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Protein

T-cell immunoglobulin and mucin domain-containing protein 4

Gene

TIMD4

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

Functioni

Phosphatidylserine receptor that enhances the engulfment of apoptotic cells. Involved in regulating T-cell proliferation and lymphotoxin signaling. Ligand for HAVCR1/TIMD1 (By similarity).By similarity

Names & Taxonomyi

Protein namesi
Recommended name:
T-cell immunoglobulin and mucin domain-containing protein 4
Short name:
TIMD-4
Alternative name(s):
T-cell immunoglobulin mucin receptor 4
Short name:
TIM-4
T-cell membrane protein 4
Gene namesi
Name:TIMD4
Synonyms:TIM4
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 5

Organism-specific databases

EuPathDBiHostDB:ENSG00000145850.8
HGNCiHGNC:25132 TIMD4
MIMi610096 gene
neXtProtiNX_Q96H15

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini25 – 314ExtracellularSequence analysisAdd BLAST290
Transmembranei315 – 335HelicalSequence analysisAdd BLAST21
Topological domaini336 – 378CytoplasmicSequence analysisAdd BLAST43

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Organism-specific databases

DisGeNETi91937
OpenTargetsiENSG00000145850
PharmGKBiPA134989118

Polymorphism and mutation databases

BioMutaiTIMD4
DMDMi296452930

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 24Sequence analysisAdd BLAST24
ChainiPRO_000004210325 – 378T-cell immunoglobulin and mucin domain-containing protein 4Add BLAST354

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi40 ↔ 112PROSITE-ProRule annotation
Disulfide bondi53 ↔ 64PROSITE-ProRule annotation
Disulfide bondi59 ↔ 111PROSITE-ProRule annotation
Glycosylationi291N-linked (GlcNAc...) asparagineSequence analysis1
Modified residuei358PhosphoserineBy similarity1

Keywords - PTMi

Disulfide bond, Glycoprotein, Phosphoprotein

Proteomic databases

PaxDbiQ96H15
PeptideAtlasiQ96H15
PRIDEiQ96H15
ProteomicsDBi76694

PTM databases

iPTMnetiQ96H15
PhosphoSitePlusiQ96H15

Expressioni

Gene expression databases

BgeeiENSG00000145850 Expressed in 98 organ(s), highest expression level in right testis
CleanExiHS_TIMD4
ExpressionAtlasiQ96H15 baseline and differential
GenevisibleiQ96H15 HS

Organism-specific databases

HPAiCAB026027
HPA015625

Interactioni

Protein-protein interaction databases

STRINGi9606.ENSP00000274532

Structurei

Secondary structure

1378
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ96H15
SMRiQ96H15
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini25 – 126Ig-like V-typeAdd BLAST102

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi136 – 214Thr-richAdd BLAST79
Compositional biasi234 – 277Ser-richAdd BLAST44

Domaini

Recognizes phosphatidyl serine via its immunoglobulin domain.

Sequence similaritiesi

Belongs to the immunoglobulin superfamily. TIM family.Curated

Keywords - Domaini

Immunoglobulin domain, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410IYS0 Eukaryota
ENOG4111VB0 LUCA
GeneTreeiENSGT00440000039800
HOGENOMiHOG000074110
HOVERGENiHBG083934
InParanoidiQ96H15
OMAiQSRNSMC
OrthoDBiEOG091G0E5V
PhylomeDBiQ96H15
TreeFamiTF336163

Family and domain databases

Gene3Di2.60.40.10, 1 hit
InterProiView protein in InterPro
IPR007110 Ig-like_dom
IPR036179 Ig-like_dom_sf
IPR013783 Ig-like_fold
IPR003599 Ig_sub
IPR013106 Ig_V-set
PfamiView protein in Pfam
PF07686 V-set, 1 hit
SMARTiView protein in SMART
SM00409 IG, 1 hit
SUPFAMiSSF48726 SSF48726, 1 hit
PROSITEiView protein in PROSITE
PS50835 IG_LIKE, 1 hit

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

This entry has 2 described isoforms and 1 potential isoform that is computationally mapped.Show allAlign All

Isoform 1 (identifier: Q96H15-1) [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
MSKEPLILWL MIEFWWLYLT PVTSETVVTE VLGHRVTLPC LYSSWSHNSN
60 70 80 90 100
SMCWGKDQCP YSGCKEALIR TDGMRVTSRK SAKYRLQGTI PRGDVSLTIL
110 120 130 140 150
NPSESDSGVY CCRIEVPGWF NDVKINVRLN LQRASTTTHR TATTTTRRTT
160 170 180 190 200
TTSPTTTRQM TTTPAALPTT VVTTPDLTTG TPLQMTTIAV FTTANTCLSL
210 220 230 240 250
TPSTLPEEAT GLLTPEPSKE GPILTAESET VLPSDSWSSV ESTSADTVLL
260 270 280 290 300
TSKESKVWDL PSTSHVSMWK TSDSVSSPQP GASDTAVPEQ NKTTKTGQMD
310 320 330 340 350
GIPMSMKNEM PISQLLMIIA PSLGFVLFAL FVAFLLRGKL METYCSQKHT
360 370
RLDYIGDSKN VLNDVQHGRE DEDGLFTL
Length:378
Mass (Da):41,578
Last modified:May 18, 2010 - v2
Checksum:i6D3CC4AC89A0FE5D
GO
Isoform 2 (identifier: Q96H15-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     254-281: Missing.

