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LOC123493276 Sharpr-MPRA regulatory region 14227 [ Homo sapiens (human) ]

Gene ID: 123493276, updated on 12-Sep-2024

Summary

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Gene symbol
LOC123493276
Gene description
Sharpr-MPRA regulatory region 14227
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, Nov 2021]
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Genomic context

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See LOC123493276 in Genome Data Viewer
Location:
5p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (17190280..17190574)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (17129629..17129923)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (17190389..17190683)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene BASP1 antisense RNA 1 Neighboring gene RNA, 5S ribosomal pseudogene 180 Neighboring gene uncharacterized LOC105374664 Neighboring gene Sharpr-MPRA regulatory region 6771 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15948 Neighboring gene DDB1 and CUL4 associated factor 13 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15949 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15950 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:17218860-17219640 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:17227689-17228189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22424 Neighboring gene brain abundant membrane attached signal protein 1 Neighboring gene RNA, U6 small nuclear 1003, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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_077700.1 

    Range
    101..395
    Download
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    17190280..17190574
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    17129629..17129923
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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