PSD3_HUMAN
ID PSD3_HUMAN Reviewed; 1048 AA.
AC Q9NYI0; A6NFQ4; E9KL50; Q6B003; Q9Y2F1;
DT 10-OCT-2003, integrated into UniProtKB/Swiss-Prot.
DT 13-NOV-2007, sequence version 2.
DT 03-AUG-2022, entry version 180.
DE RecName: Full=PH and SEC7 domain-containing protein 3;
DE AltName: Full=Epididymis tissue protein Li 20mP;
DE AltName: Full=Exchange factor for ADP-ribosylation factor guanine nucleotide factor 6 D;
DE Short=Exchange factor for ARF6 D;
DE AltName: Full=Hepatocellular carcinoma-associated antigen 67;
DE AltName: Full=Pleckstrin homology and SEC7 domain-containing protein 3;
GN Name=PSD3; Synonyms=EFA6D, EFA6R, HCA67, KIAA0942;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
RC TISSUE=Brain;
RX PubMed=10231032; DOI=10.1093/dnares/6.1.63;
RA Nagase T., Ishikawa K., Suyama M., Kikuno R., Hirosawa M., Miyajima N.,
RA Tanaka A., Kotani H., Nomura N., Ohara O.;
RT "Prediction of the coding sequences of unidentified human genes. XIII. The
RT complete sequences of 100 new cDNA clones from brain which code for large
RT proteins in vitro.";
RL DNA Res. 6:63-70(1999).
RN [2]
RP SEQUENCE REVISION.
RX PubMed=12168954; DOI=10.1093/dnares/9.3.99;
RA Nakajima D., Okazaki N., Yamakawa H., Kikuno R., Ohara O., Nagase T.;
RT "Construction of expression-ready cDNA clones for KIAA genes: manual
RT curation of 330 KIAA cDNA clones.";
RL DNA Res. 9:99-106(2002).
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), AND TISSUE SPECIFICITY.
RC TISSUE=Epididymis;
RX PubMed=20736409; DOI=10.1074/mcp.m110.001719;
RA Li J., Liu F., Wang H., Liu X., Liu J., Li N., Wan F., Wang W., Zhang C.,
RA Jin S., Liu J., Zhu P., Liu Y.;
RT "Systematic mapping and functional analysis of a family of human epididymal
RT secretory sperm-located proteins.";
RL Mol. Cell. Proteomics 9:2517-2528(2010).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=16421571; DOI=10.1038/nature04406;
RA Nusbaum C., Mikkelsen T.S., Zody M.C., Asakawa S., Taudien S., Garber M.,
RA Kodira C.D., Schueler M.G., Shimizu A., Whittaker C.A., Chang J.L.,
RA Cuomo C.A., Dewar K., FitzGerald M.G., Yang X., Allen N.R., Anderson S.,
RA Asakawa T., Blechschmidt K., Bloom T., Borowsky M.L., Butler J., Cook A.,
RA Corum B., DeArellano K., DeCaprio D., Dooley K.T., Dorris L. III,
RA Engels R., Gloeckner G., Hafez N., Hagopian D.S., Hall J.L., Ishikawa S.K.,
RA Jaffe D.B., Kamat A., Kudoh J., Lehmann R., Lokitsang T., Macdonald P.,
RA Major J.E., Matthews C.D., Mauceli E., Menzel U., Mihalev A.H.,
RA Minoshima S., Murayama Y., Naylor J.W., Nicol R., Nguyen C., O'Leary S.B.,
RA O'Neill K., Parker S.C.J., Polley A., Raymond C.K., Reichwald K.,
RA Rodriguez J., Sasaki T., Schilhabel M., Siddiqui R., Smith C.L.,
RA Sneddon T.P., Talamas J.A., Tenzin P., Topham K., Venkataraman V., Wen G.,
RA Yamazaki S., Young S.K., Zeng Q., Zimmer A.R., Rosenthal A., Birren B.W.,
RA Platzer M., Shimizu N., Lander E.S.;
RT "DNA sequence and analysis of human chromosome 8.";
RL Nature 439:331-335(2006).
RN [5]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 500-1048 (ISOFORM 1).
