Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Immunoglobulin superfamily member 3

Gene

IGSF3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

Functioni

GO - Biological processi

  • lacrimal gland development Source: UniProtKB
Complete GO annotation...

Names & Taxonomyi

Protein namesi
Recommended name:
Immunoglobulin superfamily member 3
Short name:
IgSF3
Alternative name(s):
Glu-Trp-Ile EWI motif-containing protein 3
Short name:
EWI-3
Gene namesi
Name:IGSF3
Synonyms:EWI3, KIAA0466
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:5950. IGSF3.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini20 – 11241105ExtracellularSequence analysisAdd
BLAST
Transmembranei1125 – 114521HelicalSequence analysisAdd
BLAST
Topological domaini1146 – 119449CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

  • cell surface Source: UniProtKB
  • integral component of membrane Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Involvement in diseasei

Lacrimal duct defect (LCDD)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA condition resulting in the imbalance between tear production and tear drainage. Infants typically manifest persistent epiphora and/or recurrent infections of the lacrimal pathway, such as conjunctivitis. LCDD is caused by failure of the nasolacrimal duct to open into the inferior meatus.
See also OMIM:149700

Organism-specific databases

MalaCardsiIGSF3.
MIMi149700. phenotype.
PharmGKBiPA29763.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 1919Sequence analysisAdd
BLAST
Chaini20 – 11941175Immunoglobulin superfamily member 3PRO_0000320134Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi42 ↔ 120PROSITE-ProRule annotation
Glycosylationi43 – 431N-linked (GlcNAc...)Sequence analysis
Disulfide bondi167 ↔ 246PROSITE-ProRule annotation
Disulfide bondi302 ↔ 376PROSITE-ProRule annotation
Glycosylationi418 – 4181N-linked (GlcNAc...)Sequence analysis
Disulfide bondi432 ↔ 511PROSITE-ProRule annotation
Disulfide bondi566 ↔ 645PROSITE-ProRule annotation
Glycosylationi655 – 6551N-linked (GlcNAc...)Sequence analysis
Disulfide bondi701 ↔ 782PROSITE-ProRule annotation
Disulfide bondi838 ↔ 918PROSITE-ProRule annotation
Glycosylationi842 – 8421N-linked (GlcNAc...)Sequence analysis
Disulfide bondi974 ↔ 1080PROSITE-ProRule annotation
Glycosylationi1077 – 10771N-linked (GlcNAc...)Sequence analysis

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

EPDiO75054.
MaxQBiO75054.
PaxDbiO75054.
PRIDEiO75054.

PTM databases

iPTMnetiO75054.
PhosphoSiteiO75054.

Expressioni

Tissue specificityi

Expressed in a wide range of tissues with High expression in Placenta, kidney and lung.1 Publication

Gene expression databases

BgeeiO75054.
CleanExiHS_IGSF3.
GenevisibleiO75054. HS.

Organism-specific databases

HPAiHPA036305.
HPA036306.

Interactioni

Protein-protein interaction databases

BioGridi109553. 7 interactions.
STRINGi9606.ENSP00000321184.

Structurei

3D structure databases

ProteinModelPortaliO75054.
SMRiO75054. Positions 25-250.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini20 – 138119Ig-like C2-type 1Add
BLAST
Domaini143 – 262120Ig-like C2-type 2Add
BLAST
Domaini276 – 386111Ig-like C2-type 3Add
BLAST
Domaini401 – 539139Ig-like C2-type 4Add
BLAST
Domaini545 – 661117Ig-like C2-type 5Add
BLAST
Domaini676 – 803128Ig-like C2-type 6Add
BLAST
Domaini813 – 945133Ig-like C2-type 7Add
BLAST
Domaini949 – 1097149Ig-like C2-type 8Add
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi250 – 2523EWI motif

Sequence similaritiesi

Keywords - Domaini

Immunoglobulin domain, Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410IFBX. Eukaryota.
ENOG410YWQX. LUCA.
GeneTreeiENSGT00390000010278.
HOGENOMiHOG000293322.
HOVERGENiHBG107998.
InParanoidiO75054.
KOiK06522.
OMAiVEEWLLN.
OrthoDBiEOG7ZKS99.
PhylomeDBiO75054.
TreeFamiTF332702.

