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CHASERR CHD2 adjacent suppressive regulatory RNA [ Homo sapiens (human) ]

Gene ID: 100507217, updated on 10-Oct-2023

Summary

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Official Symbol
CHASERRprovided by HGNC
Official Full Name
CHD2 adjacent suppressive regulatory RNAprovided by HGNC
Primary source
HGNC:HGNC:48626
See related
AllianceGenome:HGNC:48626
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
LINC01578
Expression
Ubiquitous expression in bone marrow (RPKM 64.7), brain (RPKM 22.1) and 24 other tissues See more
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Genomic context

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See CHASERR in Genome Data Viewer
Location:
15q26.1
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (92882843..92898747)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (90645106..90661010)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (93426073..93441977)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_42698 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:93344283-93345134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10118 Neighboring gene uncharacterized LOC124903558 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:93351993-93352843 Neighboring gene ankyrin repeat and SOCS box containing 9 pseudogene 1 Neighboring gene FAM174B-LINC01578 intergenic CAGE-defined high expression enhancer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:93368032-93368688 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10121 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10122 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10124 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10125 Neighboring gene MPRA-validated peak2429 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10127 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6848 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6849 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:93425915-93426556 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10128 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10129 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:93447162-93448361 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:93460529-93461365 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:93464712-93465911 Neighboring gene microRNA 3175 Neighboring gene chromodomain helicase DNA binding protein 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:93488387-93488611 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:93492919-93494118 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:93523977-93525176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:93571676-93572182 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:93575221-93575725 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10132 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10133 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:93595001-93595610 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:93605093-93605890 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:93606687-93607483 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:93608443-93609406 Neighboring gene repulsive guidance molecule BMP co-receptor a Neighboring gene YBX2 pseudogene 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. LINC01578 affects the radiation resistance of lung cancer cells through regulating microRNA-216b-5p/TBL1XR1 axis. Wang P, et al. Bioengineered, 2022 Apr. PMID 35475502, Free PMC Article
  2. Long noncoding RNA LINC01578 drives colon cancer metastasis through a positive feedback loop with the NF-κB/YY1 axis. Liu J, et al. Mol Oncol, 2020 Dec. PMID 33040438, Free PMC Article
  3. Regulation of CHD2 expression by the Chaserr long noncoding RNA gene is essential for viability. Rom A, et al. Nat Commun, 2019 Nov 8. PMID 31704914, Free PMC Article
  4. Generation and analysis of 280,000 human expressed sequence tags. Hillier LD, et al. Genome Res, 1996 Sep. PMID 8889549
  5. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. LINC01578 affects the radiation resistance of lung cancer cells through regulating microRNA-216b-5p/TBL1XR1 axis.
    Title: LINC01578 affects the radiation resistance of lung cancer cells through regulating microRNA-216b-5p/TBL1XR1 axis.
  2. Long noncoding RNA LINC01578 drives colon cancer metastasis through a positive feedback loop with the NF-kappaB/YY1 axis.
    Title: Long noncoding RNA LINC01578 drives colon cancer metastasis through a positive feedback loop with the NF-κB/YY1 axis.
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

Potential readthrough

Included gene: CHD2

Other Names

  • long intergenic non-protein coding RNA 1578

Clone Names

  • DKFZp781D1727

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_037600.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon, compared to variant 1.
    Source sequence(s)
    AC013394, AW246969, BU848955

  2. NR_037601.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript.
    Source sequence(s)
    AA083786, AC013394, AW246969, BQ188346, BU848955

  3. NR_037602.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate splice donor site for the first exon and lacks the alternate second exon, compared to variant 1.
    Source sequence(s)
    AC013394, BQ890654

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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    92882843..92898747
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    90645106..90661010
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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