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Protein

T-lymphocyte surface antigen Ly-9

Gene

LY9

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Self-ligand receptor of the signaling lymphocytic activation molecule (SLAM) family. SLAM receptors triggered by homo- or heterotypic cell-cell interactions are modulating the activation and differentiation of a wide variety of immune cells and thus are involved in the regulation and interconnection of both innate and adaptive immune response. Activities are controlled by presence or absence of small cytoplasmic adapter proteins, SH2D1A/SAP and/or SH2D1B/EAT-2. May participate in adhesion reactions between T lymphocytes and accessory cells by homophilic interaction. Promotes T-cell differentiation into a helper T-cell Th17 phenotype leading to increased IL-17 secretion; the costimulatory activity requires SH2D1A (PubMed:22184727). Promotes recruitment of RORC to the IL-17 promoter (PubMed:22989874). May be involved in the maintenance of peripheral cell tolerance by serving as a negative regulator of the immune response. May disable autoantibody responses and inhibit IFN-gamma secretion by CD4+ T-cells. May negatively regulate the size of thymic innate CD8+ T-cells and the development of invariant natural killer T (iNKT) cells (By similarity).By similarity2 Publications

GO - Biological processi

Keywordsi

Biological processAdaptive immunity, Cell adhesion, Immunity, Innate immunity

Names & Taxonomyi

Protein namesi
Recommended name:
T-lymphocyte surface antigen Ly-9
Alternative name(s):
Cell surface molecule Ly-9
Lymphocyte antigen 9
SLAM family member 3
Short name:
SLAMF3
Signaling lymphocytic activation molecule 3
CD_antigen: CD229
Gene namesi
Name:LY9
ORF Names:CDABP0070
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

EuPathDBiHostDB:ENSG00000122224.17
HGNCiHGNC:6730 LY9
MIMi600684 gene
neXtProtiNX_Q9HBG7

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini48 – 454ExtracellularSequence analysisAdd BLAST407
Transmembranei455 – 476HelicalSequence analysisAdd BLAST22
Topological domaini477 – 655CytoplasmicSequence analysisAdd BLAST179

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Organism-specific databases

DisGeNETi4063
OpenTargetsiENSG00000122224
PharmGKBiPA30494

Polymorphism and mutation databases

BioMutaiLY9
DMDMi71152965

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 47Sequence analysisAdd BLAST47
ChainiPRO_000001485148 – 655T-lymphocyte surface antigen Ly-9Add BLAST608

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi68N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi95N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi120N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi169N-linked (GlcNAc...) asparagineSequence analysis1
Disulfide bondi172 ↔ 242PROSITE-ProRule annotation
Glycosylationi173N-linked (GlcNAc...) asparagineSequence analysis1
Disulfide bondi178 ↔ 222PROSITE-ProRule annotation
Glycosylationi285N-linked (GlcNAc...) asparagine1 Publication1
Disulfide bondi377 ↔ 446PROSITE-ProRule annotation
Disulfide bondi383 ↔ 427PROSITE-ProRule annotation
Glycosylationi413N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi424N-linked (GlcNAc...) asparagineSequence analysis1
Modified residuei603Phosphotyrosine2 Publications1

Keywords - PTMi

Disulfide bond, Glycoprotein, Phosphoprotein

Proteomic databases

PaxDbiQ9HBG7
PeptideAtlasiQ9HBG7
PRIDEiQ9HBG7
ProteomicsDBi81544
81545 [Q9HBG7-2]
81546 [Q9HBG7-3]
81547 [Q9HBG7-4]

PTM databases

iPTMnetiQ9HBG7
PhosphoSitePlusiQ9HBG7
SwissPalmiQ9HBG7

Expressioni

Tissue specificityi

Increased surface expression on T-cells of systemic lupus erythematosus (SLE) patients.1 Publication

Gene expression databases

BgeeiENSG00000122224 Expressed in 126 organ(s), highest expression level in blood
CleanExiHS_LY9
ExpressionAtlasiQ9HBG7 baseline and differential
GenevisibleiQ9HBG7 HS

