cobot-io-0.1.2.0: test/UniprotSpec.hs
{-# LANGUAGE QuasiQuotes #-}
module UniprotSpec where
import Prelude hiding (lines, unlines)
import Data.Text (Text)
import Data.Attoparsec.Text (parseOnly, endOfLine, many')
import NeatInterpolation (text)
import Test.Hspec
import Bio.Uniprot.Type
import Bio.Uniprot.Parser
idStr :: Text
idStr = "ID PDCD1_HUMAN Reviewed; 288 AA."
acStr :: Text
acStr = "AC Q15116; O00517; Q8IX89;"
dtStr :: Text
dtStr = [text|
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 17-APR-2007, sequence version 3.
DT 28-FEB-2018, entry version 163.|]
deStr :: Text
deStr = [text|
DE RecName: Full=Programmed cell death protein 1;
DE Short=Protein PD-1;
DE Short=hPD-1;
DE AltName: CD_antigen=CD279;
DE Flags: Precursor;|]
de2Str :: Text
de2Str = [text|
DE RecName: Full=Arginine biosynthesis bifunctional protein argJ;
DE Includes:
DE RecName: Full=Glutamate N-acetyltransferase;
DE EC=2.3.1.35;
DE AltName: Full=Ornithine acetyltransferase;
DE Short=OATase;
DE AltName: Full=Ornithine transacetylase;
DE Includes:
DE RecName: Full=Amino-acid acetyltransferase;
DE EC=2.3.1.1;
DE AltName: Full=N-acetylglutamate synthase;
DE Short=AGS;
DE Contains:
DE RecName: Full=Arginine biosynthesis bifunctional protein argJ alpha chain;
DE Contains:
DE RecName: Full=Arginine biosynthesis bifunctional protein argJ beta chain;|]
gnStr :: Text
gnStr = "GN Name=PDCD1; Synonyms=PD1;"
osStr :: Text
osStr = "OS Homo sapiens (Human)."
ogStr :: Text
ogStr = [text|
OG Plasmid R6-5, Plasmid IncFII R100 (NR1), and
OG Plasmid IncFII R1-19 (R1 drd-19).|]
ocStr :: Text
ocStr = [text|
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC Catarrhini; Hominidae; Homo.|]
oxStr :: Text
oxStr = "OX NCBI_TaxID=9606;"
ohStr :: Text
ohStr = "OH NCBI_TaxID=9536; Cercopithecus hamlyni (Owl-faced monkey) (Hamlyn's monkey)."
refStr :: Text
refStr = [text|
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=7851902; DOI=10.1006/geno.1994.1562;
RA Shinohara T., Taniwaki M., Ishida Y., Kawaich M., Honjo T.;
RT "Structure and chromosomal localization of the human PD-1 gene
RT (PDCD1).";
RL Genomics 23:704-706(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=9332365; DOI=10.1016/S0378-1119(97)00260-6;
RA Finger L.R., Pu J., Wasserman R., Vibhakar R., Louie E., Hardy R.R.,
RA Burrows P.D., Billips L.D.;
RT "The human PD-1 gene: complete cDNA, genomic organization, and
RT developmentally regulated expression in B cell progenitors.";
RL Gene 197:177-187(1997).
RN [3]
RP ERRATUM.
RA Finger L.R., Pu J., Wasserman R., Vibhakar R., Louie E., Hardy R.R.,
RA Burrows P.D., Billips L.D.;
RL Gene 203:253-253(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND INVOLVEMENT IN SLEB2.
RX PubMed=12402038; DOI=10.1038/ng1020;
RA Prokunina L., Castillejo-Lopez C., Oberg F., Gunnarsson I., Berg L.,
RA Magnusson V., Brookes A.J., Tentler D., Kristjansdottir H.,
RA Grondal G., Bolstad A.I., Svenungsson E., Lundberg I., Sturfelt G.,
RA Jonssen A., Truedsson L., Lima G., Alcocer-Varela J., Jonsson R.,
RA Gyllensten U.B., Harley J.B., Alarcon-Segovia D., Steinsson K.,
RA Alarcon-Riquelme M.E.;
RT "A regulatory polymorphism in PDCD1 is associated with susceptibility
RT to systemic lupus erythematosus in humans.";
RL Nat. Genet. 32:666-669(2002).
RN [5]
RP NUCLEOTIDE SEQUENCE [MRNA].
RA He X., Xu L., Liu Y., Zeng Y.;
RT "Cloning of PD-1 cDNA from activated peripheral leukocytes.";
RL Submitted (FEB-2003) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Livingston R.J., Shaffer T., McFarland I., Nguyen C.P., Stanaway I.B.,
RA Rajkumar N., Johnson E.J., da Ponte S.H., Willa H., Ahearn M.O.,
RA Bertucci C., Acklestad J., Carroll A., Swanson J., Gildersleeve H.I.,
RA Nickerson D.A.;
RL Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A.,
RA Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M.,
RA Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y.,
RA Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M.,
RA Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K.,
RA Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S.,
RA Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J.,
RA Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y.,
RA Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N.,
RA Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S.,
RA Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y.,
RA Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T.,
RA Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y.,
RA Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S.,
RA Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T.,
RA Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M.,
RA Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T.,
RA Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K.,
RA Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R.,
RA Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [8]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA
RT project: the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [9]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G., Florea L., Halpern A.L.,
RA Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R.,
RA Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V.,
RA Hannenhalli S., Turner R., Yooseph S., Lu F., Nusskern D.R.,
RA Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H.,
RA Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G.,
RA Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W.,
RA Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [10]
RP FUNCTION.
RX PubMed=21276005; DOI=10.1111/j.1749-6632.2010.05919.x;
RA Fife B.T., Pauken K.E.;
RT "The role of the PD-1 pathway in autoimmunity and peripheral
RT tolerance.";
RL Ann. N. Y. Acad. Sci. 1217:45-59(2011).|]
ccStr :: Text
ccStr = [text|
CC -!- FUNCTION: Inhibitory cell surface receptor involved in the
CC regulation of T-cell function during immunity and tolerance. Upon
CC ligand binding, inhibits T-cell effector functions in an antigen-
CC specific manner. Possible cell death inducer, in association with
CC other factors. {ECO:0000269|PubMed:21276005}.
CC -!- SUBUNIT: Monomer. {ECO:0000250}.
CC -!- INTERACTION:
CC Q9NZQ7:CD274; NbExp=2; IntAct=EBI-4314328, EBI-4314282;
CC Q9NZQ7-1:CD274; NbExp=2; IntAct=EBI-4314328, EBI-15686469;
CC Q06124:PTPN11; NbExp=3; IntAct=EBI-4314328, EBI-297779;
CC -!- SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane
CC protein.
CC -!- DEVELOPMENTAL STAGE: Induced at programmed cell death.
CC -!- DISEASE: Systemic lupus erythematosus 2 (SLEB2) [MIM:605218]: A
CC chronic, relapsing, inflammatory, and often febrile multisystemic
CC disorder of connective tissue, characterized principally by
CC involvement of the skin, joints, kidneys and serosal membranes. It
CC is of unknown etiology, but is thought to represent a failure of
CC the regulatory mechanisms of the autoimmune system. The disease is
CC marked by a wide range of system dysfunctions, an elevated
CC erythrocyte sedimentation rate, and the formation of LE cells in
CC the blood or bone marrow. {ECO:0000269|PubMed:12402038}.
