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    B3GALT5-AS1 B3GALT5 antisense RNA 1 [ Homo sapiens (human) ]

    Gene ID: 114041, updated on 10-Oct-2023

    Summary

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    Official Symbol
    B3GALT5-AS1provided by HGNC
    Official Full Name
    B3GALT5 antisense RNA 1provided by HGNC
    Primary source
    HGNC:HGNC:16424
    See related
    AllianceGenome:HGNC:16424
    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
    C21orf88
    Expression
    Biased expression in colon (RPKM 5.0), thyroid (RPKM 0.6) and 7 other tissues See more
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    Genomic context

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    See B3GALT5-AS1 in Genome Data Viewer
    Location:
    21q22.2
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (39597147..39612822, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (37981617..37997292, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (40969074..40984749, complement)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene GET1-SH3BGR readthrough Neighboring gene SH3 domain binding glutamate rich protein Neighboring gene ribosomal protein S26 pseudogene 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:40899605-40900600 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:40907492-40908386 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:40909281-40910174 Neighboring gene NANOG hESC enhancer GRCh37_chr21:40923594-40924095 Neighboring gene NANOG hESC enhancer GRCh37_chr21:40931347-40931936 Neighboring gene JCAD pseudogene 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:41005119-41006318 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:41011717-41012218 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:41012219-41012718 Neighboring gene beta-1,3-galactosyltransferase 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:41015167-41015667 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:41020756-41021302 Neighboring gene B3GALT5 ERV-L LTR promoter Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:41044997-41045632 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:41079003-41079814 Neighboring gene uncharacterized LOC107985499 Neighboring gene immunoglobulin superfamily member 5

    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. Abnormally expressed long noncoding RNA B3GALT5-AS1 may serve as a biomarker for the diagnostic and prognostic of gastric cancer. Feng W, et al. J Cell Biochem, 2020 Jan. PMID 31338903
    2. Long noncoding RNA B3GALT5-AS1 suppresses colon cancer liver metastasis via repressing microRNA-203. Wang L, et al. Aging (Albany NY), 2018 Dec 10. PMID 30530918, Free PMC Article
    3. Nineteen additional unpredicted transcripts from human chromosome 21. Reymond A, et al. Genomics, 2002 Jun. PMID 12036297
    4. Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters. Warnatz HJ, et al. Nucleic Acids Res, 2010 Oct. PMID 20494980, Free PMC Article
    5. The sequence of the human genome. Venter JC, et al. Science, 2001 Feb 16. PMID 11181995

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Abnormally expressed long noncoding RNA B3GALT5-AS1 may serve as a biomarker for the diagnostic and prognostic of gastric cancer.
      Title: Abnormally expressed long noncoding RNA B3GALT5-AS1 may serve as a biomarker for the diagnostic and prognostic of gastric cancer.
    2. Long noncoding RNA B3GALT5-AS1 suppresses colon cancer liver metastasis via repressing expression of microRNA-203.
      Title: Long noncoding RNA B3GALT5-AS1 suppresses colon cancer liver metastasis via repressing microRNA-203.
    3. The C21orf88 promoter is activated by Trichostatin A (TSA) treatment and by serum depletion according to promoter reporter assays in HEK 293 cells.
      Title: Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters.
    Submit: New GeneRIF Correction

    Phenotypes

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    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

    General gene information

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    Markers

    Clone Names

    • FLJ26079

    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_026542.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) is the longer transcript.
      Source sequence(s)
      AF064860, AF426266, BC119738, BG751912, DA218783

    2. NR_026543.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has an alternate 3' exon, as compared to variant 1.
      Source sequence(s)
      BC062296, BC080530, DA218783

    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_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      39597147..39612822 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      37981617..37997292 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_153754.1: Suppressed sequence

      Description
      NM_153754.1: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P59052.2 GenPept UniProtKB/Swiss-Prot:P59052

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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