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LOC124310621 Sharpr-MPRA regulatory region 2753 [ Homo sapiens (human) ]

Gene ID: 124310621, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124310621
Gene description
Sharpr-MPRA regulatory region 2753
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 matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Feb 2022]
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Genomic context

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See LOC124310621 in Genome Data Viewer
Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (109475569..109475863)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (121644964..121645258)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (112237849..112238143)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene erythrocyte membrane protein band 4.1 like 4B Neighboring gene RNA, U6 small nuclear 984, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20165 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20166 Neighboring gene MT-ND2 pseudogene 11 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20167 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28759 Neighboring gene protein tyrosine phosphatase non-receptor type 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28760 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28761 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28763 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28762 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28764 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28765 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:112193017-112193518 Neighboring gene HNF1 motif-containing MPRA enhancer 98 Neighboring gene microRNA 3927 Neighboring gene Y-box binding protein 1 pseudogene 6

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_078903.1 

    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    109475569..109475863
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    121644964..121645258
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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