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LOC108254686 ITGB4 intron CAGE-defined low expression enhancer [ Homo sapiens (human) ]

Gene ID: 108254686, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108254686
Gene description
ITGB4 intron CAGE-defined low expression enhancer
Gene type
biological region
Feature type(s)
misc_feature: CAGE_cluster
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 ITGB4 (integrin subunit beta 4) gene. It was defined as a low expression actively transcribed enhancer based on the presence of balanced bidirectional capped transcripts by cap analysis of gene expression (CAGE). It was validated as a functional enhancer by reporter assays in HeLa cells. [provided by RefSeq, Jul 2016]
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Genomic context

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Location:
17q25
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (75723181..75723829)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (76616399..76617047)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (73719261..73719909)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene RecQ like helicase 5 Neighboring gene uncharacterized LOC107985013 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:73662359-73663558 Neighboring gene SAP30 binding protein Neighboring gene SAP30BP antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:73684215-73684716 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:73684717-73685216 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73693087-73693798 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:73695788-73696987 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:73702471-73703670 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8975 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73717282-73717820 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73717821-73718359 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73724533-73725033 Neighboring gene integrin subunit beta 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73749848-73750621 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8978 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73754136-73754662 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73754663-73755189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12775 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8979 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8980 Neighboring gene galactokinase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73769871-73770371 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8981 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8982 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8983 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12776 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73774948-73775552 Neighboring gene H3.3 histone B

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. An atlas of active enhancers across human cell types and tissues. Andersson R, et al. Nature, 2014 Mar 27. PMID 24670763, 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

  • ITGB4 intron low CAGE FANTOM5 enhancer

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_051034.1 

    Range
    101..749
    Download
    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
    75723181..75723829
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    76616399..76617047
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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