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LOC121009628 Sharpr-MPRA regulatory region 12127 [ Homo sapiens (human) ]

Gene ID: 121009628, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121009628
Gene description
Sharpr-MPRA regulatory region 12127
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 enhancer 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 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Mar 2021]
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Genomic context

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Location:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (230667234..230667528)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (231150338..231150632)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (231531949..231532243)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC112268431 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17227 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17228 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17229 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17231 Neighboring gene tropomyosin 3 pseudogene 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17232 Neighboring gene RNA, U6 small nuclear 451, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17233 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12411 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17234 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17235 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17236 Neighboring gene CRISPRi-validated cis-regulatory element chr2.6880 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231524789-231525345 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17241 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231531133-231531998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17242 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17243 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17246 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17247 Neighboring gene formin-like protein 16 Neighboring gene long intergenic non-protein coding RNA 1907 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12412 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231585879-231586402 Neighboring gene calcium binding protein 39 Neighboring gene BANF1 pseudogene 3

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_074024.1 

    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
    230667234..230667528
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    231150338..231150632
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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