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    AFDN-DT AFDN divergent transcript [ Homo sapiens (human) ]

    Gene ID: 653483, updated on 10-Oct-2023

    Summary

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    Official Symbol
    AFDN-DTprovided by HGNC
    Official Full Name
    AFDN divergent transcriptprovided by HGNC
    Primary source
    HGNC:HGNC:21236
    See related
    AllianceGenome:HGNC:21236
    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
    HGC6.4; XBP1SBM; AFDN-AS1; C6orf124; MLLT4-AS1; dJ431P23.3
    Expression
    Broad expression in prostate (RPKM 1.2), testis (RPKM 1.0) and 22 other tissues See more
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    Genomic context

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    Location:
    6q27
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (167823890..167826796, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (169162096..169165002, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (168224570..168227476, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene serine palmitoyltransferase long chain base subunit 2 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:168167604-168168104 Neighboring gene long intergenic non-protein coding RNA 1558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:168199638-168200171 Neighboring gene uncharacterized LOC441179 Neighboring gene Sharpr-MPRA regulatory region 935 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17792 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25461 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17793 Neighboring gene afadin, adherens junction formation factor Neighboring gene Sharpr-MPRA regulatory region 4710 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:168264804-168266003 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:168294093-168294968 Neighboring gene uncharacterized LOC107986673 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:168375775-168376684 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:168378524-168379100 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:168379101-168379677 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:168380255-168380830 Neighboring gene uncharacterized LOC100128124

    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. A micropeptide XBP1SBM encoded by lncRNA promotes angiogenesis and metastasis of TNBC via XBP1s pathway. Wu S, et al. Oncogene, 2022 Apr. PMID 35197570
    2. Tumour suppressive long non-coding RNA AFDN-DT inhibits gastric cancer invasion via transcriptional regulation. Lai Y, et al. J Cell Mol Med, 2020 Mar. PMID 31981317, Free PMC Article
    3. Decreased expression of the long non-coding RNA MLLT4 antisense RNA 1 is a potential biomarker and an indicator of a poor prognosis for gastric cancer. Lai Y, et al. Oncol Lett, 2017 Sep. PMID 28927028, Free PMC Article
    4. Complete DNA sequence and characterization of a 330-kb VNTR-rich region on chromosome 6q27 that is commonly deleted in ovarian cancer. Minaguchi T, et al. DNA Res, 1999 Apr 30. PMID 10382971
    5. RIG-I regulates myeloid differentiation by promoting TRIM25-mediated ISGylation. Wu SF, et al. Proc Natl Acad Sci U S A, 2020 Jun 23. PMID 32513696, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Tumour suppressive long non-coding RNA AFDN-DT inhibits gastric cancer invasion via transcriptional regulation.
      Title: Tumour suppressive long non-coding RNA AFDN-DT inhibits gastric cancer invasion via transcriptional regulation.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Other Names

    • AFDN antisense RNA 1 (head to head)
    • MLLT4 antisense RNA 1 (head to head)
    • MLLT4 antisense RNA 1 (non-protein coding)
    • XBP1s binding micropeptide

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  

    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_027906.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AB016898, DC331926, DC427335

    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
      167823890..167826796 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      169162096..169165002 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001042508.3: Suppressed sequence

      Description
      NM_001042508.3: This RefSeq was permanently suppressed because it is now thought that this gene does not encode a protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y6Z5.1 GenPept UniProtKB/Swiss-Prot:Q9Y6Z5

    Gene LinkOut

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

    Molecular Biology Databases
    Research Materials
    Miscellaneous