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CRNDE colorectal neoplasia differentially expressed [ Homo sapiens (human) ]

Gene ID: 643911, updated on 5-Mar-2024

Summary

Official Symbol
CRNDEprovided by HGNC
Official Full Name
colorectal neoplasia differentially expressedprovided by HGNC
Primary source
HGNC:HGNC:37078
See related
Ensembl:ENSG00000245694 MIM:615624; AllianceGenome:HGNC:37078
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
CRNDEP; PNAS-108; lincIRX5; LINC00180; NCRNA00180
Summary
This gene is transcribed into multiple transcript variants, some of which may function as non-coding RNAs. One of the transcript variants encodes a putative short protein that is localized to the nucleus (PMID:25978564). Expression of this locus is increased in proliferating tissues, including certain tumors such as colorectal adenomas and adenocarcinomas. Transcription from this gene is negatively regulated by insulin and insulin-like growth factors, and may regulate the expression of genes involved in metabolism. [provided by RefSeq, May 2015]
Expression
Biased expression in testis (RPKM 14.7), lung (RPKM 2.1) and 8 other tissues See more
Orthologs
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Genomic context

See CRNDE in Genome Data Viewer
Location:
16q12.2
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (54918863..54928886, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (60716970..60726999, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (54952775..54962798, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101927480 Neighboring gene uncharacterized LOC105371275 Neighboring gene uncharacterized LOC105371276 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7503 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7504 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7505 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7506 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:54965529-54966728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:54968431-54969182 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:54969183-54969932 Neighboring gene uncharacterized LOC124903692 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:54970502-54971064 Neighboring gene iroquois homeobox 5

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Other Names

  • colorectal neoplasia differentially expressed (non-protein coding)
  • long intergenic non-protein coding RNA 180

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_034105.4 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1, also known as h) is the reference variant.
    Source sequence(s)
    BM974647, DB455235, FJ466685
    Related
    ENST00000701876.1
  2. NR_034106.3 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2, also known as g) differs in the 5' terminal exon, resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AC106738, BF692451, BM974647, FJ466685
  3. NR_110453.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3, also known as c1a) contains an alternate internal exon, resulting in a longer transcript, compared to variant 1.
    Source sequence(s)
    BM974647, DB446128, DB455235, FJ466685
  4. NR_110454.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4, also known as i1b) differs in the 5' terminal exon and uses an alternate splice site at an internal exon, resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AC106738, BF692451, BM974647, CV575277
    Related
    ENST00000501177.9
  5. NR_170995.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC106738, AC108084

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
    54918863..54928886 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    60716970..60726999 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001308963.2: Suppressed sequence

    Description
    NM_001308963.2: This RefSeq was removed because it is now thought that this gene does not encode a protein.