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LOC123497906 Sharpr-MPRA regulatory region 3669 [ Homo sapiens (human) ]

Gene ID: 123497906, updated on 10-Oct-2023

Summary

Gene symbol
LOC123497906
Gene description
Sharpr-MPRA regulatory region 3669
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 HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 13:Ctcf, distal CTCF/candidate insulator without open chromatin). [provided by RefSeq, Dec 2021]
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Genomic context

See LOC123497906 in Genome Data Viewer
Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (72524022..72524316)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (73005140..73005434)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (71819849..71820143)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16081 Neighboring gene Y-box binding protein 1 pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22649 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22650 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22651 Neighboring gene zinc finger protein 366 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16082 Neighboring gene uncharacterized LOC102503427 Neighboring gene TNPO1 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22652 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:71930309-71930809 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:72004631-72005132 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:72005133-72005632 Neighboring gene ribosomal protein L7 pseudogene 22

Genomic regions, transcripts, and products

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_077760.1 

    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
    72524022..72524316
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    73005140..73005434
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)