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

T-cell immunoglobulin and mucin domain-containing protein 4

Gene

Timd4

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 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/TIMD1.3 Publications

GO - Molecular functioni

  • phosphatidylserine binding Source: MGI
Complete GO annotation...

Names & Taxonomyi

Protein namesi
Recommended name:
T-cell immunoglobulin and mucin domain-containing protein 4
Short name:
TIMD-4
Alternative name(s):
Spleen, mucin-containing, knockout of lymphotoxin protein
Short name:
SMUCKLER
T-cell immunoglobulin mucin receptor 4
Short name:
TIM-4
T-cell membrane protein 4
Gene namesi
Name:Timd4
Synonyms:Tim4
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 11

Organism-specific databases

MGIiMGI:2445125. Timd4.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini23 – 279ExtracellularSequence analysisAdd BLAST257
Transmembranei280 – 300HelicalSequence analysisAdd BLAST21
Topological domaini301 – 343CytoplasmicSequence analysisAdd BLAST43

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 22Sequence analysisAdd BLAST22
ChainiPRO_000004210423 – 343T-cell immunoglobulin and mucin domain-containing protein 4Add BLAST321

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi40 ↔ 112PROSITE-ProRule annotation1 Publication
Disulfide bondi53 ↔ 64PROSITE-ProRule annotation1 Publication
Disulfide bondi59 ↔ 111PROSITE-ProRule annotation1 Publication
Glycosylationi220N-linked (GlcNAc...)Sequence analysis1
Modified residuei323PhosphoserineCombined sources1
Modified residuei325PhosphoserineCombined sources1
Modified residuei331PhosphoserineCombined sources1

Keywords - PTMi

Disulfide bond, Glycoprotein, Phosphoprotein

Proteomic databases

PaxDbiQ6U7R4.
PeptideAtlasiQ6U7R4.
PRIDEiQ6U7R4.

PTM databases

iPTMnetiQ6U7R4.
PhosphoSitePlusiQ6U7R4.

Expressioni

Tissue specificityi

Predominantly expressed in lymphoid tissues, such as spleen, lymph nodes, and Peyer patches. Also expressed in fetal liver, salivary gland, and spleen stromal cells, predominantly in the marginal zone and to a lesser extent throughout the white pulp. Not expressed by bone marrow-derived cells. In spleen, expressed mostly by stromal cells in T- and B-cell areas, but not by T or B-lymphocytes.2 Publications

Inductioni

Down-regulated in lymphotoxin deficient mice.1 Publication

Gene expression databases

BgeeiENSMUSG00000055546.
GenevisibleiQ6U7R4. MM.

Interactioni

Subunit structurei

Homodimer.2 Publications

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000069456.

Structurei

Secondary structure

1343
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi26 – 31Combined sources6
Beta strandi36 – 38Combined sources3
Turni47 – 49Combined sources3
Beta strandi51 – 58Combined sources8
Beta strandi61 – 63Combined sources3
Beta strandi67 – 71Combined sources5
Beta strandi73 – 81Combined sources9
Beta strandi84 – 86Combined sources3
Helixi90 – 92Combined sources3
Beta strandi97 – 99Combined sources3
Helixi104 – 106Combined sources3
Beta strandi108 – 115Combined sources8
Beta strandi117 – 120Combined sources4
Beta strandi123 – 132Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3BI9X-ray2.95X24-134[»]
3BIAX-ray2.20X24-134[»]
3BIBX-ray2.50X24-134[»]
ProteinModelPortaliQ6U7R4.
SMRiQ6U7R4.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ6U7R4.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini23 – 128Ig-like V-typeAdd BLAST106

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi135 – 269Thr-richAdd BLAST135

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.
InParanoidiQ6U7R4.
OMAiKINVRLN.
OrthoDBiEOG091G0E5V.
PhylomeDBiQ6U7R4.
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]

Sequencei

Sequence statusi: Complete.

