TAFA4 TAFA chemokine like family member 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TAFA4provided by HGNC
Official Full Name: TAFA chemokine like family member 4provided by HGNC
Primary source: HGNC:HGNC:21591
See related: Ensembl:ENSG00000163377 MIM:617498; AllianceGenome:HGNC:21591
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-4; FAM19A4
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. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Nov 2011]
Expression: Biased expression in adrenal (RPKM 8.7), gall bladder (RPKM 0.7) and 1 other tissue See more
Orthologs: mouse all
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Genomic context

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 (68731766..68932547, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (68769008..68969284, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (68780917..68981698, complement)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Signals from the TAFA4-PTEN-PU.1 axis alleviate nasal allergy by modulating the expression of FcepsilonRI in mast cells.
Title: Signals from the TAFA4-PTEN-PU.1 axis alleviate nasal allergy by modulating the expression of FcεRI in mast cells.
FAM19A4/miR124-2 Methylation Testing and Human Papillomavirus (HPV) 16/18 Genotyping in HPV-Positive Women Under the Age of 30 Years.
Title: FAM19A4/miR124-2 Methylation Testing and Human Papillomavirus (HPV) 16/18 Genotyping in HPV-Positive Women Under the Age of 30 Years.
Full genotyping and FAM19A4/miR124-2 methylation analysis in high-risk human papillomavirus-positive samples from women over 30 years participating in cervical cancer screening in Orebro, Sweden.
Title: Full genotyping and FAM19A4/miR124-2 methylation analysis in high-risk human papillomavirus-positive samples from women over 30 years participating in cervical cancer screening in Örebro, Sweden.
Clinical Regression of High-Grade Cervical Intraepithelial Neoplasia Is Associated With Absence of FAM19A4/miR124-2 DNA Methylation (CONCERVE Study).
Title: Clinical Regression of High-Grade Cervical Intraepithelial Neoplasia Is Associated With Absence of FAM19A4/miR124-2 DNA Methylation (CONCERVE Study).
Risk-stratification of HPV-positive women with low-grade cytology by FAM19A4/miR124-2 methylation and HPV genotyping.
Title: Risk-stratification of HPV-positive women with low-grade cytology by FAM19A4/miR124-2 methylation and HPV genotyping.
Methylation markers FAM19A4 and miR124-2 as triage strategy for primary human papillomavirus screen positive women: A large European multicenter study.
Title: Methylation markers FAM19A4 and miR124-2 as triage strategy for primary human papillomavirus screen positive women: A large European multicenter study.
Expression of p16 and HPV E4 on biopsy samples and methylation of FAM19A4 and miR124-2 on cervical cytology samples in the classification of cervical squamous intraepithelial lesions.
Title: Expression of p16 and HPV E4 on biopsy samples and methylation of FAM19A4 and miR124-2 on cervical cytology samples in the classification of cervical squamous intraepithelial lesions.
FAM19A4/miR124-2 methylation in invasive cervical cancer: A retrospective cross-sectional worldwide study.
Title: FAM19A4/miR124-2 methylation in invasive cervical cancer: A retrospective cross-sectional worldwide study.
The use of molecular markers for cervical screening of women living with HIV in South Africa.
Title: The use of molecular markers for cervical screening of women living with HIV in South Africa.
Among HPV positive women aged >/=30 years, a negative FAM19A4/miR124-2 methylation test provides a similar safety in terms of long-term CIN3+ risk compared with a negative cytology test, while the CIN3+risk following a positive methylation test justifies immediate colposcopy referral.
Title: Long-term CIN3+ risk of HPV positive women after triage with FAM19A4/miR124-2 methylation analysis.

Submit: New GeneRIF Correction See all GeneRIFs (20)

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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D3S2987 (e-PCR)
- UniSTS:27397

L18063 (e-PCR)
- UniSTS:54283

D3S3540 (e-PCR)
- UniSTS:28947

SHGC-111854 (e-PCR)
- UniSTS:168782

AB063062 (e-PCR)
- UniSTS:479828

SHGC-112013 (e-PCR)
- UniSTS:183636

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 macrophage chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
involved_in macrophage chemotaxis	ISS Inferred from Sequence or Structural Similarity more info
involved_in phagocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in phagocytosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of membrane potential	IEA Inferred from Electronic Annotation more info
involved_in regulation of sensory perception of pain	IEA Inferred from Electronic Annotation 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
involved_in superoxide anion generation	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
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
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
located_in synaptic vesicle membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: chemokine-like protein TAFA-4

Names: family with sequence similarity 19 (chemokine (C-C motif)-like), member A4; family with sequence similarity 19 member A4, C-C motif chemokine like; protein FAM19A4

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)

NM_001005527.3 → NP_001005527.1 chemokine-like protein TAFA-4 precursor

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)

AC096922, BC031566, DA017279

Consensus CDS

CCDS2907.1

UniProtKB/Swiss-Prot

A8MVT2, Q96LR4

Conserved Domains (1) summary

pfam12020
Location:50 → 138

TAFA; TAFA family
NM_182522.5 → NP_872328.1 chemokine-like protein TAFA-4 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.

Source sequence(s)

AC096922, AY325117

Consensus CDS

CCDS2907.1

UniProtKB/Swiss-Prot

A8MVT2, Q96LR4

Related

ENSP00000295569.7, ENST00000295569.12

Conserved Domains (1) summary

pfam12020
Location:50 → 138

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

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

68731766..68932547 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011533372.2 → XP_011531674.1 chemokine-like protein TAFA-4 isoform X1

Conserved Domains (1) summary

pfam12020
Location:50 → 124

TAFA; TAFA family
XM_011533371.2 → XP_011531673.1 chemokine-like protein TAFA-4 isoform X1

Conserved Domains (1) summary

pfam12020
Location:50 → 124

TAFA; TAFA family