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

    Gene ID: 100507217, updated on 10-Dec-2024

    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
    MIM:620993; 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
    NEDFSAB; LINC01578
    Summary
    Predicted to be involved in several processes, including adipose tissue development; regulation of gene expression; and thymus development. Predicted to be part of chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Dec 2024]
    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_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (92882843..92898747)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (90645106..90661010)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Neurodevelopmental Disorder Caused by Deletion of CHASERR, a lncRNA Gene. Ganesh VS, et al. N Engl J Med, 2024 Oct 24. PMID 39442041
    2. 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
    3. 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
    4. 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
    5. Generation and analysis of 280,000 human expressed sequence tags. Hillier LD, et al. Genome Res, 1996 Sep. PMID 8889549

    See all (6) citations in PubMed

    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)

    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_2024_08

    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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