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ATP2A1-AS1 ATP2A1 antisense RNA 1 [ Homo sapiens (human) ]

Gene ID: 100289092, updated on 10-Oct-2023

Summary

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Official Symbol
ATP2A1-AS1provided by HGNC
Official Full Name
ATP2A1 antisense RNA 1provided by HGNC
Primary source
HGNC:HGNC:51370
See related
Ensembl:ENSG00000260442 AllianceGenome:HGNC:51370
Gene type
ncRNA
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Expression
Biased expression in esophagus (RPKM 2.7), prostate (RPKM 2.4) and 13 other tissues See more
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Genomic context

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Location:
16p11.2
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (28878957..28879921, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (29159457..29160421, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (28890278..28891242, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10645 Neighboring gene MPRA-validated peak2552 silencer Neighboring gene microRNA 4721 Neighboring gene Tu translation elongation factor, mitochondrial Neighboring gene SH2B adaptor protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10646 Neighboring gene Sharpr-MPRA regulatory region 4004 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7314 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:28885274-28885774 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:28885775-28886275 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10648 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10649 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:28890195-28890968 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7315 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7316 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:28894492-28895301 Neighboring gene ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:28917069-28917917 Neighboring gene rabaptin, RAB GTPase binding effector protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10650 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10651 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7317 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7318 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:28937019-28937602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10652 Neighboring gene CD19 molecule

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. Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation. Brandenberger R, et al. Nat Biotechnol, 2004 Jun. PMID 15146197

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

Pathways from PubChem

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General gene information

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Markers

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_046287.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript.
    Source sequence(s)
    AI015924, BX099641, CK823011
    Related
    ENST00000561547.5

  2. NR_046288.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site, compared to variant 1.
    Source sequence(s)
    AI015924, AI825432, CK823011, CN276695

  3. NR_046289.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site, compared to variant 1.
    Source sequence(s)
    AI015924, CK823011, CK823012
    Related
    ENST00000566956.2

  4. NR_046290.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site, compared to variant 1.
    Source sequence(s)
    AI015924, AW451408, CK823011, CN276695

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    28878957..28879921 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    29159457..29160421 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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