RC TISSUE=Hepatoma;
RX PubMed=12097419; DOI=10.4049/jimmunol.169.2.1102;
RA Wang Y., Han K.-J., Pang X.-W., Vaughan H.A., Qu W., Dong X.-Y.,
RA Peng J.-R., Zhao H.-T., Rui J.-A., Leng X.-S., Cebon J., Burgess A.W.,
RA Chen W.-F.;
RT "Large scale identification of human hepatocellular carcinoma-associated
RT antigens by autoantibodies.";
RL J. Immunol. 169:1102-1109(2002).
RN [6]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 500-1048 (ISOFORM 1).
RA Hong W., Tham J.M., Li H.;
RT "Cloning and expression of EFA6R, an exchange factor of ARF6 homolog.";
RL Submitted (JUN-2002) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 506-1048 (ISOFORMS 1 AND 2).
RC TISSUE=Brain;
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 project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-770 AND SER-1020, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=18669648; DOI=10.1073/pnas.0805139105;
RA Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
RA Elledge S.J., Gygi S.P.;
RT "A quantitative atlas of mitotic phosphorylation.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-76, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Liver;
RX PubMed=24275569; DOI=10.1016/j.jprot.2013.11.014;
RA Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L.,
RA Ye M., Zou H.;
RT "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver
RT phosphoproteome.";
RL J. Proteomics 96:253-262(2014).
CC -!- FUNCTION: Guanine nucleotide exchange factor for ARF6. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000250|UniProtKB:Q2PFD7}.
CC Cell projection, ruffle membrane {ECO:0000250|UniProtKB:Q2PFD7}.
CC Postsynaptic density {ECO:0000250|UniProtKB:Q2PFD7}. Note=In interphase
CC associated with the plasma membrane, in particular with membrane
CC ruffling regions. {ECO:0000250|UniProtKB:Q2PFD7}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1;
CC IsoId=Q9NYI0-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9NYI0-2; Sequence=VSP_023029;
CC Name=3;
CC IsoId=Q9NYI0-3; Sequence=VSP_029155, VSP_029156, VSP_023029;
CC -!- TISSUE SPECIFICITY: Isoform 2 is expressed in epididymis (at protein
CC level). {ECO:0000269|PubMed:20736409}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF61269.2; Type=Erroneous initiation; Evidence={ECO:0000305};
CC Sequence=AAH75044.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC Sequence=AAH75045.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC Sequence=BAA76786.2; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; AB023159; BAA76786.2; ALT_INIT; mRNA.
DR EMBL; GU727648; ADU87649.1; -; mRNA.
DR EMBL; AC009884; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AC087821; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AC090420; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AC100800; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AC120051; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AF519767; AAM74203.1; -; mRNA.
DR EMBL; AF243495; AAF61269.2; ALT_INIT; mRNA.
DR EMBL; BC075044; AAH75044.1; ALT_INIT; mRNA.
DR EMBL; BC075045; AAH75045.1; ALT_INIT; mRNA.
DR CCDS; CCDS34854.1; -. [Q9NYI0-3]
DR CCDS; CCDS43720.1; -. [Q9NYI0-2]
DR RefSeq; NP_056125.3; NM_015310.3. [Q9NYI0-2]
DR RefSeq; NP_996792.1; NM_206909.2. [Q9NYI0-3]
DR AlphaFoldDB; Q9NYI0; -.
DR SMR; Q9NYI0; -.
DR BioGRID; 116943; 55.
DR IntAct; Q9NYI0; 30.
DR MINT; Q9NYI0; -.
DR STRING; 9606.ENSP00000324127; -.
DR iPTMnet; Q9NYI0; -.
DR PhosphoSitePlus; Q9NYI0; -.
DR SwissPalm; Q9NYI0; -.
DR BioMuta; PSD3; -.
DR DMDM; 160332377; -.
DR EPD; Q9NYI0; -.
DR jPOST; Q9NYI0; -.
DR MassIVE; Q9NYI0; -.
DR MaxQB; Q9NYI0; -.
DR PaxDb; Q9NYI0; -.
DR PeptideAtlas; Q9NYI0; -.
DR PRIDE; Q9NYI0; -.
