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LOC124310638 Sharpr-MPRA regulatory region 1336 [ Homo sapiens (human) ]

Gene ID: 124310638, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124310638
Gene description
Sharpr-MPRA regulatory region 1336
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 23:Low, low signal proximal to active elements) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Feb 2022]
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Genomic context

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Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (123725490..123725784)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (135923310..135923604)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (126487769..126488063)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene DENN domain containing 1A Neighboring gene microRNA 7150 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:126323227-126323788 Neighboring gene uncharacterized LOC105376266 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20251 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28943 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:126417147-126417647 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28945 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28946 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28947 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28948 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28950 Neighboring gene VISTA enhancer hs314 Neighboring gene uncharacterized LOC124902336 Neighboring gene phosphatidylinositol glycan anchor biosynthesis class F pseudogene 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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_078919.1 

    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
    123725490..123725784
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    135923310..135923604
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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