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LOC121847956 Sharpr-MPRA regulatory region 4122 [ Homo sapiens (human) ]

Gene ID: 121847956, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121847956
Gene description
Sharpr-MPRA regulatory region 4122
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 4:PromP, inactive/poised promoter, highly conserved). [provided by RefSeq, Jul 2021]
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Genomic context

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Location:
15q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (72168408..72168702)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (69985135..69985429)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (72460749..72461043)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene myosin IXA Neighboring gene RNA, U2 small nuclear 65, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:72394409-72394919 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9710 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6616 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9711 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9712 Neighboring gene ribosomal protein L21 pseudogene 115 Neighboring gene uncharacterized LOC124903522 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9713 Neighboring gene SUMO peptidase family member, NEDD8 specific Neighboring gene GRAM domain containing 2A Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr15:72485963-72486586 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9714 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6617 Neighboring gene Sharpr-MPRA regulatory region 1213 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9715 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6618 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6619 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:72529434-72530633 Neighboring gene pyruvate kinase M1/2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6620 Neighboring gene poly(ADP-ribose) polymerase family member 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_075982.1 

    Range
    101..395
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    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    72168408..72168702
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    69985135..69985429
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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