CC Note=Disease susceptibility is associated with variations
CC affecting the gene represented in this entry.|]
peStr :: Text
peStr = "PE 1: Evidence at protein level;"
kwStr :: Text
kwStr = [text|
KW 3D-structure; Apoptosis; Complete proteome; Disulfide bond;
KW Glycoprotein; Immunity; Immunoglobulin domain; Membrane; Polymorphism;
KW Reference proteome; Signal; Systemic lupus erythematosus;
KW Transmembrane; Transmembrane helix.|]
drStr :: Text
drStr = [text|
DR EMBL; L27440; AAC41700.1; -; Genomic_DNA.
DR EMBL; U64863; AAC51773.1; -; mRNA.
DR EMBL; AF363458; AAN64003.1; -; Genomic_DNA.
DR EMBL; AY238517; AAO63583.1; -; mRNA.
DR EMBL; EF064716; ABK41899.1; -; Genomic_DNA.
DR EMBL; AK313848; BAG36577.1; -; mRNA.
DR EMBL; CH471063; EAW71298.1; -; Genomic_DNA.
DR EMBL; BC074740; AAH74740.1; -; mRNA.
DR CCDS; CCDS33428.1; -.
DR PIR; A55737; A55737.
DR RefSeq; NP_005009.2; NM_005018.2.
DR UniGene; Hs.158297; -.
DR PDB; 2M2D; NMR; -; A=34-150.
DR PDB; 3RRQ; X-ray; 2.10 A; A=32-160.
DR PDB; 4ZQK; X-ray; 2.45 A; B=33-150.
DR PDB; 5B8C; X-ray; 2.15 A; C/F/I/L=32-160.
DR PDB; 5GGR; X-ray; 3.30 A; Y/Z=26-150.
DR PDB; 5GGS; X-ray; 2.00 A; Y/Z=26-148.
DR PDB; 5IUS; X-ray; 2.89 A; A/B=26-146.
DR PDB; 5JXE; X-ray; 2.90 A; A/B=33-146.
DR PDB; 5WT9; X-ray; 2.40 A; G=1-167.
DR PDBsum; 2M2D; -.
DR PDBsum; 3RRQ; -.
DR PDBsum; 4ZQK; -.
DR PDBsum; 5B8C; -.
DR PDBsum; 5GGR; -.
DR PDBsum; 5GGS; -.
DR PDBsum; 5IUS; -.
DR PDBsum; 5JXE; -.
DR PDBsum; 5WT9; -.
DR ProteinModelPortal; Q15116; -.
DR SMR; Q15116; -.
DR BioGrid; 111160; 61.
DR DIP; DIP-44126N; -.
DR IntAct; Q15116; 5.
DR MINT; Q15116; -.
DR STRING; 9606.ENSP00000335062; -.
DR ChEMBL; CHEMBL3307223; -.
DR DrugBank; DB05916; CT-011.
DR DrugBank; DB09035; Nivolumab.
DR DrugBank; DB09037; Pembrolizumab.
DR GuidetoPHARMACOLOGY; 2760; -.
DR iPTMnet; Q15116; -.
DR PhosphoSitePlus; Q15116; -.
DR BioMuta; PDCD1; -.
DR DMDM; 145559515; -.
DR PaxDb; Q15116; -.
DR PeptideAtlas; Q15116; -.
DR PRIDE; Q15116; -.
DR DNASU; 5133; -.
DR Ensembl; ENST00000334409; ENSP00000335062; ENSG00000188389.
DR Ensembl; ENST00000618185; ENSP00000480684; ENSG00000276977.
DR GeneID; 5133; -.
DR KEGG; hsa:5133; -.
DR UCSC; uc002wcq.5; human.
DR CTD; 5133; -.
DR DisGeNET; 5133; -.
DR EuPathDB; HostDB:ENSG00000188389.10; -.
DR GeneCards; PDCD1; -.
DR H-InvDB; HIX0030684; -.
DR HGNC; HGNC:8760; PDCD1.
DR HPA; CAB038418; -.
DR HPA; HPA035981; -.
DR MalaCards; PDCD1; -.
DR MIM; 109100; phenotype.
DR MIM; 600244; gene.
DR MIM; 605218; phenotype.
DR neXtProt; NX_Q15116; -.
DR OpenTargets; ENSG00000188389; -.
DR Orphanet; 802; Multiple sclerosis.
DR Orphanet; 536; Systemic lupus erythematosus.
DR PharmGKB; PA33110; -.
DR eggNOG; ENOG410J26W; Eukaryota.
DR eggNOG; ENOG41116U6; LUCA.
DR GeneTree; ENSGT00390000013662; -.
DR HOGENOM; HOG000253959; -.
DR HOVERGEN; HBG053534; -.
DR InParanoid; Q15116; -.
DR KO; K06744; -.
DR OMA; DFQWREK; -.
DR OrthoDB; EOG091G0EE8; -.
DR PhylomeDB; Q15116; -.
DR TreeFam; TF336181; -.
DR Reactome; R-HSA-389948; PD-1 signaling.
DR SIGNOR; Q15116; -.
DR ChiTaRS; PDCD1; human.
DR GeneWiki; Programmed_cell_death_1; -.
DR GenomeRNAi; 5133; -.
DR PRO; PR:Q15116; -.
DR Proteomes; UP000005640; Chromosome 2.
DR Bgee; ENSG00000188389; -.
DR CleanEx; HS_PDCD1; -.
DR ExpressionAtlas; Q15116; baseline and differential.
DR Genevisible; Q15116; HS.
DR GO; GO:0009897; C:external side of plasma membrane; IEA:Ensembl.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0005886; C:plasma membrane; TAS:Reactome.
DR GO; GO:0004871; F:signal transducer activity; TAS:ProtInc.
DR GO; GO:0006915; P:apoptotic process; TAS:ProtInc.
DR GO; GO:0006959; P:humoral immune response; TAS:ProtInc.
DR GO; GO:0007275; P:multicellular organism development; TAS:ProtInc.
DR GO; GO:0043066; P:negative regulation of apoptotic process; IEA:Ensembl.
DR GO; GO:0002644; P:negative regulation of tolerance induction; IEA:Ensembl.
DR GO; GO:0070234; P:positive regulation of T cell apoptotic process; IDA:UniProtKB.
DR GO; GO:0031295; P:T cell costimulation; TAS:Reactome.
DR Gene3D; 2.60.40.10; -; 1.
DR InterPro; IPR007110; Ig-like_dom.
DR InterPro; IPR036179; Ig-like_dom_sf.
DR InterPro; IPR013783; Ig-like_fold.
DR InterPro; IPR003599; Ig_sub.
DR InterPro; IPR013106; Ig_V-set.
DR Pfam; PF07686; V-set; 1.
DR SMART; SM00409; IG; 1.
DR SMART; SM00406; IGv; 1.
DR SUPFAM; SSF48726; SSF48726; 1.
DR PROSITE; PS50835; IG_LIKE; 1.|]
ftStr :: Text
ftStr = [text|
FT SIGNAL 1 20 {ECO:0000255}.
FT CHAIN 21 288 Programmed cell death protein 1.
FT /FTId=PRO_0000014892.