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

Q6U7R4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKGLLLLWL VTELWWLYLT PAASEDTIIG FLGQPVTLPC HYLSWSQSRN
60 70 80 90 100
SMCWGKGSCP NSKCNAELLR TDGTRIISRK STKYTLLGKV QFGEVSLTIS
110 120 130 140 150
NTNRGDSGVY CCRIEVPGWF NDVKKNVRLE LRRATTTKKP TTTTRPTTTP
160 170 180 190 200
YVTTTTPELL PTTVMTTSVL PTTTPPQTLA TTAFSTAVTT CPSTTPGSFS
210 220 230 240 250
QETTKGSAFT TESETLPASN HSQRSMMTIS TDIAVLRPTG SNPGILPSTS
260 270 280 290 300
QLTTQKTTLT TSESLQKTTK SHQINSRQTI LIIACCVGFV LMVLLFLAFL
310 320 330 340
LRGKVTGANC LQRHKRPDNT EDSDSVLNDM SHGRDDEDGI FTL
Length:343
Mass (Da):37,548
Last modified:September 27, 2005 - v2
Checksum:iD2D5539A7CDB8290
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti12T → M in strain: C57BL/6. 1 Publication1
Natural varianti209F → I in strain: C57BL/6. 1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY376717 mRNA. Translation: AAR23484.1.
AY376716 mRNA. Translation: AAR23483.1.
CCDSiCCDS36137.1.
RefSeqiNP_848874.3. NM_178759.4.
UniGeneiMm.69002.

Genome annotation databases

EnsembliENSMUST00000068877; ENSMUSP00000069456; ENSMUSG00000055546.
GeneIDi276891.
KEGGimmu:276891.
UCSCiuc007iox.1. mouse.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY376717 mRNA. Translation: AAR23484.1.
AY376716 mRNA. Translation: AAR23483.1.
CCDSiCCDS36137.1.
RefSeqiNP_848874.3. NM_178759.4.
UniGeneiMm.69002.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3BI9X-ray2.95X24-134[»]
3BIAX-ray2.20X24-134[»]
3BIBX-ray2.50X24-134[»]
ProteinModelPortaliQ6U7R4.
SMRiQ6U7R4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000069456.

PTM databases

iPTMnetiQ6U7R4.
PhosphoSitePlusiQ6U7R4.

Proteomic databases

PaxDbiQ6U7R4.
PeptideAtlasiQ6U7R4.
PRIDEiQ6U7R4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000068877; ENSMUSP00000069456; ENSMUSG00000055546.
GeneIDi276891.
KEGGimmu:276891.
UCSCiuc007iox.1. mouse.

Organism-specific databases

CTDi91937.
MGIiMGI:2445125. Timd4.

Phylogenomic databases

eggNOGiENOG410IYS0. Eukaryota.
ENOG4111VB0. LUCA.
GeneTreeiENSGT00440000039800.
HOGENOMiHOG000074110.
HOVERGENiHBG083934.
InParanoidiQ6U7R4.
OMAiKINVRLN.
OrthoDBiEOG091G0E5V.
PhylomeDBiQ6U7R4.
TreeFamiTF336163.

Miscellaneous databases

EvolutionaryTraceiQ6U7R4.
PROiQ6U7R4.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000055546.
GenevisibleiQ6U7R4. MM.

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_MOUSE
AccessioniPrimary (citable) accession number: Q6U7R4
Secondary accession number(s): Q6U7R3, Q8CIC7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 27, 2005
Last sequence update: September 27, 2005
Last modified: November 2, 2016
This is version 96 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Miscellaneous

Belongs to the T-cell and airway phenotype regulator (Tapr) locus, a single chromosomal region that confers reduced T-helper type 2 responsiveness and protects against airway hyperactivity (AHR), the hallmark of human asthma.
Low expression of Timd4 is associated with lymphotoxin deficiency.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.