Note: No experimental confirmation available.
Show »
Length:350
Mass (Da):38,536
Checksum:iCA6C452EFBD371B6
GO

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
B5MCV9B5MCV9_HUMAN
T-cell immunoglobulin and mucin dom...
TIMD4
80Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti67A → T in AK301337 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_049946240V → A2 PublicationsCorresponds to variant dbSNP:rs6873053Ensembl.1
Natural variantiVAR_049947365V → M. Corresponds to variant dbSNP:rs7731575Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_045474254 – 281Missing in isoform 2. 1 PublicationAdd BLAST28

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK301337 mRNA No translation available.
AC008491 Genomic DNA No translation available.
AC026777 Genomic DNA No translation available.
BC008988 mRNA Translation: AAH08988.1
CCDSiCCDS4332.1 [Q96H15-1]
CCDS54943.1 [Q96H15-2]
RefSeqiNP_001140198.1, NM_001146726.1 [Q96H15-2]
NP_612388.2, NM_138379.2 [Q96H15-1]
UniGeneiHs.334907

Genome annotation databases

EnsembliENST00000274532; ENSP00000274532; ENSG00000145850 [Q96H15-1]
ENST00000407087; ENSP00000385973; ENSG00000145850 [Q96H15-2]
GeneIDi91937
KEGGihsa:91937
UCSCiuc003lwh.2 human [Q96H15-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK301337 mRNA No translation available.
AC008491 Genomic DNA No translation available.
AC026777 Genomic DNA No translation available.
BC008988 mRNA Translation: AAH08988.1
CCDSiCCDS4332.1 [Q96H15-1]
CCDS54943.1 [Q96H15-2]
RefSeqiNP_001140198.1, NM_001146726.1 [Q96H15-2]
NP_612388.2, NM_138379.2 [Q96H15-1]
UniGeneiHs.334907

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5DZNX-ray2.30A/B/C/D/E/F/G/H22-134[»]
5F7FX-ray1.50A/B24-134[»]
5F7HX-ray2.50A/B/C/D/E/F24-134[»]
ProteinModelPortaliQ96H15
SMRiQ96H15
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9606.ENSP00000274532

PTM databases

iPTMnetiQ96H15
PhosphoSitePlusiQ96H15

Polymorphism and mutation databases

BioMutaiTIMD4
DMDMi296452930

Proteomic databases

PaxDbiQ96H15
PeptideAtlasiQ96H15
PRIDEiQ96H15
ProteomicsDBi76694

Protocols and materials databases

DNASUi91937
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000274532; ENSP00000274532; ENSG00000145850 [Q96H15-1]
ENST00000407087; ENSP00000385973; ENSG00000145850 [Q96H15-2]
GeneIDi91937
KEGGihsa:91937
UCSCiuc003lwh.2 human [Q96H15-1]

Organism-specific databases

CTDi91937
DisGeNETi91937
EuPathDBiHostDB:ENSG00000145850.8
GeneCardsiTIMD4
HGNCiHGNC:25132 TIMD4
HPAiCAB026027
HPA015625
MIMi610096 gene
neXtProtiNX_Q96H15
OpenTargetsiENSG00000145850
PharmGKBiPA134989118
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IYS0 Eukaryota
ENOG4111VB0 LUCA
GeneTreeiENSGT00440000039800
HOGENOMiHOG000074110
HOVERGENiHBG083934
InParanoidiQ96H15
OMAiQSRNSMC
OrthoDBiEOG091G0E5V
PhylomeDBiQ96H15
TreeFamiTF336163

Miscellaneous databases

GeneWikiiTIMD4
GenomeRNAii91937
PROiPR:Q96H15
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000145850 Expressed in 98 organ(s), highest expression level in right testis
CleanExiHS_TIMD4
ExpressionAtlasiQ96H15 baseline and differential
GenevisibleiQ96H15 HS

Family and domain databases

Gene3Di2.60.40.10, 1 hit
InterProiView protein in InterPro
IPR007110 Ig-like_dom
IPR036179 Ig-like_dom_sf
IPR013783 Ig-like_fold
IPR003599 Ig_sub
IPR013106 Ig_V-set
PfamiView protein in Pfam
PF07686 V-set, 1 hit
SMARTiView protein in SMART
SM00409 IG, 1 hit
SUPFAMiSSF48726 SSF48726, 1 hit
PROSITEiView protein in PROSITE
PS50835 IG_LIKE, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiTIMD4_HUMAN
AccessioniPrimary (citable) accession number: Q96H15
Secondary accession number(s): B5MCL9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 27, 2005
Last sequence update: May 18, 2010
Last modified: November 7, 2018
This is version 124 of the entry and version 2 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. Human chromosome 5
    Human chromosome 5: entries, gene names and cross-references to MIM
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Main funding by: National Institutes of Health

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