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LOC108175351 TCBA and LOC101929154 interval homotypic clusters of transcription factor binding sites enhancer [ Homo sapiens (human) ]

Gene ID: 108175351, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108175351
Gene description
TCBA and LOC101929154 interval homotypic clusters of transcription factor binding sites 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 the intergenic region between the TCBA (tubulin folding cofactor A) and LOC101929154 genes, approximately 70 kb from the TCBA 5' end. It contains multiple homotypic clusters of transcription factor binding sites (HCTs) based on the presence of multiple binding motifs for NRF1 (nuclear respiratory factor 1) and E2F4 (E2F transcription factor 4). This HCT region was validated as a functional enhancer in transgenic reporter assays in embryonic mouse brain and neural tube. Two subregions were also shown to be active enhancers by ChIP-STARR-seq in human embryonic stem cells, where one subregion is associated with the OCT4 and NANOG transcription factors and the other is marked by the H3K27ac and H3K4me1 histone modifications. [provided by RefSeq, Oct 2022]
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Genomic context

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Location:
5q14.1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (77845919..77849307)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (78327664..78331052)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (77141743..77145131)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77047116-77047753 Neighboring gene tubulin folding cofactor A Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:77068972-77069857 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:77069858-77070742 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16114 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16115 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:77105415-77106614 Neighboring gene ACTB pseudogene 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77140391-77141257 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77147023-77147532 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77147533-77148040 Neighboring gene NANOG hESC enhancer GRCh37_chr5:77167707-77168240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22703 Neighboring gene uncharacterized LOC101929154 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:77230857-77231031 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:77253041-77253552 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:77254064-77254574 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:77254575-77255085 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16117 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16118 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:77283519-77284038 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:77284039-77284558 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:77312459-77313399 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:77313400-77314339 Neighboring gene tRNA-Gln (anticodon TTG) 7-1 Neighboring gene adaptor related protein complex 3 subunit beta 1

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. Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. Gotea V, et al. Genome Res, 2010 May. PMID 20363979, Free PMC Article
  2. VISTA Enhancer Browser--a database of tissue-specific human enhancers. Visel A, et al. Nucleic Acids Res, 2007 Jan. PMID 17130149, 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77142152-77142736
  • NRF1 and E2F4 HCT enhancer
  • OCT4-NANOG hESC enhancer GRCh37_chr5:77143463-77144411
  • VISTA enhancer hs1783

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_050924.1 

    Range
    101..3489
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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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    77845919..77849307
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    78327664..78331052
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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