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LOC123956206 Sharpr-MPRA regulatory region 12136 [ Homo sapiens (human) ]

Gene ID: 123956206, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123956206
Gene description
Sharpr-MPRA regulatory region 12136
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 DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jan 2022]
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Genomic context

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Location:
7q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (106862564..106862858)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (108178600..108178894)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (106503009..106503303)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26487 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18535 Neighboring gene MPRA-validated peak6673 silencer Neighboring gene coiled-coil domain containing 71 like Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:106358550-106359749 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26488 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26489 Neighboring gene MPRA-validated peak6674 silencer Neighboring gene MPRA-validated peak6675 silencer Neighboring gene Sharpr-MPRA regulatory region 6701 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:106415535-106416734 Neighboring gene long intergenic non-protein coding RNA 2577 Neighboring gene RNA, 5S ribosomal pseudogene 236 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26490 Neighboring gene phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma Neighboring gene CRISPRi-validated cis-regulatory element chr7.4040 Neighboring gene CRISPRi-validated cis-regulatory element chr7.4041 Neighboring gene CRISPRi-validated cis-regulatory element chr7.4042 Neighboring gene CRISPRi-validated cis-regulatory element chr7.4045 Neighboring gene CRISPRi-validated cis-regulatory element chr7.4046 Neighboring gene CRISPRi-validated cis-regulatory element chr7.4048 Neighboring gene CRISPRi-validated cis-regulatory element chr7.4050 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:106681203-106681414 Neighboring gene Sharpr-MPRA regulatory region 8060 Neighboring gene PRKAR2B antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 12069 Neighboring gene protein kinase cAMP-dependent type II regulatory subunit beta

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_078400.1 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    106862564..106862858
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    108178600..108178894
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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