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SIX3-AS1 SIX3 antisense RNA 1 [ Homo sapiens (human) ]

Gene ID: 100506108, updated on 10-Oct-2023

Summary

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Official Symbol
SIX3-AS1provided by HGNC
Official Full Name
SIX3 antisense RNA 1provided by HGNC
Primary source
HGNC:HGNC:40532
See related
Ensembl:ENSG00000236502 AllianceGenome:HGNC:40532
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
SIX3OS
Expression
Low expression observed in reference dataset See more
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Genomic context

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Location:
2p21
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (44940154..44941878, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (44945419..44947143, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (45167293..45169017, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374573 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15686 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:45089860-45089961 Neighboring gene VISTA enhancer hs149 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:45153974-45154534 Neighboring gene long intergenic non-protein coding RNA 1833 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45164020-45164553 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45164554-45165086 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11434 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45166505-45167006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45167007-45167506 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45168275-45168801 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45169884-45170608 Neighboring gene NANOG hESC enhancer GRCh37_chr2:45172898-45173404 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11435 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11436 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45182266-45182972 Neighboring gene SIX homeobox 3 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45199471-45200338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45202291-45203066 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45203067-45203842 Neighboring gene keratinocyte-associated protein 2-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45227219-45228192 Neighboring gene KRTCAP2 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45232925-45233468 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45233469-45234012 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45235286-45236059 Neighboring gene SIX homeobox 2

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. Natural antisense transcripts associated with genes involved in eye development. Alfano G, et al. Hum Mol Genet, 2005 Apr 1. PMID 15703187
  2. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548

GeneRIFs: Gene References Into Functions

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

Other Names

  • SIX3 antisense RNA 1 (non-protein coding)

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in regulation of gene expression IEA
Inferred from Electronic Annotation
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_103785.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript.
    Source sequence(s)
    AC012354
    Related
    ENST00000456467.2

  2. NR_103786.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks the 5' exon and contains an alternate 5' exon, resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AC012354
    Related
    ENST00000419364.3

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    44940154..44941878 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    44945419..44947143 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Molecular Biology Databases