DR ProteomicsDB; 83232; -. [Q9NYI0-1]
DR ProteomicsDB; 83233; -. [Q9NYI0-2]
DR ProteomicsDB; 83234; -. [Q9NYI0-3]
DR Antibodypedia; 9043; 153 antibodies from 22 providers.
DR DNASU; 23362; -.
DR Ensembl; ENST00000286485.12; ENSP00000286485.8; ENSG00000156011.18. [Q9NYI0-3]
DR Ensembl; ENST00000327040.13; ENSP00000324127.8; ENSG00000156011.18. [Q9NYI0-2]
DR Ensembl; ENST00000440756.4; ENSP00000401704.3; ENSG00000156011.18. [Q9NYI0-1]
DR GeneID; 23362; -.
DR KEGG; hsa:23362; -.
DR MANE-Select; ENST00000327040.13; ENSP00000324127.8; NM_015310.4; NP_056125.3. [Q9NYI0-2]
DR UCSC; uc003wyy.4; human. [Q9NYI0-1]
DR CTD; 23362; -.
DR DisGeNET; 23362; -.
DR GeneCards; PSD3; -.
DR HGNC; HGNC:19093; PSD3.
DR HPA; ENSG00000156011; Tissue enhanced (brain).
DR MIM; 614440; gene.
DR neXtProt; NX_Q9NYI0; -.
DR OpenTargets; ENSG00000156011; -.
DR PharmGKB; PA128394629; -.
DR VEuPathDB; HostDB:ENSG00000156011; -.
DR eggNOG; KOG0932; Eukaryota.
DR GeneTree; ENSGT00940000156591; -.
DR HOGENOM; CLU_011021_1_1_1; -.
DR InParanoid; Q9NYI0; -.
DR OrthoDB; 301851at2759; -.
DR PhylomeDB; Q9NYI0; -.
DR TreeFam; TF319755; -.
DR PathwayCommons; Q9NYI0; -.
DR SignaLink; Q9NYI0; -.
DR BioGRID-ORCS; 23362; 13 hits in 1066 CRISPR screens.
DR ChiTaRS; PSD3; human.
DR GenomeRNAi; 23362; -.
DR Pharos; Q9NYI0; Tbio.
DR PRO; PR:Q9NYI0; -.
DR Proteomes; UP000005640; Chromosome 8.
DR RNAct; Q9NYI0; protein.
DR Bgee; ENSG00000156011; Expressed in Brodmann (1909) area 23 and 199 other tissues.
DR ExpressionAtlas; Q9NYI0; baseline and differential.
DR Genevisible; Q9NYI0; HS.
DR GO; GO:0070161; C:anchoring junction; IEA:UniProtKB-KW.
DR GO; GO:0014069; C:postsynaptic density; IEA:UniProtKB-SubCell.
DR GO; GO:0032587; C:ruffle membrane; ISS:UniProtKB.
DR GO; GO:0005085; F:guanyl-nucleotide exchange factor activity; IEA:UniProtKB-KW.
DR GO; GO:0032012; P:regulation of ARF protein signal transduction; IEA:InterPro.
DR CDD; cd00171; Sec7; 1.
DR Gene3D; 1.10.1000.11; -; 1.
DR Gene3D; 2.30.29.30; -; 1.
DR InterPro; IPR011993; PH-like_dom_sf.
DR InterPro; IPR041681; PH_9.
DR InterPro; IPR001849; PH_domain.
DR InterPro; IPR023394; Sec7_C_sf.
DR InterPro; IPR000904; Sec7_dom.
DR InterPro; IPR035999; Sec7_dom_sf.
DR Pfam; PF15410; PH_9; 1.
DR Pfam; PF01369; Sec7; 1.
DR SMART; SM00233; PH; 1.
DR SMART; SM00222; Sec7; 1.
DR SUPFAM; SSF48425; SSF48425; 1.
DR PROSITE; PS50003; PH_DOMAIN; 1.
DR PROSITE; PS50190; SEC7; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Cell membrane; Cell projection; Coiled coil;
KW Guanine-nucleotide releasing factor; Membrane; Phosphoprotein;
KW Reference proteome; Synapse.
