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TRAF3IP2-AS1 TRAF3IP2 antisense RNA 1 [ Homo sapiens (human) ]

Gene ID: 643749, updated on 17-Jun-2024

Summary

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Official Symbol
TRAF3IP2-AS1provided by HGNC
Official Full Name
TRAF3IP2 antisense RNA 1provided by HGNC
Primary source
HGNC:HGNC:40005
See related
Ensembl:ENSG00000231889 AllianceGenome:HGNC:40005
Gene type
ncRNA
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
C6UAS; C6orf3; BetaFAAR; NCRNA00248; TRAF3IP2-AS2
Expression
Ubiquitous expression in brain (RPKM 2.1), endometrium (RPKM 1.3) and 23 other tissues See more
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Genomic context

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See TRAF3IP2-AS1 in Genome Data Viewer
Location:
6q21
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (111483472..111602295)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (112666471..112785304)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (111804675..111923498)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene REV3 like, DNA directed polymerase zeta catalytic subunit Neighboring gene FCF1 pseudogene 5 Neighboring gene MPRA-validated peak6034 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr6:111751696-111751904 Neighboring gene MPRA-validated peak6035 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24943 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:111798355-111799247 Neighboring gene bromodomain containing 7 pseudogene 4 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:111799845-111800569 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24944 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17478 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17479 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17477 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17476 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17475 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24945 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24946 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24947 Neighboring gene uncharacterized LOC107986520 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:111828147-111828670 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:111828671-111829193 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_87727 Neighboring gene uncharacterized LOC107986522 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:111861530-111861704 Neighboring gene VISTA enhancer hs1690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:111880567-111881066 Neighboring gene MPRA-validated peak6037 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:111885602-111886274 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:111886439-111887638 Neighboring gene TRAF3 interacting protein 2 Neighboring gene TRAF3IP2 eExon liver enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24950 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:111928045-111928677 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:111941387-111941922 Neighboring gene MPRA-validated peak6038 silencer Neighboring gene uncharacterized LOC105377944 Neighboring gene Sharpr-MPRA regulatory region 7524 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:111982565-111983248 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:111983249-111983930 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:111983931-111984612 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:111998453-111999376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:112003973-112004474 Neighboring gene uncharacterized LOC105377945 Neighboring gene FYN proto-oncogene, Src family tyrosine kinase

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. The long non-coding RNA βFaar regulates islet β-cell function and survival during obesity in mice. Zhang F, et al. Nat Commun, 2021 Jun 28. PMID 34183666, Free PMC Article
  2. Genetics of long-term treatment outcome in bipolar disorder. Fabbri C, et al. Prog Neuropsychopharmacol Biol Psychiatry, 2016 Feb 4. PMID 26297903
  3. Identification of long noncoding RNAs dysregulated in the midbrain of human cocaine abusers. Bannon MJ, et al. J Neurochem, 2015 Oct. PMID 26222413, Free PMC Article
  4. IncRNA TRAF3IP2-AS1 Restrains Cervical Cancer Progression by Sponging miR-3677-3p and Acts As a Diagnostic Marker in Cervical Cancer. Luo C, et al. Crit Rev Eukaryot Gene Expr, 2022. PMID 36374810
  5. Identification of a Long Noncoding RNA TRAF3IP2-AS1 as Key Regulator of IL-17 Signaling through the SRSF10-IRF1-Act1 Axis in Autoimmune Diseases. He R, et al. J Immunol, 2021 May 15. PMID 33941656

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. IncRNA TRAF3IP2-AS1 Restrains Cervical Cancer Progression by Sponging miR-3677-3p and Acts As a Diagnostic Marker in Cervical Cancer.
    Title: IncRNA TRAF3IP2-AS1 Restrains Cervical Cancer Progression by Sponging miR-3677-3p and Acts As a Diagnostic Marker in Cervical Cancer.
  2. Low expression of TRAF3IP2-AS1 promotes progression of NONO-TFE3 translocation renal cell carcinoma by stimulating N(6)-methyladenosine of PARP1 mRNA and downregulating PTEN.
    Title: Low expression of TRAF3IP2-AS1 promotes progression of NONO-TFE3 translocation renal cell carcinoma by stimulating N(6)-methyladenosine of PARP1 mRNA and downregulating PTEN.
  3. Identification of a Long Noncoding RNA TRAF3IP2-AS1 as Key Regulator of IL-17 Signaling through the SRSF10-IRF1-Act1 Axis in Autoimmune Diseases.
    Title: Identification of a Long Noncoding RNA TRAF3IP2-AS1 as Key Regulator of IL-17 Signaling through the SRSF10-IRF1-Act1 Axis in Autoimmune Diseases.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Common variants at TRAF3IP2 are associated with susceptibility to psoriatic arthritis and psoriasis.
EBI GWAS Catalog
Genome-wide association study identifies a psoriasis susceptibility locus at TRAF3IP2.
EBI GWAS Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
EBI GWAS Catalog

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

General gene information

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Markers

Other Names

  • Beta-cell function and apoptosis regulator
  • TRAF3IP2 antisense RNA 1 (non-protein coding)
  • TRAF3IP2 antisense RNA 2 (non-protein coding)

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.

RNA

  1. NR_034108.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript.
    Source sequence(s)
    AL008730, AL136310, Z97989

  2. NR_034109.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks two alternate internal exons, compared to variant 1.
    Source sequence(s)
    AL136310, Z97989

  3. NR_034110.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate 3' splice pattern, compared to variant 1.
    Source sequence(s)
    AL008730, AL136310
    Related
    ENST00000449449.7

  4. NR_034111.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses the same first exon as variant 1, but uses an alternate set of exons for the 3' end.
    Source sequence(s)
    AL136310, BX647114
    Related
    ENST00000525151.5

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    111483472..111602295
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    112666471..112785304
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Molecular Biology Databases
Research Materials