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TAFA1 TAFA chemokine like family member 1 [ Homo sapiens (human) ]

Gene ID: 407738, updated on 5-Mar-2024

Summary

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Official Symbol
TAFA1provided by HGNC
Official Full Name
TAFA chemokine like family member 1provided by HGNC
Primary source
HGNC:HGNC:21587
See related
Ensembl:ENSG00000183662 MIM:617495; AllianceGenome:HGNC:21587
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TAFA-1; FAM19A1
Summary
This gene is a member of the TAFA family which is composed of five highly homologous genes that encode small secreted proteins. These proteins contain conserved cysteine residues at fixed positions, and are distantly related to MIP-1alpha, a member of the CC-chemokine family. The TAFA proteins are predominantly expressed in specific regions of the brain, and are postulated to function as brain-specific chemokines or neurokines that act as regulators of immune and nervous cells. [provided by RefSeq, Jul 2008]
Expression
Biased expression in brain (RPKM 6.6) and prostate (RPKM 0.3) See more
Orthologs
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Genomic context

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See TAFA1 in Genome Data Viewer
Location:
3p14.1
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (67991544..68545621)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (68036911..68591152)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (68040686..68594772)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene succinate-CoA ligase GDP-forming subunit beta Neighboring gene MPRA-validated peak4691 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr3:67603587-67603736 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20048 Neighboring gene NADH:ubiquinone oxidoreductase subunit B4 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 7041 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20049 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:67704843-67705342 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14513 Neighboring gene SUCLG2 divergent transcript Neighboring gene FAM19A1 intron homotypic cluster of transcription factor binding sites enhancer Neighboring gene COP9 signalosome subunit 8 pseudogene 2 Neighboring gene uncharacterized LOC107986019 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:68467140-68467944 Neighboring gene uncharacterized LOC105377146 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:68584830-68585382 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:68680918-68681896 Neighboring gene ribosomal protein lateral stalk subunit P0 pseudogene 8 Neighboring gene proteasome 26S subunit, ATPase 1 pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Single-nucleotide polymorphisms in chromosome 3p14.1- 3p14.2 are associated with susceptibility of type 2 diabetes with cataract. Lin HJ, et al. Mol Vis, 2010 Jul 1. PMID 20664687, Free PMC Article
  2. TAFA: a novel secreted family with conserved cysteine residues and restricted expression in the brain. Tom Tang Y, et al. Genomics, 2004 Apr. PMID 15028294
  3. Novel Adipokine, FAM19A5, Inhibits Neointima Formation After Injury Through Sphingosine-1-Phosphate Receptor 2. Wang Y, et al. Circulation, 2018 Jul 3. PMID 29453251
  4. Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. Simpson JC, et al. EMBO Rep, 2000 Sep. PMID 11256614, Free PMC Article
  5. The LIFEdb database in 2006. Mehrle A, et al. Nucleic Acids Res, 2006 Jan 1. PMID 16381901, Free PMC Article

See all (15) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Single-nucleotide polymorphisms in chromosome 3p14.1- 3p14.2 are associated with susceptibility of type 2 diabetes with cataract.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables receptor ligand activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables receptor ligand activity ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in neuroblast differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in neuroblast differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of neuroblast proliferation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of neuroblast proliferation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of signaling receptor activity ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in signal transduction IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular space IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular space ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
chemokine-like protein TAFA-1
Names
family with sequence similarity 19 (chemokine (C-C motif)-like), member A1
family with sequence similarity 19 member A1, C-C motif chemokine like
protein FAM19A1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001252216.2 → NP_001239145.1  chemokine-like protein TAFA-1 precursor

    See identical proteins and their annotated locations for NP_001239145.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC139766, AY325114, BC025746
    Consensus CDS
    CCDS54606.1
    UniProtKB/Swiss-Prot
    A8K0V3, Q7Z5A9, Q8TCL8
    Conserved Domains (1) summary
    pfam12020
    Location:41 → 129
    TAFA; TAFA family

  2. NM_213609.4 → NP_998774.2  chemokine-like protein TAFA-1 precursor

    See identical proteins and their annotated locations for NP_998774.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AK290446, BC025746, DA484048, DA485098
    Consensus CDS
    CCDS54606.1
    UniProtKB/Swiss-Prot
    A8K0V3, Q7Z5A9, Q8TCL8
    Related
    ENSP00000418575.1, ENST00000478136.6
    Conserved Domains (1) summary
    pfam12020
    Location:41 → 129
    TAFA; TAFA family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    67991544..68545621
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017006387.3 → XP_016861876.1  chemokine-like protein TAFA-1 isoform X1

    UniProtKB/Swiss-Prot
    A8K0V3, Q7Z5A9, Q8TCL8
    Conserved Domains (1) summary
    pfam12020
    Location:41 → 129
    TAFA; TAFA family

  2. XM_017006390.2 → XP_016861879.1  chemokine-like protein TAFA-1 isoform X2

    Conserved Domains (1) summary
    pfam12020
    Location:40 → 128
    TAFA; TAFA family

  3. XM_017006388.2 → XP_016861877.1  chemokine-like protein TAFA-1 isoform X2

    Conserved Domains (1) summary
    pfam12020
    Location:40 → 128
    TAFA; TAFA family

  4. XM_017006386.2 → XP_016861875.1  chemokine-like protein TAFA-1 isoform X1

    UniProtKB/Swiss-Prot
    A8K0V3, Q7Z5A9, Q8TCL8
    Related
    ENSP00000417496.1, ENST00000496687.1
    Conserved Domains (1) summary
    pfam12020
    Location:41 → 129
    TAFA; TAFA family

  5. XM_017006389.2 → XP_016861878.1  chemokine-like protein TAFA-1 isoform X2

    Conserved Domains (1) summary
    pfam12020
    Location:40 → 128
    TAFA; TAFA family

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    68036911..68591152
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054346515.1 → XP_054202490.1  chemokine-like protein TAFA-1 isoform X1

    UniProtKB/Swiss-Prot
    A8K0V3, Q7Z5A9, Q8TCL8

  2. XM_054346517.1 → XP_054202492.1  chemokine-like protein TAFA-1 isoform X2

  3. XM_054346516.1 → XP_054202491.1  chemokine-like protein TAFA-1 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q7Z5A9.1 GenPept UniProtKB/Swiss-Prot:Q7Z5A9

Gene LinkOut

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