UniProtKB - Q6U7R4 (TIMD4_MOUSE)

BLAST

>sp|Q6U7R4|TIMD4_MOUSE T-cell immunoglobulin and mucin domain-containing protein 4 OS=Mus musculus OX=10090 GN=Timd4 PE=1 SV=2
MSKGLLLLWLVTELWWLYLTPAASEDTIIGFLGQPVTLPCHYLSWSQSRNSMCWGKGSCP
NSKCNAELLRTDGTRIISRKSTKYTLLGKVQFGEVSLTISNTNRGDSGVYCCRIEVPGWF
NDVKKNVRLELRRATTTKKPTTTTRPTTTPYVTTTTPELLPTTVMTTSVLPTTTPPQTLA
TTAFSTAVTTCPSTTPGSFSQETTKGSAFTTESETLPASNHSQRSMMTISTDIAVLRPTG
SNPGILPSTSQLTTQKTTLTTSESLQKTTKSHQINSRQTILIIACCVGFVLMVLLFLAFL
LRGKVTGANCLQRHKRPDNTEDSDSVLNDMSHGRDDEDGIFTL

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History
Entry version 106 (07 Nov 2018)
Sequence version 2 (27 Sep 2005)
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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
Inferred from direct assayⁱ
- 13886198

View the complete GO annotation on QuickGO ...

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
Organismⁱ	Mus musculus (Mouse)
Taxonomic identifierⁱ	10090 [NCBI]
Taxonomic lineageⁱ	cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Dipnotetrapodomorpha › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Boreoeutheria › Euarchontoglires › Glires › Rodentia › Myomorpha › Muroidea › Muridae › Murinae › Mus › Mus
Proteomesⁱ	UP000000589 Componentⁱ: Chromosome 11

Organism-specific databases

MGIⁱ	MGI:2445125 Timd4

Topology

Feature key	Position(s)	DescriptionActions	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

Membrane

PTM / 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	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, Phosphoprotein

Proteomic databases

MaxQB - The MaxQuant DataBase More...MaxQBⁱ	Q6U7R4
PaxDbⁱ	Q6U7R4
PeptideAtlas More...PeptideAtlasⁱ	Q6U7R4
PRIDEⁱ	Q6U7R4

PTM databases

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 52 organ(s), highest expression level in peripheral lymph node
Genevisibleⁱ	Q6U7R4 MM

Interactionⁱ

Subunit structureⁱ

Homodimer.2 Publications

Binary interactionsⁱ

With	Entry	#Exp.	IntAct	Notes
Havcr1	Q5QNS5	4	EBI-16764486,EBI-20217708
Havcr1	Q5QNS5-2	2	EBI-16764486,EBI-20217763

Protein-protein interaction databases

IntActⁱ	Q6U7R4, 1 interactor
STRINGⁱ	10090.ENSMUSP00000069456

Structureⁱ

Secondary structure

Legend: HelixTurnBeta strandPDB Structure known for this area

Feature key	Position(s)	DescriptionActions	Length
Beta strandⁱ	26 – 31	Combined sources	6
Beta strandⁱ	36 – 38	Combined sources	3
Turnⁱ	47 – 49	Combined sources	3
Beta strandⁱ	51 – 58	Combined sources	8
Beta strandⁱ	61 – 63	Combined sources	3
Beta strandⁱ	67 – 71	Combined sources	5
Beta strandⁱ	73 – 81	Combined sources	9
Beta strandⁱ	84 – 86	Combined sources	3
Helixⁱ	90 – 92	Combined sources	3
Beta strandⁱ	97 – 99	Combined sources	3
Helixⁱ	104 – 106	Combined sources	3
Beta strandⁱ	108 – 115	Combined sources	8
Beta strandⁱ	117 – 120	Combined sources	4
Beta strandⁱ	123 – 132	Combined sources	10

Show more details

3D structure databases

ProteinModelPortalⁱ	Q6U7R4
SMRⁱ	Q6U7R4
ModBaseⁱ	Search...
MobiDBⁱ	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

Belongs to the immunoglobulin superfamily. TIM family.Curated

Keywords - Domainⁱ

Immunoglobulin domain, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGⁱ	ENOG410IYS0 Eukaryota ENOG4111VB0 LUCA
Ensembl GeneTree More...GeneTreeⁱ	ENSGT00440000039800
HOGENOMⁱ	HOG000074110
HOVERGENⁱ	HBG083934
InParanoidⁱ	Q6U7R4
OMAⁱ	QSRNSMC
Database of Orthologous Groups More...OrthoDBⁱ	EOG091G0E5V
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
Pfam protein domain database More...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

Sequenceⁱ

Sequence statusⁱ: Complete.

