UniProtKB - Q6U7R4 (TIMD4_MOUSE)
Protein
T-cell immunoglobulin and mucin domain-containing protein 4
Gene
Timd4
Organism
Mus musculus (Mouse)
Status
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
GO - Biological processi
- apoptotic cell clearance Source: MGI
Names & Taxonomyi
Protein namesi | Recommended name: T-cell immunoglobulin and mucin domain-containing protein 4Short 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 |
Organismi | Mus musculus (Mouse) |
Taxonomic identifieri | 10090 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Myomorpha › Muroidea › Muridae › Murinae › Mus › Mus |
Proteomesi |
|
Organism-specific databases
MGIi | MGI:2445125, Timd4 |
Subcellular locationi
Other locations
- Membrane Curated; Single-pass type I membrane protein Curated
Other locations
- integral component of membrane Source: UniProtKB-KW
Topology
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Topological domaini | 23 – 279 | ExtracellularSequence analysisAdd BLAST | 257 | |
Transmembranei | 280 – 300 | HelicalSequence analysisAdd BLAST | 21 | |
Topological domaini | 301 – 343 | CytoplasmicSequence analysisAdd BLAST | 43 |
Keywords - Cellular componenti
MembranePTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Signal peptidei | 1 – 22 | Sequence analysisAdd BLAST | 22 | |
ChainiPRO_0000042104 | 23 – 343 | T-cell immunoglobulin and mucin domain-containing protein 4Add BLAST | 321 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Disulfide bondi | 40 ↔ 112 | PROSITE-ProRule annotation1 Publication | ||
Disulfide bondi | 53 ↔ 64 | PROSITE-ProRule annotation1 Publication | ||
Disulfide bondi | 59 ↔ 111 | PROSITE-ProRule annotation1 Publication | ||
Glycosylationi | 220 | N-linked (GlcNAc...) asparagineSequence analysis | 1 | |
Modified residuei | 323 | PhosphoserineCombined sources | 1 | |
Modified residuei | 325 | PhosphoserineCombined sources | 1 | |
Modified residuei | 331 | PhosphoserineCombined sources | 1 |
Keywords - PTMi
Disulfide bond, Glycoprotein, PhosphoproteinProteomic databases
MaxQBi | Q6U7R4 |
PaxDbi | Q6U7R4 |
PeptideAtlasi | Q6U7R4 |
PRIDEi | Q6U7R4 |
PTM databases
GlyGeni | Q6U7R4, 1 site |
iPTMneti | Q6U7R4 |
PhosphoSitePlusi | Q6U7R4 |
SwissPalmi | Q6U7R4 |
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
Bgeei | ENSMUSG00000055546, Expressed in peripheral lymph node and 75 other tissues |
Genevisiblei | Q6U7R4, MM |
Interactioni
Subunit structurei
Homodimer.
2 PublicationsBinary interactionsi
Hide detailsQ6U7R4
With | #Exp. | IntAct |
---|---|---|
Havcr1 [Q5QNS5] | 4 | EBI-16764486,EBI-20217708 |
Havcr1 - isoform 2 [Q5QNS5-2] | 2 | EBI-16764486,EBI-20217763 |
Protein-protein interaction databases
IntActi | Q6U7R4, 1 interactor |
STRINGi | 10090.ENSMUSP00000069456 |
Miscellaneous databases
RNActi | Q6U7R4, protein |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | Q6U7R4 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | Q6U7R4 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 23 – 128 | Ig-like V-typeAdd BLAST | 106 |
Compositional bias
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Compositional biasi | 135 – 269 | Thr-richAdd BLAST | 135 |
Sequence similaritiesi
Keywords - Domaini
Immunoglobulin domain, Signal, Transmembrane, Transmembrane helixPhylogenomic databases
eggNOGi | ENOG502S1A2, Eukaryota |
GeneTreei | ENSGT00940000161609 |
HOGENOMi | CLU_047504_0_1_1 |
InParanoidi | Q6U7R4 |
OMAi | QSRNSMC |
OrthoDBi | 1147868at2759 |
PhylomeDBi | Q6U7R4 |
TreeFami | TF336163 |
Family and domain databases
Gene3Di | 2.60.40.10, 1 hit |
InterProi | View protein in InterPro IPR007110, Ig-like_dom IPR036179, Ig-like_dom_sf IPR013783, Ig-like_fold IPR003599, Ig_sub IPR013106, Ig_V-set |
Pfami | View protein in Pfam PF07686, V-set, 1 hit |
SMARTi | View protein in SMART SM00409, IG, 1 hit |
SUPFAMi | SSF48726, SSF48726, 1 hit |
PROSITEi | View protein in PROSITE PS50835, IG_LIKE, 1 hit |
i Sequence
Sequence statusi: Complete.
