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LOC121048711 Sharpr-MPRA regulatory region 6102 [ Homo sapiens (human) ]

Gene ID: 121048711, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121048711
Gene description
Sharpr-MPRA regulatory region 6102
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 non-DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Apr 2021]
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Genomic context

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Location:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (134795047..134795341)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (137540418..137540712)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (134513889..134514183)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene centrosomal protein 63 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20566 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20567 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20568 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20569 Neighboring gene RNA, U6 small nuclear 1174, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20570 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20571 Neighboring gene RNA, 5S ribosomal pseudogene 141 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14754 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:134565355-134565854 Neighboring gene uncharacterized LOC105374121 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20573 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20574 Neighboring gene EPH receptor B1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20575 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:134610984-134611623 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:134660519-134661204 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20576 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:134723970-134724470 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:134724471-134724971 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:134737937-134738437 Neighboring gene uncharacterized LOC102724019

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_074081.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    134795047..134795341
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    137540418..137540712
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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