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Protein

T-cell immunoglobulin and mucin domain-containing protein 4

Gene

Timd4

Organism
Mus musculus (Mouse)
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/TIMD1.3 Publications

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.

GO - Molecular functioni

  • phosphatidylserine binding Source: MGI

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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
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

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...) asparagineSequence analysis1
Modified residuei323PhosphoserineCombined sources1
Modified residuei325PhosphoserineCombined sources1
Modified residuei331PhosphoserineCombined sources1

Keywords - PTMi

Disulfide bond, Glycoprotein, Phosphoprotein

Proteomic databases

MaxQBiQ6U7R4
PaxDbiQ6U7R4
PeptideAtlasiQ6U7R4
PRIDEiQ6U7R4

PTM databases

iPTMnetiQ6U7R4
PhosphoSitePlusiQ6U7R4
SwissPalmiQ6U7R4

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 Expressed in 52 organ(s), highest expression level in peripheral lymph node
GenevisibleiQ6U7R4 MM

Interactioni

Subunit structurei

Homodimer.2 Publications

Binary interactionsi

Protein-protein interaction databases

IntActiQ6U7R4, 1 interactor
STRINGi10090.ENSMUSP00000069456

Structurei

Secondary structure

1343
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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
OMAiQSRNSMC
OrthoDBiEOG091G0E5V
PhylomeDBiQ6U7R4
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

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

Similar proteinsi

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

IntActiQ6U7R4, 1 interactor
STRINGi10090.ENSMUSP00000069456

PTM databases

iPTMnetiQ6U7R4
PhosphoSitePlusiQ6U7R4
SwissPalmiQ6U7R4

Proteomic databases

MaxQBiQ6U7R4
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
OMAiQSRNSMC
OrthoDBiEOG091G0E5V
PhylomeDBiQ6U7R4
TreeFamiTF336163

Miscellaneous databases

EvolutionaryTraceiQ6U7R4
PROiPR:Q6U7R4
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000055546 Expressed in 52 organ(s), highest expression level in peripheral lymph node
GenevisibleiQ6U7R4 MM

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_MOUSE
AccessioniPrimary (citable) accession number: Q6U7R4
Secondary accession number(s): Q6U7R3, Q8CIC7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 27, 2005
Last sequence update: September 27, 2005
Last modified: November 7, 2018
This is version 106 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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