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LOC125312416 Sharpr-MPRA regulatory region 7022 [ Homo sapiens (human) ]

Gene ID: 125312416, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125312416
Gene description
Sharpr-MPRA regulatory region 7022
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 13:Ctcf, distal CTCF/candidate insulator without open chromatin). [provided by RefSeq, May 2022]
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Genomic context

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See LOC125312416 in Genome Data Viewer
Location:
17q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (63399988..63400282)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (64270207..64270501)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (61477349..61477643)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:61259160-61260359 Neighboring gene DNAJB6 pseudogene 8 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:61310050-61310550 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:61310551-61311051 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:61382271-61382865 Neighboring gene NANOG hESC enhancer GRCh37_chr17:61423641-61424164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:61438304-61438804 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:61438805-61439305 Neighboring gene DENR pseudogene 3 Neighboring gene Sharpr-MPRA regulatory region 4360 Neighboring gene uncharacterized LOC105371856 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:61503073-61503811 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:61512442-61512609 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:61513919-61514833 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:61514834-61515748 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8815 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8816 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:61524253-61525066 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:61525067-61525879 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:61528047-61528547 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:61533342-61534200 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:61534201-61535059 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12545 Neighboring gene cytochrome b561 Neighboring gene peptidylprolyl isomerase A pseudogene 55

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_080584.1 

    Range
    101..395
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    63399988..63400282
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    64270207..64270501
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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