FT TOPO_DOM 21 170 Extracellular. {ECO:0000255}.
FT TRANSMEM 171 191 Helical. {ECO:0000255}.
FT TOPO_DOM 192 288 Cytoplasmic. {ECO:0000255}.
FT DOMAIN 35 145 Ig-like V-type.
FT CARBOHYD 49 49 N-linked (GlcNAc...) asparagine.
FT {ECO:0000255}.
FT CARBOHYD 58 58 N-linked (GlcNAc...) asparagine.
FT {ECO:0000255}.
FT CARBOHYD 74 74 N-linked (GlcNAc...) asparagine.
FT {ECO:0000255}.
FT CARBOHYD 116 116 N-linked (GlcNAc...) asparagine.
FT {ECO:0000255}.
FT DISULFID 54 123 {ECO:0000255|PROSITE-ProRule:PRU00114}.
FT VARIANT 215 215 A -> V (in dbSNP:rs2227982).
FT /FTId=VAR_031685.
FT CONFLICT 38 38 S -> F (in Ref. 2; AAC51773).
FT {ECO:0000305}.
FT CONFLICT 162 162 P -> S (in Ref. 1; AAC41700).
FT {ECO:0000305}.
FT STRAND 27 29 {ECO:0000244|PDB:5WT9}.
FT STRAND 36 38 {ECO:0000244|PDB:5GGS}.
FT STRAND 40 45 {ECO:0000244|PDB:5GGS}.
FT STRAND 50 55 {ECO:0000244|PDB:5GGS}.
FT STRAND 60 70 {ECO:0000244|PDB:5GGS}.
FT STRAND 72 74 {ECO:0000244|PDB:4ZQK}.
FT STRAND 76 83 {ECO:0000244|PDB:5GGS}.
FT STRAND 95 99 {ECO:0000244|PDB:5GGS}.
FT STRAND 103 112 {ECO:0000244|PDB:5GGS}.
FT HELIX 115 117 {ECO:0000244|PDB:5GGS}.
FT STRAND 119 131 {ECO:0000244|PDB:5GGS}.
FT STRAND 134 136 {ECO:0000244|PDB:5GGS}.
FT STRAND 140 145 {ECO:0000244|PDB:5GGS}.|]
sqStr :: Text
sqStr = [text|
SQ SEQUENCE 288 AA; 31647 MW; A5210FD40C304FB7 CRC64;
MQIPQAPWPV VWAVLQLGWR PGWFLDSPDR PWNPPTFSPA LLVVTEGDNA TFTCSFSNTS
ESFVLNWYRM SPSNQTDKLA AFPEDRSQPG QDCRFRVTQL PNGRDFHMSV VRARRNDSGT
YLCGAISLAP KAQIKESLRA ELRVTERRAE VPTAHPSPSP RPAGQFQTLV VGVVGGLLGS
LVLLVWVLAV ICSRAARGTI GARRTGQPLK EDPSAVPVFS VDYGELDFQW REKTPEPPVP
CVPEQTEYAT IVFPSGMGTS SPARRGSADG PRSAQPLRPE DGHCSWPL|]
endStr :: Text
endStr = "//"
pd1Str :: Text
pd1Str = [text|
ID PDCD1_HUMAN Reviewed; 288 AA.
AC Q15116; O00517; Q8IX89;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 17-APR-2007, sequence version 3.
DT 28-FEB-2018, entry version 163.
DE RecName: Full=Programmed cell death protein 1;
DE Short=Protein PD-1;
DE Short=hPD-1;
DE AltName: CD_antigen=CD279;
DE Flags: Precursor;
GN Name=PDCD1; Synonyms=PD1;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC Catarrhini; Hominidae; Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=7851902; DOI=10.1006/geno.1994.1562;
RA Shinohara T., Taniwaki M., Ishida Y., Kawaich M., Honjo T.;
RT "Structure and chromosomal localization of the human PD-1 gene
RT (PDCD1).";
RL Genomics 23:704-706(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=9332365; DOI=10.1016/S0378-1119(97)00260-6;
RA Finger L.R., Pu J., Wasserman R., Vibhakar R., Louie E., Hardy R.R.,
RA Burrows P.D., Billips L.D.;
RT "The human PD-1 gene: complete cDNA, genomic organization, and
RT developmentally regulated expression in B cell progenitors.";
RL Gene 197:177-187(1997).
RN [3]
RP ERRATUM.
RA Finger L.R., Pu J., Wasserman R., Vibhakar R., Louie E., Hardy R.R.,
RA Burrows P.D., Billips L.D.;
RL Gene 203:253-253(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND INVOLVEMENT IN SLEB2.
RX PubMed=12402038; DOI=10.1038/ng1020;
RA Prokunina L., Castillejo-Lopez C., Oberg F., Gunnarsson I., Berg L.,
RA Magnusson V., Brookes A.J., Tentler D., Kristjansdottir H.,
RA Grondal G., Bolstad A.I., Svenungsson E., Lundberg I., Sturfelt G.,
RA Jonssen A., Truedsson L., Lima G., Alcocer-Varela J., Jonsson R.,
RA Gyllensten U.B., Harley J.B., Alarcon-Segovia D., Steinsson K.,
RA Alarcon-Riquelme M.E.;
RT "A regulatory polymorphism in PDCD1 is associated with susceptibility
RT to systemic lupus erythematosus in humans.";
RL Nat. Genet. 32:666-669(2002).
RN [5]
RP NUCLEOTIDE SEQUENCE [MRNA].
RA He X., Xu L., Liu Y., Zeng Y.;
RT "Cloning of PD-1 cDNA from activated peripheral leukocytes.";
RL Submitted (FEB-2003) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Livingston R.J., Shaffer T., McFarland I., Nguyen C.P., Stanaway I.B.,
RA Rajkumar N., Johnson E.J., da Ponte S.H., Willa H., Ahearn M.O.,
RA Bertucci C., Acklestad J., Carroll A., Swanson J., Gildersleeve H.I.,
RA Nickerson D.A.;
RL Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A.,
RA Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M.,
RA Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y.,
RA Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M.,
RA Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K.,
RA Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S.,
RA Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J.,
RA Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y.,
RA Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N.,
RA Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S.,
RA Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y.,
RA Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T.,
RA Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y.,
RA Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S.,
RA Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T.,
RA Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M.,
RA Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T.,
RA Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K.,
RA Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R.,
RA Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [8]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA
RT project: the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [9]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G., Florea L., Halpern A.L.,
RA Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R.,
RA Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V.,
RA Hannenhalli S., Turner R., Yooseph S., Lu F., Nusskern D.R.,
RA Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H.,
RA Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G.,
RA Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W.,
RA Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [10]
RP FUNCTION.
RX PubMed=21276005; DOI=10.1111/j.1749-6632.2010.05919.x;
RA Fife B.T., Pauken K.E.;
RT "The role of the PD-1 pathway in autoimmunity and peripheral
RT tolerance.";
RL Ann. N. Y. Acad. Sci. 1217:45-59(2011).
CC -!- FUNCTION: Inhibitory cell surface receptor involved in the
CC regulation of T-cell function during immunity and tolerance. Upon
CC ligand binding, inhibits T-cell effector functions in an antigen-
CC specific manner. Possible cell death inducer, in association with
CC other factors. {ECO:0000269|PubMed:21276005}.