Family and domain databases

Gene3Di2.60.40.10. 8 hits.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003599. Ig_sub.
IPR003598. Ig_sub2.
IPR013106. Ig_V-set.
[Graphical view]
PfamiPF07686. V-set. 4 hits.
[Graphical view]
SMARTiSM00409. IG. 8 hits.
SM00408. IGc2. 4 hits.
SM00406. IGv. 4 hits.
[Graphical view]
SUPFAMiSSF48726. SSF48726. 7 hits.
PROSITEiPS50835. IG_LIKE. 7 hits.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: O75054-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MKCFFPVLSC LAVLGVVSAQ RQVTVQEGPL YRTEGSHITI WCNVSGYQGP
60 70 80 90 100
SEQNFQWSIY LPSSPEREVQ IVSTMDSSFP YAIYTQRVRG GKIFIERVQG
110 120 130 140 150
NSTLLHITDL QARDAGEYEC HTPSTDKQYF GSYSAKMNLV VIPDSLQTTA
160 170 180 190 200
MPQTLHRVEQ DPLELTCEVA SETIQHSHLS VAWLRQKVGE KPVEVISLSR
210 220 230 240 250
DFMLHSSSEY AQRQSLGEVR LDKLGRTTFR LTIFHLQPSD QGEFYCEAAE
260 270 280 290 300
WIQDPDGSWY AMTRKRSEGA VVNVQPTDKE FTVRLETEKR LHTVGEPVEF
310 320 330 340 350
RCILEAQNVP DRYFAVSWAF NSSLIATMGP NAVPVLNSEF AHREARGQLK
360 370 380 390 400
VAKESDSVFV LKIYHLRQED SGKYNCRVTE REKTVTGEFI DKESKRPKNI
410 420 430 440 450
PIIVLPLKSS ISVEVASNAS VILEGEDLRF SCSVRTAGRP QGRFSVIWQL
460 470 480 490 500
VDRQNRRSNI MWLDRDGTVQ PGSSYWERSS FGGVQMEQVQ PNSFSLGIFN
510 520 530 540 550
SRKEDEGQYE CHVTEWVRAV DGEWQIVGER RASTPISITA LEMGFAVTAI
560 570 580 590 600
SRTPGVTYSD SFDLQCIIKP HYPAWVPVSV TWRFQPVGTV EFHDLVTFTR
610 620 630 640 650
DGGVQWGDRS SSFRTRTAIE KAESSNNVRL SISRASDTEA GKYQCVAELW
660 670 680 690 700
RKNYNNTWTR LAERTSNLLE IRVLQPVTKL QVSKSKRTLT LVENKPIQLN
710 720 730 740 750
CSVKSQTSQN SHFAVLWYVH KPSDADGKLI LKTTHNSAFE YGTYAEEEGL
760 770 780 790 800
RARLQFERHV SGGLFSLTVQ RAEVSDSGSY YCHVEEWLLS PNYAWYKLAE
810 820 830 840 850
EVSGRTEVTV KQPDSRLRLS QAQGNLSVLE TRQVQLECVV LNRTSITSQL
860 870 880 890 900
MVEWFVWKPN HPERETVARL SRDATFHYGE QAAKNNLKGR LHLESPSPGV
910 920 930 940 950
YRLFIQNVAV QDSGTYSCHV EEWLPSPSGM WYKRAEDTAG QTALTVMRPD
960 970 980 990 1000
ASLQVDTVVP NATVSEKAAF QLDCSIVSRS SQDSRFAVAW YSLRTKAGGK
1010 1020 1030 1040 1050
RSSPGLEEQE EEREEEEEED DDDDDDPTER TALLSVGPDA VFGPEGSPWE
1060 1070 1080 1090 1100
GRLRFQRLSP VLYRLTVLQA SPQDTGNYSC HVEEWLPSPQ KEWYRLTEEE
1110 1120 1130 1140 1150
SAPIGIRVLD TSPTLQSIIC SNDALFYFVF FYPFPIFGIL IITILLVRFK
1160 1170 1180 1190
SRNSSKNSDG KNGVPLLWIK EPHLNYSPTC LEPPVLSIHP GAID
Length:1,194
Mass (Da):135,196
Last modified:February 26, 2008 - v3
Checksum:iC5E22EDBC81714DD
GO
Isoform 2 (identifier: O75054-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     407-408: LK → LTDNWVVKVPQHHQLLSQGHLE

