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LOC126860461 CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:102655529-102656728 [ Homo sapiens (human) ]

Gene ID: 126860461, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126860461
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:102655529-102656728
Gene type
biological region
Feature type(s)
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 region includes an enhancer that was validated by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in HCT116 colorectal carcinoma cells, where it was defined as a group 2 enhancer that depends on the BRD2, BRD4, P300/CBP, MED14 and CDK7 cofactors, with strong dependence on CDK7. A subregion was also validated as an enhancer by ChIP-STARR-seq in naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
chromosome: 8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (101643301..101644505)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (102769167..102770373)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene SAP domain containing ribonucleoprotein pseudogene Neighboring gene grainyhead like transcription factor 2 Neighboring gene probable ribosome biogenesis protein RLP24 Neighboring gene Sharpr-MPRA regulatory region 9664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:102659137-102659637 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:102668311-102669171 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27732 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27733 Neighboring gene neurocalcin delta Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:102762302-102763501 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27734 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27735 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:102799260-102799806 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:102799807-102800353 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27736 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19433 Neighboring gene small nucleolar RNA U13 Neighboring gene PDCL3 pseudogene 2

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. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, Free PMC Article
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, Free PMC Article
  3. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 27731
  • H3K4me1 hESC enhancer GRCh37_chr8:102655905-102656404

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_084961.2 

    Range
    101..1305
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    GenBank, FASTA, Sequence Viewer (Graphics)

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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    101643301..101644505
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    102769167..102770373
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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