CC -!- SUBUNIT: Monomer. {ECO:0000250}.
CC -!- INTERACTION:
CC Q9NZQ7:CD274; NbExp=2; IntAct=EBI-4314328, EBI-4314282;
CC Q9NZQ7-1:CD274; NbExp=2; IntAct=EBI-4314328, EBI-15686469;
CC Q06124:PTPN11; NbExp=3; IntAct=EBI-4314328, EBI-297779;
CC -!- SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane
CC protein.
CC -!- DEVELOPMENTAL STAGE: Induced at programmed cell death.
CC -!- DISEASE: Systemic lupus erythematosus 2 (SLEB2) [MIM:605218]: A
CC chronic, relapsing, inflammatory, and often febrile multisystemic
CC disorder of connective tissue, characterized principally by
CC involvement of the skin, joints, kidneys and serosal membranes. It
CC is of unknown etiology, but is thought to represent a failure of
CC the regulatory mechanisms of the autoimmune system. The disease is
CC marked by a wide range of system dysfunctions, an elevated
CC erythrocyte sedimentation rate, and the formation of LE cells in
CC the blood or bone marrow. {ECO:0000269|PubMed:12402038}.
CC Note=Disease susceptibility is associated with variations
CC affecting the gene represented in this entry.
DR EMBL; L27440; AAC41700.1; -; Genomic_DNA.
DR EMBL; U64863; AAC51773.1; -; mRNA.
DR EMBL; AF363458; AAN64003.1; -; Genomic_DNA.
DR EMBL; AY238517; AAO63583.1; -; mRNA.
DR EMBL; EF064716; ABK41899.1; -; Genomic_DNA.
DR EMBL; AK313848; BAG36577.1; -; mRNA.
DR EMBL; CH471063; EAW71298.1; -; Genomic_DNA.
DR EMBL; BC074740; AAH74740.1; -; mRNA.
DR CCDS; CCDS33428.1; -.
DR PIR; A55737; A55737.
DR RefSeq; NP_005009.2; NM_005018.2.
DR UniGene; Hs.158297; -.
DR PDB; 2M2D; NMR; -; A=34-150.
DR PDB; 3RRQ; X-ray; 2.10 A; A=32-160.
DR PDB; 4ZQK; X-ray; 2.45 A; B=33-150.
DR PDB; 5B8C; X-ray; 2.15 A; C/F/I/L=32-160.
DR PDB; 5GGR; X-ray; 3.30 A; Y/Z=26-150.
DR PDB; 5GGS; X-ray; 2.00 A; Y/Z=26-148.
DR PDB; 5IUS; X-ray; 2.89 A; A/B=26-146.
DR PDB; 5JXE; X-ray; 2.90 A; A/B=33-146.
DR PDB; 5WT9; X-ray; 2.40 A; G=1-167.
DR PDBsum; 2M2D; -.
DR PDBsum; 3RRQ; -.
DR PDBsum; 4ZQK; -.
DR PDBsum; 5B8C; -.
DR PDBsum; 5GGR; -.
DR PDBsum; 5GGS; -.
DR PDBsum; 5IUS; -.
DR PDBsum; 5JXE; -.
DR PDBsum; 5WT9; -.
DR ProteinModelPortal; Q15116; -.
DR SMR; Q15116; -.
DR BioGrid; 111160; 61.
DR DIP; DIP-44126N; -.
DR IntAct; Q15116; 5.
DR MINT; Q15116; -.
DR STRING; 9606.ENSP00000335062; -.
DR ChEMBL; CHEMBL3307223; -.
DR DrugBank; DB05916; CT-011.
DR DrugBank; DB09035; Nivolumab.
DR DrugBank; DB09037; Pembrolizumab.
DR GuidetoPHARMACOLOGY; 2760; -.
DR iPTMnet; Q15116; -.
DR PhosphoSitePlus; Q15116; -.
DR BioMuta; PDCD1; -.
DR DMDM; 145559515; -.
DR PaxDb; Q15116; -.
DR PeptideAtlas; Q15116; -.
DR PRIDE; Q15116; -.
DR DNASU; 5133; -.
DR Ensembl; ENST00000334409; ENSP00000335062; ENSG00000188389.
DR Ensembl; ENST00000618185; ENSP00000480684; ENSG00000276977.
DR GeneID; 5133; -.
DR KEGG; hsa:5133; -.
DR UCSC; uc002wcq.5; human.
DR CTD; 5133; -.
DR DisGeNET; 5133; -.
DR EuPathDB; HostDB:ENSG00000188389.10; -.
DR GeneCards; PDCD1; -.
DR H-InvDB; HIX0030684; -.
DR HGNC; HGNC:8760; PDCD1.
DR HPA; CAB038418; -.
DR HPA; HPA035981; -.
DR MalaCards; PDCD1; -.
DR MIM; 109100; phenotype.
DR MIM; 600244; gene.
DR MIM; 605218; phenotype.
DR neXtProt; NX_Q15116; -.
DR OpenTargets; ENSG00000188389; -.
DR Orphanet; 802; Multiple sclerosis.
DR Orphanet; 536; Systemic lupus erythematosus.
DR PharmGKB; PA33110; -.
DR eggNOG; ENOG410J26W; Eukaryota.
DR eggNOG; ENOG41116U6; LUCA.
DR GeneTree; ENSGT00390000013662; -.
DR HOGENOM; HOG000253959; -.
DR HOVERGEN; HBG053534; -.
DR InParanoid; Q15116; -.
DR KO; K06744; -.
DR OMA; DFQWREK; -.
DR OrthoDB; EOG091G0EE8; -.
DR PhylomeDB; Q15116; -.
DR TreeFam; TF336181; -.
DR Reactome; R-HSA-389948; PD-1 signaling.
DR SIGNOR; Q15116; -.
DR ChiTaRS; PDCD1; human.
DR GeneWiki; Programmed_cell_death_1; -.
DR GenomeRNAi; 5133; -.
DR PRO; PR:Q15116; -.
DR Proteomes; UP000005640; Chromosome 2.
DR Bgee; ENSG00000188389; -.
DR CleanEx; HS_PDCD1; -.
DR ExpressionAtlas; Q15116; baseline and differential.
DR Genevisible; Q15116; HS.
DR GO; GO:0009897; C:external side of plasma membrane; IEA:Ensembl.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0005886; C:plasma membrane; TAS:Reactome.
DR GO; GO:0004871; F:signal transducer activity; TAS:ProtInc.
DR GO; GO:0006915; P:apoptotic process; TAS:ProtInc.
DR GO; GO:0006959; P:humoral immune response; TAS:ProtInc.
DR GO; GO:0007275; P:multicellular organism development; TAS:ProtInc.
DR GO; GO:0043066; P:negative regulation of apoptotic process; IEA:Ensembl.
DR GO; GO:0002644; P:negative regulation of tolerance induction; IEA:Ensembl.
DR GO; GO:0070234; P:positive regulation of T cell apoptotic process; IDA:UniProtKB.
DR GO; GO:0031295; P:T cell costimulation; TAS:Reactome.
DR Gene3D; 2.60.40.10; -; 1.
DR InterPro; IPR007110; Ig-like_dom.
DR InterPro; IPR036179; Ig-like_dom_sf.
DR InterPro; IPR013783; Ig-like_fold.
