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LOC120893132 Sharpr-MPRA regulatory region 301 [ Homo sapiens (human) ]

Gene ID: 120893132, updated on 10-Oct-2023

Summary

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Gene symbol
LOC120893132
Gene description
Sharpr-MPRA regulatory region 301
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 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Mar 2021]
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Genomic context

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See LOC120893132 in Genome Data Viewer
Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (39133117..39133411)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (39000506..39000800)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (39598789..39599083)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904088 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 800 Neighboring gene NANOG hESC enhancer GRCh37_chr1:39517634-39518135 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:39530834-39531126 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 692 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 801 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 803 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:39568667-39569222 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 693 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 694 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 695 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 804 Neighboring gene microtubule actin crosslinking factor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:39599569-39600336 Neighboring gene RNA, U6 small nuclear 608, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:39606647-39607470 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:39605822-39606646 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:39607555-39608294 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:39637465-39637991 Neighboring gene RNA, 5S ribosomal pseudogene 44 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:39648813-39650012 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:39657180-39657722 Neighboring gene Sharpr-MPRA regulatory region 6545 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 806 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 807 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:39679473-39680191 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 696 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 697 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:39691029-39691222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 808 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 809 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:39698122-39698932 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:39764567-39764723 Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 8

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_073891.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    39133117..39133411
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    39000506..39000800
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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