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LOC125424380 Sharpr-MPRA regulatory region 13635 [ Homo sapiens (human) ]

Gene ID: 125424380, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125424380
Gene description
Sharpr-MPRA regulatory region 13635
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 19:H4K20, transcription, primarily H4K20me1, more intronic). [provided by RefSeq, May 2022]
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Genomic context

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Location:
22q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (17063739..17064033)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (17740460..17740754)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene vomeronasal 1 receptor 9 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13427 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18609 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18610 Neighboring gene cat eye syndrome chromosome region, candidate 7 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_62188 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_62204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:17538919-17539419 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13428 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_62270 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_62296 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13429 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13430 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13431 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13432 Neighboring gene interleukin 17 receptor A Neighboring gene ribosomal protein L31 pseudogene 62 Neighboring gene MPRA-validated peak4440 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18611 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr22:17587847-17589046 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13433 Neighboring gene transmembrane protein 121B

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

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_081115.1 

    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    17063739..17064033
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    17740460..17740754
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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