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LOC123956185 Sharpr-MPRA regulatory region 1794 [ Homo sapiens (human) ]

Gene ID: 123956185, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123956185
Gene description
Sharpr-MPRA regulatory region 1794
Gene type
biological region
Feature type(s)
regulatory: silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional repressive element by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 16:ElonW, transcriptional elongation, weaker H3K36me3). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123956185 in Genome Data Viewer
Location:
7q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (99055586..99055880)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (100288911..100289205)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (98653209..98653503)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene transformation/transcription domain associated protein Neighboring gene uncharacterized LOC101927550 Neighboring gene RNF14 pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:98631759-98632259 Neighboring gene SMAD specific E3 ubiquitin protein ligase 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:98695995-98696849 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:98696850-98697703 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:98700145-98701344 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:98706490-98706992 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26311 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18400 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18401 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18402 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:98749275-98749496 Neighboring gene karyopherin subunit alpha 7 Neighboring gene Sharpr-MPRA regulatory region 10979 Neighboring gene Sharpr-MPRA regulatory region 10425 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:98848211-98848712 Neighboring gene uncharacterized LOC105375421 Neighboring gene myosin heavy chain 16 (pseudogene)

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-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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)

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_078379.1 

    Range
    101..395
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    99055586..99055880
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    100288911..100289205
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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