DR InterPro; IPR003599; Ig_sub.
DR InterPro; IPR013106; Ig_V-set.
DR Pfam; PF07686; V-set; 1.
DR SMART; SM00409; IG; 1.
DR SMART; SM00406; IGv; 1.
DR SUPFAM; SSF48726; SSF48726; 1.
DR PROSITE; PS50835; IG_LIKE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Apoptosis; Complete proteome; Disulfide bond;
KW Glycoprotein; Immunity; Immunoglobulin domain; Membrane; Polymorphism;
KW Reference proteome; Signal; Systemic lupus erythematosus;
KW Transmembrane; Transmembrane helix.
FT SIGNAL 1 20 {ECO:0000255}.
FT CHAIN 21 288 Programmed cell death protein 1.
FT /FTId=PRO_0000014892.
FT TOPO_DOM 21 170 Extracellular. {ECO:0000255}.
FT TRANSMEM 171 191 Helical. {ECO:0000255}.
FT TOPO_DOM 192 288 Cytoplasmic. {ECO:0000255}.
FT DOMAIN 35 145 Ig-like V-type.
FT CARBOHYD 49 49 N-linked (GlcNAc...) asparagine.
FT {ECO:0000255}.
FT CARBOHYD 58 58 N-linked (GlcNAc...) asparagine.
FT {ECO:0000255}.
FT CARBOHYD 74 74 N-linked (GlcNAc...) asparagine.
FT {ECO:0000255}.
FT CARBOHYD 116 116 N-linked (GlcNAc...) asparagine.
FT {ECO:0000255}.
FT DISULFID 54 123 {ECO:0000255|PROSITE-ProRule:PRU00114}.
FT VARIANT 215 215 A -> V (in dbSNP:rs2227982).
FT /FTId=VAR_031685.
FT CONFLICT 38 38 S -> F (in Ref. 2; AAC51773).
FT {ECO:0000305}.
FT CONFLICT 162 162 P -> S (in Ref. 1; AAC41700).
FT {ECO:0000305}.
FT STRAND 27 29 {ECO:0000244|PDB:5WT9}.
FT STRAND 36 38 {ECO:0000244|PDB:5GGS}.
FT STRAND 40 45 {ECO:0000244|PDB:5GGS}.
FT STRAND 50 55 {ECO:0000244|PDB:5GGS}.
FT STRAND 60 70 {ECO:0000244|PDB:5GGS}.
FT STRAND 72 74 {ECO:0000244|PDB:4ZQK}.
FT STRAND 76 83 {ECO:0000244|PDB:5GGS}.
FT STRAND 95 99 {ECO:0000244|PDB:5GGS}.
FT STRAND 103 112 {ECO:0000244|PDB:5GGS}.
FT HELIX 115 117 {ECO:0000244|PDB:5GGS}.
FT STRAND 119 131 {ECO:0000244|PDB:5GGS}.
FT STRAND 134 136 {ECO:0000244|PDB:5GGS}.
FT STRAND 140 145 {ECO:0000244|PDB:5GGS}.
SQ SEQUENCE 288 AA; 31647 MW; A5210FD40C304FB7 CRC64;
MQIPQAPWPV VWAVLQLGWR PGWFLDSPDR PWNPPTFSPA LLVVTEGDNA TFTCSFSNTS
ESFVLNWYRM SPSNQTDKLA AFPEDRSQPG QDCRFRVTQL PNGRDFHMSV VRARRNDSGT
YLCGAISLAP KAQIKESLRA ELRVTERRAE VPTAHPSPSP RPAGQFQTLV VGVVGGLLGS
LVLLVWVLAV ICSRAARGTI GARRTGQPLK EDPSAVPVFS VDYGELDFQW REKTPEPPVP
CVPEQTEYAT IVFPSGMGTS SPARRGSADG PRSAQPLRPE DGHCSWPL
//|]
idAns :: ID
idAns = ID "PDCD1_HUMAN" Reviewed 288
acAns :: AC
acAns = AC ["Q15116", "O00517", "Q8IX89"]
dtAns :: DT
dtAns = DT "01-NOV-1997" "Swiss-Prot" "17-APR-2007" 3 "28-FEB-2018" 163
deAns :: DE
deAns = DE (Just (Name "Programmed cell death protein 1" ["Protein PD-1", "hPD-1"] []))
[CDAntigen "CD279"] [] [] [] [Precursor]
de2Ans :: DE
de2Ans = DE (Just (Name "Arginine biosynthesis bifunctional protein argJ" [] [])) [] []
[DE (Just (Name "Glutamate N-acetyltransferase" [] ["2.3.1.35"]))
[Simple (Name "Ornithine acetyltransferase" ["OATase"] []),
Simple (Name "Ornithine transacetylase" [] [])]
[] [] [] [],
DE (Just (Name "Amino-acid acetyltransferase" [] ["2.3.1.1"]))
[Simple (Name "N-acetylglutamate synthase" ["AGS"] [])]
[] [] [] []
]
[DE (Just (Name "Arginine biosynthesis bifunctional protein argJ alpha chain" [] []))
[] [] [] [] [],
DE (Just (Name "Arginine biosynthesis bifunctional protein argJ beta chain" [] []))
[] [] [] [] []]
[]
gnAns :: [GN]
gnAns = [GN (Just "PDCD1") ["PD1"] [] []]
osAns :: OS
osAns = OS "Homo sapiens (Human)"
ogAns :: OG
ogAns = Plasmid ["R6-5", "IncFII R100 (NR1)", "IncFII R1-19 (R1 drd-19)"]
ocAns :: OC
ocAns = OC ["Eukaryota", "Metazoa", "Chordata", "Craniata",
"Vertebrata", "Euteleostomi", "Mammalia", "Eutheria",
"Euarchontoglires", "Primates", "Haplorrhini", "Catarrhini",
"Hominidae", "Homo"]
ohAns :: OH
ohAns = OH "9536" "Cercopithecus hamlyni (Owl-faced monkey) (Hamlyn's monkey)"
oxAns :: OX
oxAns = OX "NCBI_TaxID" "9606"
refAns :: [Reference]
refAns = [Reference 1 "NUCLEOTIDE SEQUENCE [GENOMIC DNA]" [] [(PubMed,"7851902"),(DOI,"10.1006/geno.1994.1562")] [] ["Shinohara T.","Taniwaki M.","Ishida Y.","Kawaich M.","Honjo T."] (Just "Structure and chromosomal localization of the human PD-1 gene (PDCD1).") "Genomics 23:704-706(1994)",
Reference 2 "NUCLEOTIDE SEQUENCE [MRNA]" [] [(PubMed,"9332365"),(DOI,"10.1016/S0378-1119(97)00260-6")] [] ["Finger L.R.","Pu J.","Wasserman R.","Vibhakar R.","Louie E.","Hardy R.R.","Burrows P.D.","Billips L.D."] (Just "The human PD-1 gene: complete cDNA, genomic organization, and developmentally regulated expression in B cell progenitors.") "Gene 197:177-187(1997)",
Reference 3 "ERRATUM" [] [] [] ["Finger L.R.","Pu J.","Wasserman R.","Vibhakar R.","Louie E.","Hardy R.R.","Burrows P.D.","Billips L.D."] Nothing "Gene 203:253-253(1997)",
Reference 4 "NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND INVOLVEMENT IN SLEB2" [] [(PubMed,"12402038"),(DOI,"10.1038/ng1020")] [] ["Prokunina L.","Castillejo-Lopez C.","Oberg F.","Gunnarsson I.","Berg L.","Magnusson V.","Brookes A.J.","Tentler D.","Kristjansdottir H.","Grondal G.","Bolstad A.I.","Svenungsson E.","Lundberg I.","Sturfelt G.","Jonssen A.","Truedsson L.","Lima G.","Alcocer-Varela J.","Jonsson R.","Gyllensten U.B.","Harley J.B.","Alarcon-Segovia D.","Steinsson K.","Alarcon-Riquelme M.E."] (Just "A regulatory polymorphism in PDCD1 is associated with susceptibility to systemic lupus erythematosus in humans.") "Nat. Genet. 32:666-669(2002)",