: The displayed sequence is further processed into a mature form. Sequence processingi
Q6U7R4-1 [UniParc]FASTAAdd to basket
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
Natural variant
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Natural varianti | 12 | T → M in strain: C57BL/6. 1 Publication | 1 | |
Natural varianti | 209 | F → 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 |
CCDSi | CCDS36137.1 |
RefSeqi | NP_848874.3, NM_178759.4 |
Genome annotation databases
Ensembli | ENSMUST00000068877; ENSMUSP00000069456; ENSMUSG00000055546 |
GeneIDi | 276891 |
KEGGi | mmu:276891 |
UCSCi | uc007iox.1, mouse |
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 |
CCDSi | CCDS36137.1 |
RefSeqi | NP_848874.3, NM_178759.4 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
3BI9 | X-ray | 2.95 | X | 24-134 | [»] | |
3BIA | X-ray | 2.20 | X | 24-134 | [»] | |
3BIB | X-ray | 2.50 | X | 24-134 | [»] | |
SMRi | Q6U7R4 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
IntActi | Q6U7R4, 1 interactor |
STRINGi | 10090.ENSMUSP00000069456 |
PTM databases
GlyGeni | Q6U7R4, 1 site |
iPTMneti | Q6U7R4 |
PhosphoSitePlusi | Q6U7R4 |
SwissPalmi | Q6U7R4 |
Proteomic databases
MaxQBi | Q6U7R4 |
PaxDbi | Q6U7R4 |
PeptideAtlasi | Q6U7R4 |
PRIDEi | Q6U7R4 |
Protocols and materials databases
ABCDi | Q6U7R4, 10 sequenced antibodies |
Antibodypediai | 2737, 433 antibodies |
Genome annotation databases
Ensembli | ENSMUST00000068877; ENSMUSP00000069456; ENSMUSG00000055546 |
GeneIDi | 276891 |
KEGGi | mmu:276891 |
UCSCi | uc007iox.1, mouse |
Organism-specific databases
CTDi | 91937 |
MGIi | MGI:2445125, Timd4 |
Phylogenomic databases
eggNOGi | ENOG502S1A2, Eukaryota |
GeneTreei | ENSGT00940000161609 |
HOGENOMi | CLU_047504_0_1_1 |
InParanoidi | Q6U7R4 |
OMAi | QSRNSMC |
OrthoDBi | 1147868at2759 |
PhylomeDBi | Q6U7R4 |
TreeFami | TF336163 |
Miscellaneous databases
BioGRID-ORCSi | 276891, 4 hits in 19 CRISPR screens |
EvolutionaryTracei | Q6U7R4 |
PROi | PR:Q6U7R4 |
RNActi | Q6U7R4, protein |
SOURCEi | Search... |
Gene expression databases
Bgeei | ENSMUSG00000055546, Expressed in peripheral lymph node and 75 other tissues |
Genevisiblei | Q6U7R4, MM |
Family and domain databases
Gene3Di | 2.60.40.10, 1 hit |
InterProi | View protein in InterPro IPR007110, Ig-like_dom IPR036179, Ig-like_dom_sf IPR013783, Ig-like_fold IPR003599, Ig_sub IPR013106, Ig_V-set |
Pfami | View protein in Pfam PF07686, V-set, 1 hit |
SMARTi | View protein in SMART SM00409, IG, 1 hit |
SUPFAMi | SSF48726, SSF48726, 1 hit |
PROSITEi | View protein in PROSITE PS50835, IG_LIKE, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | TIMD4_MOUSE | |
Accessioni | Q6U7R4Primary (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: | February 10, 2021 | |
This is version 118 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- MGD cross-references
Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families