Organism-specific databases

HPAiHPA050917

Interactioni

Subunit structurei

Interacts with SH2D1A, SH2D1B and INPP5D. Interacts (via phosphorylated cytoplasmic domain) with PTPN11; the interaction is blocked by SH2D1A.3 Publications

Protein-protein interaction databases

BioGridi110241, 4 interactors
ELMiQ9HBG7
IntActiQ9HBG7, 3 interactors
STRINGi9606.ENSP00000357020

Structurei

3D structure databases

ProteinModelPortaliQ9HBG7
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini48 – 158Ig-like V-type 1Add BLAST111
Domaini159 – 235Ig-like C2-type 1Add BLAST77
Domaini251 – 363Ig-like V-type 2Add BLAST113
Domaini364 – 452Ig-like C2-type 2Add BLAST89

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi601 – 606ITSM 1By similarity6
Motifi624 – 629ITSM 2By similarity6

Domaini

The ITSMs (immunoreceptor tyrosine-based switch motifs) with the consensus sequence T-X-Y-X-X-[VI] present in SLAM family receptors have overlapping specificity for activating and inhibitory SH2 domain-containing binding partners. Especially they mediate the interaction with the SH2 domain of SH2D1A and SH2D1B. A 'three-pronged' mechanism is proposed involving threonine (position -2), phosphorylated tyrosine (position 0) and valine/isoleucine (position +3).By similarity1 Publication

Keywords - Domaini

Immunoglobulin domain, Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410JJ3F Eukaryota
ENOG410ZAYK LUCA
GeneTreeiENSGT00530000063114
HOGENOMiHOG000013143
HOVERGENiHBG030765
InParanoidiQ9HBG7
KOiK06570
OMAiCRVSLTC
OrthoDBiEOG091G0KKU
PhylomeDBiQ9HBG7
TreeFamiTF334964

Family and domain databases

Gene3Di2.60.40.10, 4 hits
InterProiView protein in InterPro
IPR007110 Ig-like_dom
IPR036179 Ig-like_dom_sf
IPR013783 Ig-like_fold
IPR003599 Ig_sub
SMARTiView protein in SMART
SM00409 IG, 2 hits
SUPFAMiSSF48726 SSF48726, 4 hits
PROSITEiView protein in PROSITE
PS50835 IG_LIKE, 2 hits

Sequences (4+)i

Sequence statusi: Complete.

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

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket
Note: Experimental confirmation may be lacking for some isoforms.

This entry has 4 described isoforms and 5 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: Q9HBG7-1) [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
MVAPKSHTDD WAPGPFSSKP QRSQLQIFSS VLQTSLLFLL MGLRASGKDS
60 70 80 90 100
APTVVSGILG GSVTLPLNIS VDTEIENVIW IGPKNALAFA RPKENVTIMV
110 120 130 140 150
KSYLGRLDIT KWSYSLCISN LTLNDAGSYK AQINQRNFEV TTEEEFTLFV
160 170 180 190 200
YEQLQEPQVT MKSVKVSENF SCNITLMCSV KGAEKSVLYS WTPREPHASE
210 220 230 240 250
SNGGSILTVS RTPCDPDLPY ICTAQNPVSQ RSSLPVHVGQ FCTDPGASRG
260 270 280 290 300
GTTGETVVGV LGEPVTLPLA LPACRDTEKV VWLFNTSIIS KEREEAATAD
310 320 330 340 350
PLIKSRDPYK NRVWVSSQDC SLKISQLKIE DAGPYHAYVC SEASSVTSMT
360 370 380 390 400
HVTLLIYRRL RKPKITWSLR HSEDGICRIS LTCSVEDGGN TVMYTWTPLQ
410 420 430 440 450
KEAVVSQGES HLNVSWRSSE NHPNLTCTAS NPVSRSSHQF LSENICSGPE
460 470 480 490 500
RNTKLWIGLF LMVCLLCVGI FSWCIWKRKG RCSVPAFCSS QAEAPADTPE
510 520 530 540 550
PTAGHTLYSV LSQGYEKLDT PLRPARQQPT PTSDSSSDSN LTTEEDEDRP
560 570 580 590 600
EVHKPISGRY EVFDQVTQEG AGHDPAPEGQ ADYDPVTPYV TEVESVVGEN
610 620 630 640 650
TMYAQVFNLQ GKTPVSQKEE SSATIYCSIR KPQVVPPPQQ NDLEIPESPT

