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Protein

T-cell immunoglobulin and mucin domain-containing protein 4

Gene

TIMD4

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-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

GO - Molecular functioni

Complete GO annotation...

Enzyme and pathway databases

BioCyciZFISH:ENSG00000145850-MONOMER.

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

HGNCiHGNC:25132. TIMD4.

Subcellular locationi

Topology

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

GO - Cellular componenti

Complete GO annotation...

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...)Sequence analysis1
Modified residuei358PhosphoserineBy similarity1

Keywords - PTMi

Disulfide bond, Glycoprotein, Phosphoprotein

Proteomic databases

PaxDbiQ96H15.
PeptideAtlasiQ96H15.
PRIDEiQ96H15.

PTM databases

iPTMnetiQ96H15.
PhosphoSitePlusiQ96H15.

Expressioni

Gene expression databases

BgeeiENSG00000145850.
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
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi25 – 31Combined sources7
Beta strandi36 – 38Combined sources3
Turni47 – 49Combined sources3
Beta strandi51 – 58Combined sources8
Beta strandi68 – 71Combined sources4
Beta strandi73 – 81Combined sources9
Beta strandi84 – 86Combined sources3
Helixi90 – 92Combined sources3
Beta strandi97 – 101Combined sources5
Helixi104 – 106Combined sources3
Beta strandi108 – 115Combined sources8
Beta strandi117 – 120Combined sources4
Beta strandi123 – 133Combined sources11

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...

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.
OMAiKINVRLN.
OrthoDBiEOG091G0E5V.
PhylomeDBiQ96H15.
TreeFamiTF336163.

Family and domain databases

Gene3Di2.60.40.10. 1 hit.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003599. Ig_sub.
IPR013106. Ig_V-set.
[Graphical view]
PfamiPF07686. V-set. 1 hit.
[Graphical view]
SMARTiSM00409. IG. 1 hit.
[Graphical view]
SUPFAMiSSF48726. SSF48726. 1 hit.
PROSITEiPS50835. IG_LIKE. 1 hit.
[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: 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

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 → A.2 PublicationsCorresponds to variant rs6873053dbSNPEnsembl.1
Natural variantiVAR_049947365V → M.Corresponds to variant rs7731575dbSNPEnsembl.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

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.

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.
GeneCardsiTIMD4.
HGNCiHGNC:25132. TIMD4.
HPAiCAB026027.
HPA015625.
MIMi610096. gene.
neXtProtiNX_Q96H15.
OpenTargetsiENSG00000145850.
PharmGKBiPA134989118.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IYS0. Eukaryota.
ENOG4111VB0. LUCA.
GeneTreeiENSGT00440000039800.
HOGENOMiHOG000074110.
HOVERGENiHBG083934.
InParanoidiQ96H15.
OMAiKINVRLN.
OrthoDBiEOG091G0E5V.
PhylomeDBiQ96H15.
TreeFamiTF336163.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000145850-MONOMER.

Miscellaneous databases

GeneWikiiTIMD4.
GenomeRNAii91937.
PROiQ96H15.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000145850.
CleanExiHS_TIMD4.
ExpressionAtlasiQ96H15. baseline and differential.
GenevisibleiQ96H15. HS.

Family and domain databases

Gene3Di2.60.40.10. 1 hit.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003599. Ig_sub.
IPR013106. Ig_V-set.
[Graphical view]
PfamiPF07686. V-set. 1 hit.
[Graphical view]
SMARTiSM00409. IG. 1 hit.
[Graphical view]
SUPFAMiSSF48726. SSF48726. 1 hit.
PROSITEiPS50835. IG_LIKE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiTIMD4_HUMAN
AccessioniPrimary (citable) accession number: Q96H15
Secondary accession number(s): B5MCL9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 27, 2005
Last sequence update: May 18, 2010
Last modified: November 2, 2016
This is version 114 of the entry and version 2 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

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 5
    Human chromosome 5: 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.