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

Q6U7R4-1 [UniParc]FASTA Add 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

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
The Consensus CDS (CCDS) project More...CCDSⁱ	CCDS36137.1
NCBI Reference Sequences More...RefSeqⁱ	NP_848874.3, NM_178759.4
UniGeneⁱ	Mm.69002

Genome annotation databases

Ensemblⁱ	ENSMUST00000068877; ENSMUSP00000069456; ENSMUSG00000055546
GeneIDⁱ	276891
KEGGⁱ	mmu:276891
UCSC genome browser More...UCSCⁱ	uc007iox.1 mouse

Keywords - Coding sequence diversityⁱ

Polymorphism

Similar proteinsⁱ

50% Identity

Protein	Similar proteins		Species	Score	Length	Source
Q6U7R4	T-cell immunoglobulin and mucin domain-containing protein 4		MESAU		345	UniRef50_Q6U7R4
Uncharacterized protein		RAT		339
T-cell immunoglobulin and mucin domain-containing protein 4		Yangtze finless porpoise		359
T-cell immunoglobulin and mucin domain-containing protein 4		BALAS		361
Uncharacterized protein		PIG		361
+32

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
UniGeneⁱ	Mm.69002

3D structure databases

Select the link destinations: Protein Data Bank Europe More...PDBeⁱ Protein Data Bank RCSB More...RCSB PDBⁱ Protein Data Bank Japan More...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	[»]
ProteinModelPortalⁱ	Q6U7R4
SMRⁱ	Q6U7R4
ModBaseⁱ	Search...
MobiDBⁱ	Search...

Protein-protein interaction databases

IntActⁱ	Q6U7R4, 1 interactor
STRINGⁱ	10090.ENSMUSP00000069456

PTM databases

iPTMnetⁱ	Q6U7R4
PhosphoSitePlusⁱ	Q6U7R4
SwissPalmⁱ	Q6U7R4

Proteomic databases

MaxQBⁱ	Q6U7R4
PaxDbⁱ	Q6U7R4
PeptideAtlasⁱ	Q6U7R4
PRIDEⁱ	Q6U7R4

Protocols and materials databases

Structural Biology Knowledgebase	Search...

Structural Biology Knowledgebase

Search...

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	ENOG410IYS0 Eukaryota ENOG4111VB0 LUCA
GeneTreeⁱ	ENSGT00440000039800
HOGENOMⁱ	HOG000074110
HOVERGENⁱ	HBG083934
InParanoidⁱ	Q6U7R4
OMAⁱ	QSRNSMC
OrthoDBⁱ	EOG091G0E5V
PhylomeDBⁱ	Q6U7R4
TreeFamⁱ	TF336163

Miscellaneous databases

EvolutionaryTraceⁱ	Q6U7R4
Protein Ontology More...PROⁱ	PR:Q6U7R4
SOURCEⁱ	Search...

Gene expression databases

Bgeeⁱ	ENSMUSG00000055546 Expressed in 52 organ(s), highest expression level in peripheral lymph node
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...

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:	November 7, 2018
	This is version 106 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, Complete proteome, Reference proteome

Documents

SIMILARITY comments
Index of protein domains and families
MGD cross-references
Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
PDB cross-references
Index of Protein Data Bank (PDB) cross-references

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UniParc

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UniProtKB - Q6U7R4 (TIMD4_MOUSE)

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T-cell immunoglobulin and mucin domain-containing protein 4

Timd4

Select a section on the left to see content.

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Miscellaneous

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

Organism-specific databases

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Other locations

Other locations

Topology

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Amino acid modifications

Keywords - PTMi

Proteomic databases

PTM databases

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

Gene expression databases

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Protein-protein interaction databases

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

3D structure databases

Miscellaneous databases

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Compositional bias

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Keywords - Domaini

Phylogenomic databases

Family and domain databases

Natural variant

Sequence databases

Genome annotation databases

Keywords - Coding sequence diversityi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

3D structure databases

Protein-protein interaction databases

PTM databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Miscellaneous databases

Gene expression databases

Family and domain databases

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Documents

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Functionⁱ

GO - Molecular functionⁱ

Names & Taxonomyⁱ

Subcellular locationⁱ

PTM / Processingⁱ

Keywords - PTMⁱ

Expressionⁱ

Interactionⁱ

Structureⁱ

Family & Domainsⁱ

Sequence similaritiesⁱ

Keywords - Domainⁱ

Keywords - Coding sequence diversityⁱ

Cross-referencesⁱ

Entry informationⁱ

Miscellaneousⁱ

Keywords - Technical termⁱ