YENFT
Length:655
Mass (Da):72,139
Last modified:July 19, 2005 - v3
Checksum:i84ABA3056D69E80A
GO
Isoform 2 (identifier: Q9HBG7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     500-513: Missing.

Show »
Length:641
Mass (Da):70,655
Checksum:i8649951FCE64465C
GO
Isoform 3 (identifier: Q9HBG7-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     359-448: Missing.
     500-513: Missing.
     524-554: PARQQPTPTSDSSSDSNLTTEEDEDRPEVHK → Q

Show »
Length:521
Mass (Da):57,320
Checksum:i615B60DC9AB6766E
GO
Isoform 4 (identifier: Q9HBG7-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     152-193: EQLQEPQVTM...EKSVLYSWTP → APFIEKLSVH...AEPRVSVREG

Note: No experimental confirmation available.
Show »
Length:655
Mass (Da):71,961
Checksum:iB096694A12285C5C
GO

Computationally mapped potential isoform sequencesi

There are 5 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
Q5VYH9Q5VYH9_HUMAN
T-lymphocyte surface antigen Ly-9
LY9
565Annotation score:
Q5VYI1Q5VYI1_HUMAN
T-lymphocyte surface antigen Ly-9
LY9
341Annotation score:
A0A0C4DFU4A0A0C4DFU4_HUMAN
T-lymphocyte surface antigen Ly-9
LY9
193Annotation score:
V9GY30V9GY30_HUMAN
T-lymphocyte surface antigen Ly-9
LY9
61Annotation score:
R4GNG7R4GNG7_HUMAN
T-lymphocyte surface antigen Ly-9
LY9
71Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti171Missing in AAG14995 (PubMed:10970093).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_033612602M → V Decreases interaction with SH2D1A and INPP5D 2-fold, reduced T-cell response. 3 PublicationsCorresponds to variant dbSNP:rs509749Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_043328152 – 193EQLQE…YSWTP → APFIEKLSVHVIEGDHRTLL EGSGLESIISTLAEPRVSVR EG in isoform 4. 1 PublicationAdd BLAST42
Alternative sequenceiVSP_002524359 – 448Missing in isoform 3. 1 PublicationAdd BLAST90
Alternative sequenceiVSP_002525500 – 513Missing in isoform 2 and isoform 3. 2 PublicationsAdd BLAST14
Alternative sequenceiVSP_002526524 – 554PARQQ…PEVHK → Q in isoform 3. 1 PublicationAdd BLAST31

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF244129 mRNA Translation: AAG14995.1
AK292048 mRNA Translation: BAF84737.1
AL121985 Genomic DNA No translation available.
AL354714 Genomic DNA No translation available.
CH471121 Genomic DNA Translation: EAW52699.1
BC064485 mRNA Translation: AAH64485.1
L42621 mRNA Translation: AAA92623.1
AY007142 mRNA Translation: AAG02002.1
CCDSiCCDS30916.1 [Q9HBG7-1]
CCDS65695.1 [Q9HBG7-2]
RefSeqiNP_001028839.1, NM_001033667.2
NP_001248385.1, NM_001261456.1 [Q9HBG7-2]
NP_002339.2, NM_002348.3 [Q9HBG7-1]
UniGeneiHs.403857

