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PRANCR progenitor renewal associated non-coding RNA [ Homo sapiens (human) ]

Gene ID: 101928062, updated on 10-Oct-2023

Summary

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Official Symbol
PRANCRprovided by HGNC
Official Full Name
progenitor renewal associated non-coding RNAprovided by HGNC
Primary source
HGNC:HGNC:51126
See related
Ensembl:ENSG00000257815 MIM:619085; AllianceGenome:HGNC:51126
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
CNOT2-DT; LINC01481
Expression
Ubiquitous expression in bone marrow (RPKM 4.1), testis (RPKM 2.9) and 25 other tissues See more
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Genomic context

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Location:
12q15
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (70222190..70243360, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (70201585..70222753, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (70615970..70637140, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene histone PARylation factor 1 pseudogene Neighboring gene MPRA-validated peak1797 silencer Neighboring gene MPRA-validated peak1798 silencer Neighboring gene long intergenic non-protein coding RNA 2821 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:70636499-70637698 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6658 Neighboring gene MPRA-validated peak1799 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:70650862-70651362 Neighboring gene NANOG hESC enhancer GRCh37_chr12:70652346-70652879 Neighboring gene CCR4-NOT transcription complex subunit 2 Neighboring gene MPRA-validated peak1802 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4656 Neighboring gene MPRA-validated peak1805 silencer Neighboring gene potassium calcium-activated channel subfamily M regulatory beta subunit 4 Neighboring gene MPRA-validated peak1806 silencer Neighboring gene RNA, U4 small nuclear 65, pseudogene

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 genome-wide long noncoding RNA CRISPRi screen identifies PRANCR as a novel regulator of epidermal homeostasis. Cai P, et al. Genome Res, 2020 Jan. PMID 31804951, 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

What's a GeneRIF?
  1. The Long Noncoding RNA PRANCR Is Associated with Alternative Splicing of Fibronectin-1 in Keratinocytes.
    Title: The Long Noncoding RNA PRANCR Is Associated with Alternative Splicing of Fibronectin-1 in Keratinocytes.
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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Other Names

  • CNOT2 divergent transcript
  • long intergenic non-protein coding RNA 1481

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_120459.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript.
    Source sequence(s)
    CA418524, HY002672
    Related
    ENST00000549651.1

  2. NR_120460.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in both the 5' and 3' exon structures, resulting in a shorter transcript compared to variant 1.
    Source sequence(s)
    HY013176

  3. NR_120461.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in both the 5' and 3' exon structures, resulting in a shorter transcript compared to variant 1.
    Source sequence(s)
    DB462634, HY013176, HY048577
    Related
    ENST00000550216.1

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
    70222190..70243360 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    70201585..70222753 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Molecular Biology Databases