Reference 5 "NUCLEOTIDE SEQUENCE [MRNA]" [] [] [] ["He X.","Xu L.","Liu Y.","Zeng Y."] (Just "Cloning of PD-1 cDNA from activated peripheral leukocytes.") "Submitted (FEB-2003) to the EMBL/GenBank/DDBJ databases",
Reference 6 "NUCLEOTIDE SEQUENCE [GENOMIC DNA]" [] [] [] ["Livingston R.J.","Shaffer T.","McFarland I.","Nguyen C.P.","Stanaway I.B.","Rajkumar N.","Johnson E.J.","da Ponte S.H.","Willa H.","Ahearn M.O.","Bertucci C.","Acklestad J.","Carroll A.","Swanson J.","Gildersleeve H.I.","Nickerson D.A."] Nothing "Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases",
Reference 7 "NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]" [] [(PubMed,"14702039"),(DOI,"10.1038/ng1285")] [] ["Ota T.","Suzuki Y.","Nishikawa T.","Otsuki T.","Sugiyama T.","Irie R.","Wakamatsu A.","Hayashi K.","Sato H.","Nagai K.","Kimura K.","Makita H.","Sekine M.","Obayashi M.","Nishi T.","Shibahara T.","Tanaka T.","Ishii S.","Yamamoto J.","Saito K.","Kawai Y.","Isono Y.","Nakamura Y.","Nagahari K.","Murakami K.","Yasuda T.","Iwayanagi T.","Wagatsuma M.","Shiratori A.","Sudo H.","Hosoiri T.","Kaku Y.","Kodaira H.","Kondo H.","Sugawara M.","Takahashi M.","Kanda K.","Yokoi T.","Furuya T.","Kikkawa E.","Omura Y.","Abe K.","Kamihara K.","Katsuta N.","Sato K.","Tanikawa M.","Yamazaki M.","Ninomiya K.","Ishibashi T.","Yamashita H.","Murakawa K.","Fujimori K.","Tanai H.","Kimata M.","Watanabe M.","Hiraoka S.","Chiba Y.","Ishida S.","Ono Y.","Takiguchi S.","Watanabe S.","Yosida M.","Hotuta T.","Kusano J.","Kanehori K.","Takahashi-Fujii A.","Hara H.","Tanase T.-O.","Nomura Y.","Togiya S.","Komai F.","Hara R.","Takeuchi K.","Arita M.","Imose N.","Musashino K.","Yuuki H.","Oshima A.","Sasaki N.","Aotsuka S.","Yoshikawa Y.","Matsunawa H.","Ichihara T.","Shiohata N.","Sano S.","Moriya S.","Momiyama H.","Satoh N.","Takami S.","Terashima Y.","Suzuki O.","Nakagawa S.","Senoh A.","Mizoguchi H.","Goto Y.","Shimizu F.","Wakebe H.","Hishigaki H.","Watanabe T.","Sugiyama A.","Takemoto M.","Kawakami B.","Yamazaki M.","Watanabe K.","Kumagai A.","Itakura S.","Fukuzumi Y.","Fujimori Y.","Komiyama M.","Tashiro H.","Tanigami A.","Fujiwara T.","Ono T.","Yamada K.","Fujii Y.","Ozaki K.","Hirao M.","Ohmori Y.","Kawabata A.","Hikiji T.","Kobatake N.","Inagaki H.","Ikema Y.","Okamoto S.","Okitani R.","Kawakami T.","Noguchi S.","Itoh T.","Shigeta K.","Senba T.","Matsumura K.","Nakajima Y.","Mizuno T.","Morinaga M.","Sasaki M.","Togashi T.","Oyama M.","Hata H.","Watanabe M.","Komatsu T.","Mizushima-Sugano J.","Satoh T.","Shirai Y.","Takahashi Y.","Nakagawa K.","Okumura K.","Nagase T.","Nomura N.","Kikuchi H.","Masuho Y.","Yamashita R.","Nakai K.","Yada T.","Nakamura Y.","Ohara O.","Isogai T.","Sugano S."] (Just "Complete sequencing and characterization of 21,243 full-length human cDNAs.") "Nat. Genet. 36:40-45(2004)",
Reference 8 "NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]" [] [(PubMed,"15489334"),(DOI,"10.1101/gr.2596504")] ["The MGC Project Team;"] [] (Just "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).") "Genome Res. 14:2121-2127(2004)",
Reference 9 "NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]" [] [] [] ["Mural R.J.","Istrail S.","Sutton G.","Florea L.","Halpern A.L.","Mobarry C.M.","Lippert R.","Walenz B.","Shatkay H.","Dew I.","Miller J.R.","Flanigan M.J.","Edwards N.J.","Bolanos R.","Fasulo D.","Halldorsson B.V.","Hannenhalli S.","Turner R.","Yooseph S.","Lu F.","Nusskern D.R.","Shue B.C.","Zheng X.H.","Zhong F.","Delcher A.L.","Huson D.H.","Kravitz S.A.","Mouchard L.","Reinert K.","Remington K.A.","Clark A.G.","Waterman M.S.","Eichler E.E.","Adams M.D.","Hunkapiller M.W.","Myers E.W.","Venter J.C."] Nothing "Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases",
Reference 10 "FUNCTION" [] [(PubMed,"21276005"),(DOI,"10.1111/j.1749-6632.2010.05919.x")] [] ["Fife B.T.","Pauken K.E."] (Just "The role of the PD-1 pathway in autoimmunity and peripheral tolerance.") "Ann. N. Y. Acad. Sci. 1217:45-59(2011)"]
ccAns :: [CC]
ccAns = [CC "FUNCTION" "Inhibitory cell surface receptor involved in the regulation of T-cell function during immunity and tolerance. Upon ligand binding, inhibits T-cell effector functions in an antigen-specific manner. Possible cell death inducer, in association with other factors.",
CC "SUBUNIT" "Monomer.",
CC "INTERACTION" "Q9NZQ7:CD274; NbExp=2; IntAct=EBI-4314328, EBI-4314282; Q9NZQ7-1:CD274; NbExp=2; IntAct=EBI-4314328, EBI-15686469; Q06124:PTPN11; NbExp=3; IntAct=EBI-4314328, EBI-297779;",
CC "SUBCELLULAR LOCATION" "Membrane; Single-pass type I membrane protein.",
CC "DEVELOPMENTAL STAGE" "Induced at programmed cell death.",
CC "DISEASE" "Systemic lupus erythematosus 2 (SLEB2) [MIM:605218]: A chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys and serosal membranes. It is of unknown etiology, but is thought to represent a failure of the regulatory mechanisms of the autoimmune system. The disease is marked by a wide range of system dysfunctions, an elevated erythrocyte sedimentation rate, and the formation of LE cells in the blood or bone marrow."]
