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LOC124310603 Sharpr-MPRA regulatory region 10311 [ Homo sapiens (human) ]

Gene ID: 124310603, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124310603
Gene description
Sharpr-MPRA regulatory region 10311
Gene type
biological region
Feature type(s)
regulatory: silencer
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 repressive element 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 Repressive non-DNase unmatched - State 17:Gen3', transcription 3' end of genes, highly expressed, more exonic). [provided by RefSeq, Feb 2022]
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Genomic context

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See LOC124310603 in Genome Data Viewer
Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (96392247..96392541)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (108563968..108564262)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (99154529..99154823)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene SLC35D2-HSD17B3 readthrough Neighboring gene hydroxysteroid 17-beta dehydrogenase 3 Neighboring gene RNA, U6 small nuclear 1160, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:99051559-99052109 Neighboring gene solute carrier family 35 member D2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:99104760-99105284 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:99105285-99105808 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110853 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20077 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20078 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110866 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110873 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28653 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20079 Neighboring gene zinc finger protein 367 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20080 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:99180933-99181466 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:99181467-99182000 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:99182517-99183716 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:99185787-99186288 Neighboring gene NSA2 pseudogene 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20083 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20084 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20085 Neighboring gene hyaluronan binding protein 4 Neighboring gene cell division cycle 14B

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_078883.1 

    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    96392247..96392541
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    108563968..108564262
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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