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LOC122757920 Sharpr-MPRA regulatory region 4561 [ Homo sapiens (human) ]

Gene ID: 122757920, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122757920
Gene description
Sharpr-MPRA regulatory region 4561
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 DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Sep 2021]
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Genomic context

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Location:
2p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (38692727..38693021)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (38699661..38699955)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (38919869..38920163)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2613 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11373 Neighboring gene ribosomal protein lateral stalk subunit P0 pseudogene 6 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11374 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15608 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:38763105-38763715 Neighboring gene Sharpr-MPRA regulatory region 10245 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:38779519-38779723 Neighboring gene heterogeneous nuclear ribonucleoprotein L like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11376 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11377 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11378 Neighboring gene CRISPRi-validated cis-regulatory element chr2.1526 Neighboring gene CRISPRi-validated cis-regulatory element chr2.1528 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:38893008-38893520 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:38893521-38894033 Neighboring gene uncharacterized LOC124905993 Neighboring gene galactose mutarotase Neighboring gene MPRA-validated peak3666 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11379 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15609 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:38967980-38968152 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11380 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11381 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15610 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:38982351-38983102 Neighboring gene serine and arginine rich splicing factor 7 Neighboring gene tetratricopeptide repeat domain 39D, pseudogene

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_076912.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    38692727..38693021
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    38699661..38699955
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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