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LOC106799838 nonconserved acetylation island sequence 85 enhancer [ Homo sapiens (human) ]

Gene ID: 106799838, updated on 10-Oct-2023

Summary

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Gene symbol
LOC106799838
Gene description
nonconserved acetylation island sequence 85 enhancer
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 region, which is not conserved between human and mouse at the sequence level, is located in an intron of the ITGAE (integrin alpha E) gene on chromosome 17. The major subregion can function as an enhancer by reporter assays in human Jurkat T cells, and it represents a histone acetylation island in human T cells based on the diacetylation of histone H3 at lysines 9 and 14. Two subregions marked by the H3K4me1 histone modification were also shown to be active enhancers by ChIP-STARR-seq in naive human embryonic stem cells. This locus also includes two accessible chromatin subregions that were validated as enhancers based on their 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) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC106799838 in Genome Data Viewer
Location:
17p13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (3794907..3797050)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (3683571..3685732)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (3698786..3700173)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene P2RX5-TAX1BP3 readthrough (NMD candidate) Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:3591902-3592810 Neighboring gene purinergic receptor P2X 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11512 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11513 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:3598520-3599036 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11514 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8018 Neighboring gene MPRA-validated peak2690 silencer Neighboring gene MPRA-validated peak2691 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:3627127-3627882 Neighboring gene integrin subunit alpha E Neighboring gene Sharpr-MPRA regulatory region 669 Neighboring gene histone H3 associated protein kinase Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:3658435-3659138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11515 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11516 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11517 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:3697478-3698200 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:3701060-3701958 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11521 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:3716184-3716689 Neighboring gene nuclear cap binding subunit 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:3735506-3735685 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8021 Neighboring gene uncharacterized LOC124903897

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. Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns. Roh TY, et al. Genome Res, 2007 Jan. PMID 17135569, Free PMC Article
  2. Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Roh TY, et al. Genes Dev, 2005 Mar 1. PMID 15706033, Free PMC Article
  3. 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
  4. 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

  • ATAC-STARR-seq lymphoblastoid active region 11518
  • ATAC-STARR-seq lymphoblastoid active region 11519
  • H3K4me1 hESC enhancer GRCh37_chr17:3698201-3698922
  • H3K4me1 hESC enhancer GRCh37_chr17:3698923-3699644
  • non-conserved AI 85

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_046137.3 

    Range
    101..2244
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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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    3794907..3797050
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    3683571..3685732
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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