drAns :: [DR]
drAns = [DR "EMBL" "L27440" ["AAC41700.1","-","Genomic_DNA"],
DR "EMBL" "U64863" ["AAC51773.1","-","mRNA"],
DR "EMBL" "AF363458" ["AAN64003.1","-","Genomic_DNA"],
DR "EMBL" "AY238517" ["AAO63583.1","-","mRNA"],
DR "EMBL" "EF064716" ["ABK41899.1","-","Genomic_DNA"],
DR "EMBL" "AK313848" ["BAG36577.1","-","mRNA"],
DR "EMBL" "CH471063" ["EAW71298.1","-","Genomic_DNA"],
DR "EMBL" "BC074740" ["AAH74740.1","-","mRNA"],
DR "CCDS" "CCDS33428.1" ["-"],
DR "PIR" "A55737" ["A55737"],
DR "RefSeq" "NP_005009.2" ["NM_005018.2"],
DR "UniGene" "Hs.158297" ["-"],
DR "PDB" "2M2D" ["NMR","-","A=34-150"],
DR "PDB" "3RRQ" ["X-ray","2.10 A","A=32-160"],
DR "PDB" "4ZQK" ["X-ray","2.45 A","B=33-150"],
DR "PDB" "5B8C" ["X-ray","2.15 A","C/F/I/L=32-160"],
DR "PDB" "5GGR" ["X-ray","3.30 A","Y/Z=26-150"],
DR "PDB" "5GGS" ["X-ray","2.00 A","Y/Z=26-148"],
DR "PDB" "5IUS" ["X-ray","2.89 A","A/B=26-146"],
DR "PDB" "5JXE" ["X-ray","2.90 A","A/B=33-146"],
DR "PDB" "5WT9" ["X-ray","2.40 A","G=1-167"],
DR "PDBsum" "2M2D" ["-"],
DR "PDBsum" "3RRQ" ["-"],
DR "PDBsum" "4ZQK" ["-"],
DR "PDBsum" "5B8C" ["-"],
DR "PDBsum" "5GGR" ["-"],
DR "PDBsum" "5GGS" ["-"],
DR "PDBsum" "5IUS" ["-"],
DR "PDBsum" "5JXE" ["-"],
DR "PDBsum" "5WT9" ["-"],
DR "ProteinModelPortal" "Q15116" ["-"],
DR "SMR" "Q15116" ["-"],
DR "BioGrid" "111160" ["61"],
DR "DIP" "DIP-44126N" ["-"],
DR "IntAct" "Q15116" ["5"],
DR "MINT" "Q15116" ["-"],
DR "STRING" "9606.ENSP00000335062" ["-"],
DR "ChEMBL" "CHEMBL3307223" ["-"],
DR "DrugBank" "DB05916" ["CT-011"],
DR "DrugBank" "DB09035" ["Nivolumab"],
DR "DrugBank" "DB09037" ["Pembrolizumab"],
DR "GuidetoPHARMACOLOGY" "2760" ["-"],
DR "iPTMnet" "Q15116" ["-"],
DR "PhosphoSitePlus" "Q15116" ["-"],
DR "BioMuta" "PDCD1" ["-"],
DR "DMDM" "145559515" ["-"],
DR "PaxDb" "Q15116" ["-"],
DR "PeptideAtlas" "Q15116" ["-"],
DR "PRIDE" "Q15116" ["-"],
DR "DNASU" "5133" ["-"],
DR "Ensembl" "ENST00000334409" ["ENSP00000335062","ENSG00000188389"],
DR "Ensembl" "ENST00000618185" ["ENSP00000480684","ENSG00000276977"],
DR "GeneID" "5133" ["-"],
DR "KEGG" "hsa:5133" ["-"],
DR "UCSC" "uc002wcq.5" ["human"],
DR "CTD" "5133" ["-"],
DR "DisGeNET" "5133" ["-"],
DR "EuPathDB" "HostDB:ENSG00000188389.10" ["-"],
DR "GeneCards" "PDCD1" ["-"],
DR "H-InvDB" "HIX0030684" ["-"],
DR "HGNC" "HGNC:8760" ["PDCD1"],
DR "HPA" "CAB038418" ["-"],
DR "HPA" "HPA035981" ["-"],
DR "MalaCards" "PDCD1" ["-"],
DR "MIM" "109100" ["phenotype"],
DR "MIM" "600244" ["gene"],
DR "MIM" "605218" ["phenotype"],
DR "neXtProt" "NX_Q15116" ["-"],
DR "OpenTargets" "ENSG00000188389" ["-"],
DR "Orphanet" "802" ["Multiple sclerosis"],
DR "Orphanet" "536" ["Systemic lupus erythematosus"],
DR "PharmGKB" "PA33110" ["-"],
DR "eggNOG" "ENOG410J26W" ["Eukaryota"],
DR "eggNOG" "ENOG41116U6" ["LUCA"],
DR "GeneTree" "ENSGT00390000013662" ["-"],
DR "HOGENOM" "HOG000253959" ["-"],
DR "HOVERGEN" "HBG053534" ["-"],
DR "InParanoid" "Q15116" ["-"],
DR "KO" "K06744" ["-"],
DR "OMA" "DFQWREK" ["-"],
DR "OrthoDB" "EOG091G0EE8" ["-"],
DR "PhylomeDB" "Q15116" ["-"],
DR "TreeFam" "TF336181" ["-"],
DR "Reactome" "R-HSA-389948" ["PD-1 signaling"],
DR "SIGNOR" "Q15116" ["-"],
DR "ChiTaRS" "PDCD1" ["human"],
DR "GeneWiki" "Programmed_cell_death_1" ["-"],
DR "GenomeRNAi" "5133" ["-"],
DR "PRO" "PR:Q15116" ["-"],
DR "Proteomes" "UP000005640" ["Chromosome 2"],
DR "Bgee" "ENSG00000188389" ["-"],
DR "CleanEx" "HS_PDCD1" ["-"],
DR "ExpressionAtlas" "Q15116" ["baseline and differential"],
DR "Genevisible" "Q15116" ["HS"],
DR "GO" "GO:0009897" ["C:external side of plasma membrane","IEA:Ensembl"],
DR "GO" "GO:0016021" ["C:integral component of membrane","IEA:UniProtKB-KW"],
DR "GO" "GO:0005886" ["C:plasma membrane","TAS:Reactome"],
DR "GO" "GO:0004871" ["F:signal transducer activity","TAS:ProtInc"],
DR "GO" "GO:0006915" ["P:apoptotic process","TAS:ProtInc"],
DR "GO" "GO:0006959" ["P:humoral immune response","TAS:ProtInc"],
DR "GO" "GO:0007275" ["P:multicellular organism development","TAS:ProtInc"],
DR "GO" "GO:0043066" ["P:negative regulation of apoptotic process","IEA:Ensembl"],
DR "GO" "GO:0002644" ["P:negative regulation of tolerance induction","IEA:Ensembl"],
DR "GO" "GO:0070234" ["P:positive regulation of T cell apoptotic process","IDA:UniProtKB"],
DR "GO" "GO:0031295" ["P:T cell costimulation","TAS:Reactome"],
DR "Gene3D" "2.60.40.10" ["-","1"],
DR "InterPro" "IPR007110" ["Ig-like_dom"],
DR "InterPro" "IPR036179" ["Ig-like_dom_sf"],
DR "InterPro" "IPR013783" ["Ig-like_fold"],
DR "InterPro" "IPR003599" ["Ig_sub"],
