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LOC124625897 Sharpr-MPRA regulatory region 5519 [ Homo sapiens (human) ]

Gene ID: 124625897, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124625897
Gene description
Sharpr-MPRA regulatory region 5519
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 HepG2 liver carcinoma cells (group: HepG2 Repressive DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Mar 2022]
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Genomic context

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See LOC124625897 in Genome Data Viewer
Location:
12p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (7162653..7162947)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (7175815..7176109)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene C1RL antisense RNA 1 Neighboring gene RNA, U6 small nuclear 485, pseudogene Neighboring gene retinol binding protein 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4198 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:7283265-7283766 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4199 Neighboring gene calsyntenin 3 Neighboring gene uncharacterized LOC124902869 Neighboring gene MPRA-validated peak1553 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:7340767-7341268 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:7341269-7341768 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5916 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7342139-7342855 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7342856-7343571 Neighboring gene peroxisomal biogenesis factor 5

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

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_079579.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    7162653..7162947
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_021160008.1 Reference GRCh38.p14 PATCHES

    Range
    90339..90633
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    7175815..7176109
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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