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LOC123575580 Sharpr-MPRA regulatory region 837 [ Homo sapiens (human) ]

Gene ID: 123575580, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123575580
Gene description
Sharpr-MPRA regulatory region 837
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 21:Repr, strong Polycomb repression). [provided by RefSeq, Dec 2021]
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Genomic context

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Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (142174964..142175258)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (142705495..142705791)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (141554529..141554823)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:141488095-141488596 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16470 Neighboring gene Nedd4 family interacting protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23316 Neighboring gene uncharacterized LOC107986455 Neighboring gene uncharacterized LOC124901096 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:141560390-141560908 Neighboring gene MPRA-validated peak5506 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141563869-141564765 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141564766-141565661 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141566635-141567164 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:141580673-141581872 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:141585270-141585770 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:141595973-141596142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23317 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:141612188-141612688 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141616039-141616767 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:141625205-141625997 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:141625998-141626789 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141659038-141659604 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141659605-141660171 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:141690483-141690984 Neighboring gene NANOG hESC enhancer GRCh37_chr5:141699157-141699901 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141702584-141703548 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141703549-141704511 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:141711019-141711518 Neighboring gene SPRY4 intronic transcript 1 Neighboring gene SPRY4 antisense RNA 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:141721844-141723043 Neighboring gene sprouty RTK signaling antagonist 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141734625-141735426 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141735427-141736228 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16471 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:141740409-141740647 Neighboring gene Sharpr-MPRA regulatory region 738 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141743173-141743894 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23319 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:141768171-141768672 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:141771555-141772234 Neighboring gene Sharpr-MPRA regulatory region 12170

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_077841.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    142174964..142175258
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    142705495..142705791
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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