Show »
Length:1,214
Mass (Da):137,516
Checksum:i78BA82F1F6D072BA
GO

Sequence cautioni

The sequence AAC72013.1 differs from that shown. Reason: Frameshift at positions 829 and 861. Curated
The sequence BAA32311.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti932 – 9321Y → S in AAC72013 (PubMed:9790749).Curated
Sequence conflicti1013 – 10131R → RE in AAC72013 (PubMed:9790749).Curated
Sequence conflicti1047 – 10471S → N in AAC72013 (PubMed:9790749).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti51 – 511S → P.
Corresponds to variant rs3965246 [ dbSNP | Ensembl ].
VAR_039134
Natural varianti1020 – 10201D → E.1 Publication
Corresponds to variant rs647711 [ dbSNP | Ensembl ].
VAR_039135
Natural varianti1073 – 10731Q → R.
Corresponds to variant rs6703791 [ dbSNP | Ensembl ].
VAR_039136

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei407 – 4082LK → LTDNWVVKVPQHHQLLSQGH LE in isoform 2. 1 PublicationVSP_031609

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF031174 mRNA. Translation: AAC72013.1. Frameshift.
AB007935 mRNA. Translation: BAA32311.2. Different initiation.
AL355794 Genomic DNA. No translation available.
AL356748 Genomic DNA. No translation available.
CCDSiCCDS30813.1. [O75054-1]
CCDS30814.1. [O75054-2]
RefSeqiNP_001007238.1. NM_001007237.2. [O75054-1]
NP_001533.2. NM_001542.3. [O75054-2]
XP_005270850.1. XM_005270793.2. [O75054-2]
XP_011539617.1. XM_011541315.1. [O75054-2]
UniGeneiHs.171057.

Genome annotation databases

EnsembliENST00000318837; ENSP00000321184; ENSG00000143061. [O75054-2]
ENST00000369483; ENSP00000358495; ENSG00000143061. [O75054-2]
ENST00000369486; ENSP00000358498; ENSG00000143061. [O75054-1]
GeneIDi3321.
KEGGihsa:3321.
UCSCiuc001egr.3. human. [O75054-1]

Keywords - Coding sequence diversityi

Alternative splicing, Chromosomal rearrangement, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF031174 mRNA. Translation: AAC72013.1. Frameshift.
AB007935 mRNA. Translation: BAA32311.2. Different initiation.
AL355794 Genomic DNA. No translation available.
AL356748 Genomic DNA. No translation available.
CCDSiCCDS30813.1. [O75054-1]
CCDS30814.1. [O75054-2]
RefSeqiNP_001007238.1. NM_001007237.2. [O75054-1]
NP_001533.2. NM_001542.3. [O75054-2]
XP_005270850.1. XM_005270793.2. [O75054-2]
XP_011539617.1. XM_011541315.1. [O75054-2]
UniGeneiHs.171057.

3D structure databases

ProteinModelPortaliO75054.
SMRiO75054. Positions 25-250.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi109553. 7 interactions.
STRINGi9606.ENSP00000321184.

PTM databases

iPTMnetiO75054.
PhosphoSiteiO75054.

Proteomic databases

EPDiO75054.
MaxQBiO75054.
PaxDbiO75054.
PRIDEiO75054.

