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CRE1 CRE1 CAGE-defined tissue-specific enhancer [ Homo sapiens (human) ]

Gene ID: 108348016, updated on 17-Sep-2024

Summary

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Gene symbol
CRE1
Gene description
CRE1 CAGE-defined tissue-specific enhancer
Gene type
biological region
Feature type(s)
misc_feature: conserved_region
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic element is located in an intron of the TMEM161B-AS1 (TMEM161B antisense RNA 1) gene. It was defined as a tissue-specific transcribed enhancer based on the presence of balanced bidirectional capped transcripts by cap analysis of gene expression (CAGE) in neural tissues, and on genomic conservation analysis. It was validated as a functional tissue-specific enhancer by transgenic reporter assays in both zebrafish and mice. [provided by RefSeq, Jul 2016]
Orthologs
mouse all
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Genomic context

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See CRE1 in Genome Data Viewer
Location:
5q14.3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (88396337..88397591)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (88877403..88878657)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (87692154..87693408)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene TMEM161B divergent transcript Neighboring gene small nucleolar RNA SNORA70 Neighboring gene RPS3A pseudogene 22 Neighboring gene long intergenic non-protein coding RNA 2060 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22757 Neighboring gene MIR9-2 host gene Neighboring gene H3 histone pseudogene 23

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Visel A, et al. Nat Genet, 2008 Feb. PMID 18176564, Free PMC Article
  2. In vivo enhancer analysis of human conserved non-coding sequences. Pennacchio LA, et al. Nature, 2006 Nov 23. PMID 17086198
  3. Ultraconserved elements in the human genome. Bejerano G, et al. Science, 2004 May 28. PMID 15131266
  4. An atlas of active enhancers across human cell types and tissues. Andersson R, et al. Nature, 2014 Mar 27. PMID 24670763, Free PMC Article
  5. VISTA Enhancer Browser--a database of tissue-specific human enhancers. Visel A, et al. Nucleic Acids Res, 2007 Jan. PMID 17130149, 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 Variation Viewer (GRCh37.p13)

General gene information

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Homology

Other Names

  • FANTOM5 human-zebrafish conserved CRE1 enhancer
  • VISTA enhancer hs268
  • cis-regulatory element 1
  • ultraconserved element uc.165

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.

Genomic

  1. NG_051156.1 

    Range
    101..1355
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    88396337..88397591
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    88877403..88878657
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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