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

Gene ID: 653483, updated on 26-Oct-2024

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; LINC01558; 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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See AFDN-DT in Genome Data Viewer
Location:
6q27
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (167823890..167826796, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (169162096..169165002, complement)
RS_2024_09 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)

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
  • long intergenic non-protein coding RNA 1558

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_2024_08

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