Protocols and materials databases

DNASUi3321.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000318837; ENSP00000321184; ENSG00000143061. [O75054-2]
ENST00000369483; ENSP00000358495; ENSG00000143061. [O75054-2]
ENST00000369486; ENSP00000358498; ENSG00000143061. [O75054-1]
GeneIDi3321.
KEGGihsa:3321.
UCSCiuc001egr.3. human. [O75054-1]

Organism-specific databases

CTDi3321.
GeneCardsiIGSF3.
H-InvDBHIX0000930.
HGNCiHGNC:5950. IGSF3.
HPAiHPA036305.
HPA036306.
MalaCardsiIGSF3.
MIMi149700. phenotype.
603491. gene.
neXtProtiNX_O75054.
PharmGKBiPA29763.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IFBX. Eukaryota.
ENOG410YWQX. LUCA.
GeneTreeiENSGT00390000010278.
HOGENOMiHOG000293322.
HOVERGENiHBG107998.
InParanoidiO75054.
KOiK06522.
OMAiVEEWLLN.
OrthoDBiEOG7ZKS99.
PhylomeDBiO75054.
TreeFamiTF332702.

Miscellaneous databases

ChiTaRSiIGSF3. human.
GenomeRNAii3321.
NextBioi13168.
PROiO75054.
SOURCEiSearch...

Gene expression databases

BgeeiO75054.
CleanExiHS_IGSF3.
GenevisibleiO75054. HS.

Family and domain databases

Gene3Di2.60.40.10. 8 hits.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003599. Ig_sub.
IPR003598. Ig_sub2.
IPR013106. Ig_V-set.
[Graphical view]
PfamiPF07686. V-set. 4 hits.
[Graphical view]
SMARTiSM00409. IG. 8 hits.
SM00408. IGc2. 4 hits.
SM00406. IGv. 4 hits.
[Graphical view]
SUPFAMiSSF48726. SSF48726. 7 hits.
PROSITEiPS50835. IG_LIKE. 7 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Molecular cloning of a human cDNA IGSF3 encoding an immunoglobulin-like membrane protein: expression and mapping to chromosome band 1p13."
    Saupe S., Roizes G., Peter M., Boyle S., Gardiner K., De Sario A.
    Genomics 52:305-311(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), TISSUE SPECIFICITY, VARIANT GLU-1020.
  2. "Characterization of cDNA clones in size-fractionated cDNA libraries from human brain."
    Seki N., Ohira M., Nagase T., Ishikawa K., Miyajima N., Nakajima D., Nomura N., Ohara O.
    DNA Res. 4:345-349(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Brain.
  3. "Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones."
    Nakajima D., Okazaki N., Yamakawa H., Kikuno R., Ohara O., Nagase T.
    DNA Res. 9:99-106(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: SEQUENCE REVISION.
  4. "The DNA sequence and biological annotation of human chromosome 1."
    Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.
    , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
    Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "EWI-2 is a major CD9 and CD81 partner and member of a novel Ig protein subfamily."
    Stipp C.S., Kolesnikova T.V., Hemler M.E.
    J. Biol. Chem. 276:40545-40554(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: DOMAIN EWI MOTIF.
  6. "Shuffling of genes within low-copy repeats on 22q11 (LCR22) by Alu-mediated recombination events during evolution."
    Babcock M., Pavlicek A., Spiteri E., Kashork C.D., Ioshikhes I., Shaffer L.G., Jurka J., Morrow B.E.
    Genome Res. 13:2519-2532(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: BREAKPOINTS.
  7. "Identification of an IGSF3 mutation in a family with congenital nasolacrimal duct obstruction."
    Foster J., Kapoor S., Diaz-Horta O., Singh A., Abad C., Rastogi A., Moharana R., Tekeli O., Walz K., Tekin M.
    Clin. Genet. 86:589-591(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: INVOLVEMENT IN LCDD.

Entry informationi

Entry nameiIGSF3_HUMAN
AccessioniPrimary (citable) accession number: O75054
Secondary accession number(s): A6NJZ6, A6NMC7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 26, 2008
Last sequence update: February 26, 2008
Last modified: May 11, 2016
This is version 119 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Miscellaneous

Likely interchromosomal Alu-mediated fusion between IGSF3 on 1p13.1 and GGT on 22q11.2. Breakpoints occurred inside Alu elements as well as in the 5' or 3' ends of them.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.