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CISTR chondrogenesis-associated transcript [ Homo sapiens (human) ]

Gene ID: 102216268, updated on 10-Mar-2024

Summary

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Official Symbol
CISTRprovided by HGNC
Official Full Name
chondrogenesis-associated transcriptprovided by HGNC
Primary source
HGNC:HGNC:49426
See related
Ensembl:ENSG00000260492 AllianceGenome:HGNC:49426
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
re52431; CISTRACT; CISTR-ACT
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

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Location:
12q13.13
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (53746337..53757034, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (53712091..53722788, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (54144231..54150818, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6427 Neighboring gene ATP synthase membrane subunit c locus 2 Neighboring gene Sharpr-MPRA regulatory region 7415 Neighboring gene calcium binding and coiled-coil domain 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:54118812-54120011 Neighboring gene uncharacterized LOC105369774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:54133003-54133792 Neighboring gene CALCOCO1-CISTR intergenic nontranscribed DNase I hypersensitive site-defined enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:54141521-54142049 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:54142050-54142577 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:54144138-54144726 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4517 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4518 Neighboring gene uncharacterized LOC105378250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6429 Neighboring gene uncharacterized LOC105378250 Neighboring gene RN7SK pseudogene 289

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 misplaced lncRNA causes brachydactyly in humans. Maass PG, et al. J Clin Invest, 2012 Nov. PMID 23093776, Free PMC Article
  2. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article

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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Homology

Other Names

  • chondrogenic regulator lncRNA
  • cis- and trans-chromosomal chondrogenic regulator transcript

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_104332.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript.
    Source sequence(s)
    AC076968, DA125942, HY042141

  2. NR_104333.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks two exons and contains an alternate 5' terminal exon, which results in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AC076968, DA125942

  3. NR_186107.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC076968

  4. NR_186108.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC076968
    Related
    ENST00000663667.1

  5. NR_186109.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC076968
    Related
    ENST00000669269.1

  6. NR_186110.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC076968

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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    53746337..53757034 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    53712091..53722788 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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