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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...

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)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini25 – 314290ExtracellularSequence analysisAdd
BLAST
Transmembranei315 – 33521HelicalSequence analysisAdd
BLAST
Topological domaini336 – 37843CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134989118.

Polymorphism and mutation databases

BioMutaiTIMD4.
DMDMi296452930.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2424Sequence analysisAdd
BLAST
Chaini25 – 378354T-cell immunoglobulin and mucin domain-containing protein 4PRO_0000042103Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi40 ↔ 112PROSITE-ProRule annotation
Disulfide bondi53 ↔ 64PROSITE-ProRule annotation
Disulfide bondi59 ↔ 111PROSITE-ProRule annotation
Glycosylationi291 – 2911N-linked (GlcNAc...)Sequence analysis
Modified residuei358 – 3581PhosphoserineBy similarity

Keywords - PTMi

Disulfide bond, Glycoprotein, Phosphoprotein

Proteomic databases

PaxDbiQ96H15.
PRIDEiQ96H15.

PTM databases

iPTMnetiQ96H15.
PhosphoSiteiQ96H15.

Expressioni

Gene expression databases

BgeeiQ96H15.
CleanExiHS_TIMD4.
ExpressionAtlasiQ96H15. baseline and differential.
GenevisibleiQ96H15. HS.

Organism-specific databases

HPAiCAB026027.
HPA015625.

Interactioni

Protein-protein interaction databases

STRINGi9606.ENSP00000274532.

Structurei

Secondary structure

1
378
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi25 – 317Combined sources
Beta strandi36 – 383Combined sources
Turni47 – 493Combined sources
Beta strandi51 – 588Combined sources
Beta strandi68 – 714Combined sources
Beta strandi73 – 819Combined sources
Beta strandi84 – 863Combined sources
Helixi90 – 923Combined sources
Beta strandi97 – 1015Combined sources
Helixi104 – 1063Combined sources
Beta strandi108 – 1158Combined sources
Beta strandi117 – 1204Combined sources
Beta strandi123 – 13311Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 32-134.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini25 – 126102Ig-like V-typeAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi136 – 21479Thr-richAdd
BLAST
Compositional biasi234 – 27744Ser-richAdd
BLAST

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.
OrthoDBiEOG7R2BK4.
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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti67 – 671A → T in AK301337 (PubMed:14702039).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti240 – 2401V → A.2 Publications
Corresponds to variant rs6873053 [ dbSNP | Ensembl ].
VAR_049946
Natural varianti365 – 3651V → M.
Corresponds to variant rs7731575 [ dbSNP | Ensembl ].
VAR_049947

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei254 – 28128Missing in isoform 2. 1 PublicationVSP_045474Add
BLAST

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
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. Positions 32-134.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9606.ENSP00000274532.

PTM databases

iPTMnetiQ96H15.
PhosphoSiteiQ96H15.

Polymorphism and mutation databases

BioMutaiTIMD4.
DMDMi296452930.

Proteomic databases

PaxDbiQ96H15.
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.
GeneCardsiTIMD4.
HGNCiHGNC:25132. TIMD4.
HPAiCAB026027.
HPA015625.
MIMi610096. gene.
neXtProtiNX_Q96H15.
PharmGKBiPA134989118.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IYS0. Eukaryota.
ENOG4111VB0. LUCA.
GeneTreeiENSGT00440000039800.
HOGENOMiHOG000074110.
HOVERGENiHBG083934.
InParanoidiQ96H15.
OMAiKINVRLN.
OrthoDBiEOG7R2BK4.
PhylomeDBiQ96H15.
TreeFamiTF336163.

Miscellaneous databases

GeneWikiiTIMD4.
GenomeRNAii91937.
PROiQ96H15.
SOURCEiSearch...

Gene expression databases

BgeeiQ96H15.
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...

Publicationsi

  1. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2), VARIANT ALA-240.
    Tissue: Synovium.
  2. "The DNA sequence and comparative analysis of human chromosome 5."
    Schmutz J., Martin J., Terry A., Couronne O., Grimwood J., Lowry S., Gordon L.A., Scott D., Xie G., Huang W., Hellsten U., Tran-Gyamfi M., She X., Prabhakar S., Aerts A., Altherr M., Bajorek E., Black S.
    , Branscomb E., Caoile C., Challacombe J.F., Chan Y.M., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Glavina T., Gomez M., Gonzales E., Goodstein D., Grigoriev I., Groza M., Hammon N., Hawkins T., Haydu L., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Lopez F., Lou Y., Martinez D., Medina C., Morgan J., Nandkeshwar R., Noonan J.P., Pitluck S., Pollard M., Predki P., Priest J., Ramirez L., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wheeler J., Wu K., Yang J., Dickson M., Cheng J.-F., Eichler E.E., Olsen A., Pennacchio L.A., Rokhsar D.S., Richardson P., Lucas S.M., Myers R.M., Rubin E.M.
    Nature 431:268-274(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), VARIANT ALA-240.
    Tissue: Brain.

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: June 8, 2016
This is version 110 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.