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

    Gene ID: 407738, updated on 28-Oct-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (67991544..68545621)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (68036911..68591152)
    RS_2024_09 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 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_2024_08

    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

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