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LOC124310571 Sharpr-MPRA regulatory region 7656 [ Homo sapiens (human) ]

Gene ID: 124310571, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124310571
Gene description
Sharpr-MPRA regulatory region 7656
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 HepG2 liver carcinoma cells (group: HepG2 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 LOC124310571 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 (81676094..81676388)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (93828163..93828457)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (84291009..84291303)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene CST complex subunit TEN1-like Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:84138078-84139277 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:84164162-84164662 Neighboring gene VISTA enhancer hs1118 Neighboring gene uncharacterized LOC105376106 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:84207247-84208446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:84210105-84210800 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr9:84210801-84211494 Neighboring gene NANOG hESC enhancer GRCh37_chr9:84236633-84237248 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:84237249-84237864 Neighboring gene NANOG hESC enhancer GRCh37_chr9:84238663-84239186 Neighboring gene TLE family member 1, transcriptional corepressor Neighboring gene VISTA enhancer hs1359 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:84278031-84278532 Neighboring gene Sharpr-MPRA regulatory region 9381 Neighboring gene VISTA enhancer hs556 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:84303773-84304487 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19976 Neighboring gene TLE1 divergent transcript Neighboring gene ReSE screen-validated silencer GRCh37_chr9:84349086-84349247 Neighboring gene RNA, U6 small nuclear 1035, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:84375421-84375922 Neighboring gene NANOG hESC enhancer GRCh37_chr9:84398794-84399306 Neighboring gene NANOG hESC enhancer GRCh37_chr9:84434914-84435503 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr9:84458661-84459441 Neighboring gene RNA, 5S ribosomal pseudogene 287

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_078850.1 

    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
    81676094..81676388
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    93828163..93828457
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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