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LOC124375244 Sharpr-MPRA regulatory region 6589 [ Homo sapiens (human) ]

Gene ID: 124375244, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124375244
Gene description
Sharpr-MPRA regulatory region 6589
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 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Feb 2022]
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Genomic context

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Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (136541197..136541491)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (148773056..148773350)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (139435649..139435943)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene SEC16 homolog A, endoplasmic reticulum export factor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20522 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139378131-139378875 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20524 Neighboring gene chromosome 9 putative open reading frame 163 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:139392592-139393791 Neighboring gene notch receptor 1 Neighboring gene uncharacterized LOC124902310 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139420763-139421634 Neighboring gene microRNA 4673 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29311 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139433302-139433969 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20525 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139434130-139434814 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139436183-139436865 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20526 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20527 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20528 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20529 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139441357-139442268 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:139444236-139445435 Neighboring gene microRNA 4674 Neighboring gene NOTCH1 associated lncRNA in T cell acute lymphoblastic leukemia 1

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_078965.1 

    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
    136541197..136541491
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    148773056..148773350
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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