Genome annotation databases

EnsembliENST00000263285; ENSP00000263285; ENSG00000122224 [Q9HBG7-1]
ENST00000368037; ENSP00000357016; ENSG00000122224 [Q9HBG7-2]
GeneIDi4063
KEGGihsa:4063
UCSCiuc001fwt.5 human [Q9HBG7-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF244129 mRNA Translation: AAG14995.1
AK292048 mRNA Translation: BAF84737.1
AL121985 Genomic DNA No translation available.
AL354714 Genomic DNA No translation available.
CH471121 Genomic DNA Translation: EAW52699.1
BC064485 mRNA Translation: AAH64485.1
L42621 mRNA Translation: AAA92623.1
AY007142 mRNA Translation: AAG02002.1
CCDSiCCDS30916.1 [Q9HBG7-1]
CCDS65695.1 [Q9HBG7-2]
RefSeqiNP_001028839.1, NM_001033667.2
NP_001248385.1, NM_001261456.1 [Q9HBG7-2]
NP_002339.2, NM_002348.3 [Q9HBG7-1]
UniGeneiHs.403857

3D structure databases

ProteinModelPortaliQ9HBG7
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi110241, 4 interactors
ELMiQ9HBG7
IntActiQ9HBG7, 3 interactors
STRINGi9606.ENSP00000357020

PTM databases

iPTMnetiQ9HBG7
PhosphoSitePlusiQ9HBG7
SwissPalmiQ9HBG7

Polymorphism and mutation databases

BioMutaiLY9
DMDMi71152965

Proteomic databases

PaxDbiQ9HBG7
PeptideAtlasiQ9HBG7
PRIDEiQ9HBG7
ProteomicsDBi81544
81545 [Q9HBG7-2]
81546 [Q9HBG7-3]
81547 [Q9HBG7-4]

Protocols and materials databases

DNASUi4063
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000263285; ENSP00000263285; ENSG00000122224 [Q9HBG7-1]
ENST00000368037; ENSP00000357016; ENSG00000122224 [Q9HBG7-2]
GeneIDi4063
KEGGihsa:4063
UCSCiuc001fwt.5 human [Q9HBG7-1]

Organism-specific databases

CTDi4063
DisGeNETi4063
EuPathDBiHostDB:ENSG00000122224.17
GeneCardsiLY9
HGNCiHGNC:6730 LY9
HPAiHPA050917
MIMi600684 gene
neXtProtiNX_Q9HBG7
OpenTargetsiENSG00000122224
PharmGKBiPA30494
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410JJ3F Eukaryota
ENOG410ZAYK LUCA
GeneTreeiENSGT00530000063114
HOGENOMiHOG000013143
HOVERGENiHBG030765
InParanoidiQ9HBG7
KOiK06570
OMAiCRVSLTC
OrthoDBiEOG091G0KKU
PhylomeDBiQ9HBG7
TreeFamiTF334964

Miscellaneous databases

GeneWikiiLY9
GenomeRNAii4063
PROiPR:Q9HBG7
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000122224 Expressed in 126 organ(s), highest expression level in blood
CleanExiHS_LY9
ExpressionAtlasiQ9HBG7 baseline and differential
GenevisibleiQ9HBG7 HS

Family and domain databases

Gene3Di2.60.40.10, 4 hits
InterProiView protein in InterPro
IPR007110 Ig-like_dom
IPR036179 Ig-like_dom_sf
IPR013783 Ig-like_fold
IPR003599 Ig_sub
SMARTiView protein in SMART
SM00409 IG, 2 hits
SUPFAMiSSF48726 SSF48726, 4 hits
PROSITEiView protein in PROSITE
PS50835 IG_LIKE, 2 hits
ProtoNetiSearch...

Entry informationi

Entry nameiLY9_HUMAN
AccessioniPrimary (citable) accession number: Q9HBG7
Secondary accession number(s): A8K7N3
, Q14775, Q5VYI3, Q6P2J4, Q9H4N5, Q9NQ24
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 20, 2002
Last sequence update: July 19, 2005
Last modified: November 7, 2018
This is version 144 of the entry and version 3 of the sequence. See 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

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. Human cell differentiation molecules
    CD nomenclature of surface proteins of human leucocytes and list of entries
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Main funding by: National Institutes of Health

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