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LOC121009643 Sharpr-MPRA regulatory region 12774 [ Homo sapiens (human) ]

Gene ID: 121009643, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121009643
Gene description
Sharpr-MPRA regulatory region 12774
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 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Mar 2021]
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Genomic context

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See LOC121009643 in Genome Data Viewer
Location:
3p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (13613769..13614063)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (13614228..13614522)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (13655269..13655563)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19491 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13521871-13522527 Neighboring gene Sharpr-MPRA regulatory region 12997 Neighboring gene HDAC11 antisense RNA 1 Neighboring gene histone deacetylase 11 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19492 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13557470-13558398 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13559772-13560661 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:13567399-13568002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13573992-13574615 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13574616-13575238 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13577465-13577965 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13584863-13585400 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13591988-13592596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13592597-13593203 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:13597673-13598460 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14087 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13600925-13601426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13601427-13601926 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13610405-13611364 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13612969-13613685 Neighboring gene fibulin 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13618331-13619084 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13619085-13619838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13639373-13639873 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13663487-13664060 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13664061-13664635 Neighboring gene small nucleolar RNA, H/ACA box 93 Neighboring gene uncharacterized LOC100293612 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19493 Neighboring gene long intergenic non-protein coding RNA 620

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_074040.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    13613769..13614063
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    13614228..13614522
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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