FT CHAIN 1..1048
FT /note="PH and SEC7 domain-containing protein 3"
FT /id="PRO_0000120205"
FT DOMAIN 534..734
FT /note="SEC7"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00189"
FT DOMAIN 785..898
FT /note="PH"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00145"
FT REGION 36..57
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 104..126
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 310..342
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 364..383
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 395..434
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 741..769
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 999..1048
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 922..952
FT /evidence="ECO:0000255"
FT COMPBIAS 395..429
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 741..761
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1007..1026
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1027..1048
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 76
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:24275569"
FT MOD_RES 770
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18669648"
FT MOD_RES 1009
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q2PFD7"
FT MOD_RES 1011
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q2PFD7"
FT MOD_RES 1012
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q2PFD7"
FT MOD_RES 1014
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q2PFD7"
FT MOD_RES 1020
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18669648"
FT VAR_SEQ 1..534
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:10231032"
FT /id="VSP_029155"
FT VAR_SEQ 535..545
FT /note="KGTPEIAFWGS -> MGSSWCLYGCC (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:10231032"
FT /id="VSP_029156"
FT VAR_SEQ 695
FT /note="Missing (in isoform 2 and isoform 3)"
FT /evidence="ECO:0000303|PubMed:10231032,
FT ECO:0000303|PubMed:15489334, ECO:0000303|PubMed:20736409"
FT /id="VSP_023029"
FT VARIANT 186
FT /note="T -> M (in dbSNP:rs7016219)"
FT /id="VAR_036947"
FT VARIANT 186
FT /note="T -> P (in dbSNP:rs7003060)"
FT /id="VAR_036948"
FT VARIANT 293
FT /note="P -> L (in dbSNP:rs13263453)"
FT /id="VAR_036949"
SQ SEQUENCE 1048 AA; 116034 MW; BE879B65AB390162 CRC64;
MEGRSAAAET FVWVNNASAH SQSVAKAKYE FLFGRSEGKA PDTSDHGGST LLPPNVTNEF
PEYGTMEEGG EGLRASLEFD GEALPCHPQE QQGVQPLTGC HSGLDSVTEG PKDVREAPSQ
SHLKEQSLQP IDSLISALKA TEARIISGTL QATKVLDQDA VSSFSVQQVE KELDTASRKT
QRVNKTLPAG QKNLPEIPLS AEVTTEESFY LSIQKDLTAL LTGDTQAEIS QIMNNGRKGA
VCVQEPSCPL ASLGSSAVTC HSAGSVGFLK EQRSALGREH PGGCDRSSSM GRPGRVKHVE
FQGVEILWTG GDKRETQHPI DFETSLQRTA SPDSKESSKV PRHLISSAGL CNSSSLTENV
WDESWKAPSE RPGTSSGTFS PVRLDESGED EVFLQENKQH LEKTPKPERD RERISEQEEH
VKGEDEDILG PGYTEDSTDV YSSQFETILD NTSLYYSAES LETLYSEPDS YFSFEMPLTP
MIQQRIKEGG QFLERTSGGG HQDILSVSAD GGIVMGYSSG VTNGLNDASD SIYTKGTPEI
AFWGSNAGVK TTRLEAHSEM GSTEILEKET PENLSNGTSS NVEAAKRLAK RLYQLDRFKR
SDVAKHLGKN NEFSKLVAEE YLKFFDFTGM TLDQSLRYFF KAFSLVGETQ ERERVLIHFS
NRYFYCNPDT IASQDGVHCL TCAIMLLNTD LHGHVNIGKK MTCQEFIANL QGVNEGVDFS
KDLLKALYNS IKNEKLEWAV DDEEKKKSPS ESTEEKANGT HPKTISRIGS TTNPFLDIPH
DPNAAVYKSG FLARKIHADM DGKKTPRGKR GWKTFYAVLK GTVLYLQKDE YKPEKALSEE
DLKNAVSVHH ALASKATDYE KKPNVFKLKT ADWRVLLFQT QSPEEMQGWI NKINCVAAVF
SAPPFPAAIG SQKKFSRPLL PATTTKLSQE EQLKSHESKL KQITTELAEH RSYPPDKKVK
AKDVDEYKLK DHYLEFEKTR YEMYVSILKE GGKELLSNDE SEAAGLKKSH SSPSLNPDTS
PITAKVKRNV SERKDHRPET PSIKQKVT