DR "InterPro" "IPR013106" ["Ig_V-set"],
DR "Pfam" "PF07686" ["V-set","1"],
DR "SMART" "SM00409" ["IG","1"],
DR "SMART" "SM00406" ["IGv","1"],
DR "SUPFAM" "SSF48726" ["SSF48726","1"],
DR "PROSITE" "PS50835" ["IG_LIKE","1"]]
peAns :: PE
peAns = EvidenceAtProteinLevel
kwAns :: KW
kwAns = KW ["3D-structure", "Apoptosis", "Complete proteome", "Disulfide bond",
"Glycoprotein", "Immunity", "Immunoglobulin domain", "Membrane", "Polymorphism",
"Reference proteome", "Signal", "Systemic lupus erythematosus",
"Transmembrane", "Transmembrane helix"]
ftAns :: [FT]
ftAns = [FT "SIGNAL" (ExactEP 1) (ExactEP 20) [],
FT "CHAIN" (ExactEP 21) (ExactEP 288) ["Programmed cell death protein 1","/FTId=PRO_0000014892"],
FT "TOPO_DOM" (ExactEP 21) (ExactEP 170) ["Extracellular"],
FT "TRANSMEM" (ExactEP 171) (ExactEP 191) ["Helical"],
FT "TOPO_DOM" (ExactEP 192) (ExactEP 288) ["Cytoplasmic"],
FT "DOMAIN" (ExactEP 35) (ExactEP 145) ["Ig-like V-type"],
FT "CARBOHYD" (ExactEP 49) (ExactEP 49) ["N-linked (GlcNAc...) asparagine"],
FT "CARBOHYD" (ExactEP 58) (ExactEP 58) ["N-linked (GlcNAc...) asparagine"],
FT "CARBOHYD" (ExactEP 74) (ExactEP 74) ["N-linked (GlcNAc...) asparagine"],
FT "CARBOHYD" (ExactEP 116) (ExactEP 116) ["N-linked (GlcNAc...) asparagine"],
FT "DISULFID" (ExactEP 54) (ExactEP 123) [],
FT "VARIANT" (ExactEP 215) (ExactEP 215) ["A -> V (in dbSNP:rs2227982)","/FTId=VAR_031685"],
FT "CONFLICT" (ExactEP 38) (ExactEP 38) ["S -> F (in Ref. 2; AAC51773)"],
FT "CONFLICT" (ExactEP 162) (ExactEP 162) ["P -> S (in Ref. 1; AAC41700)"],
FT "STRAND" (ExactEP 27) (ExactEP 29) [],
FT "STRAND" (ExactEP 36) (ExactEP 38) [],
FT "STRAND" (ExactEP 40) (ExactEP 45) [],
FT "STRAND" (ExactEP 50) (ExactEP 55) [],
FT "STRAND" (ExactEP 60) (ExactEP 70) [],
FT "STRAND" (ExactEP 72) (ExactEP 74) [],
FT "STRAND" (ExactEP 76) (ExactEP 83) [],
FT "STRAND" (ExactEP 95) (ExactEP 99) [],
FT "STRAND" (ExactEP 103) (ExactEP 112) [],
FT "HELIX" (ExactEP 115) (ExactEP 117) [],
FT "STRAND" (ExactEP 119) (ExactEP 131) [],
FT "STRAND" (ExactEP 134) (ExactEP 136) [],
FT "STRAND" (ExactEP 140) (ExactEP 145) []]
sqAns :: SQ
sqAns = SQ 288 31647 "A5210FD40C304FB7"
"MQIPQAPWPVVWAVLQLGWRPGWFLDSPDRPWNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQDCRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTERRAEVPTAHPSPSPRPAGQFQTLVVGVVGGLLGSLVLLVWVLAVICSRAARGTIGARRTGQPLKEDPSAVPVFSVDYGELDFQWREKTPEPPVPCVPEQTEYATIVFPSGMGTSSPARRGSADGPRSAQPLRPEDGHCSWPL"
endAns :: ()
endAns = ()
uniprotSectionSpec :: Spec
uniprotSectionSpec =
describe "Individual Uniprot sections parishioner" $ do
it "parses ID lines" $
parseOnly parseID idStr `shouldBe` Right idAns
it "parses AC lines" $
parseOnly parseAC acStr `shouldBe` Right acAns
it "parses DT lines" $
parseOnly parseDT dtStr `shouldBe` Right dtAns
it "parses DE lines" $ do
parseOnly parseDE deStr `shouldBe` Right deAns
parseOnly parseDE de2Str `shouldBe` Right de2Ans
it "parses GN lines" $
parseOnly parseGN gnStr `shouldBe` Right gnAns
it "parses OS lines" $
parseOnly parseOS osStr `shouldBe` Right osAns
it "parses OG lines (non-PD1)" $
parseOnly parseOG ogStr `shouldBe` Right ogAns
it "parses OC lines" $
parseOnly parseOC ocStr `shouldBe` Right ocAns
it "parses OX lines (non-PD1)" $
parseOnly parseOX oxStr `shouldBe` Right oxAns
it "parses OH lines (non-PD1)" $
parseOnly parseOH ohStr `shouldBe` Right ohAns
it "parses REF lines" $ do
let parseManyRef = (:) <$> parseRef <*> many' (endOfLine *> parseRef)
parseOnly parseManyRef refStr `shouldBe` Right refAns
it "parses CC lines" $ do
let parseManyCC = (:) <$> parseCC <*> many' (endOfLine *> parseCC)
parseOnly parseManyCC ccStr `shouldBe` Right ccAns
it "parses DR lines" $ do
let parseManyDR = (:) <$> parseDR <*> many' (endOfLine *> parseDR)
parseOnly parseManyDR drStr `shouldBe` Right drAns
it "parses PE lines" $
parseOnly parsePE peStr `shouldBe` Right peAns
it "parses KW lines" $
parseOnly parseKW kwStr `shouldBe` Right kwAns
it "parses FT lines" $ do
let parseManyFT = (:) <$> parseFT <*> many' (endOfLine *> parseFT)
parseOnly parseManyFT ftStr `shouldBe` Right ftAns
it "parses SQ lines" $ do
parseOnly parseSQ sqStr `shouldBe` Right sqAns
it "parses End lines" $
parseOnly parseEnd endStr `shouldBe` Right endAns
uniprotFullSpec :: Spec
uniprotFullSpec =
describe "Full Uniprot record parser" $ do
it "parses PD1 example" $ do
let record = Record idAns acAns dtAns deAns
gnAns osAns [] ocAns
oxAns [] refAns ccAns
drAns peAns (Just kwAns) ftAns sqAns
parseOnly parseRecord pd1Str `shouldBe` Right record