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LOC125146428 Sharpr-MPRA regulatory region 3906 [ Homo sapiens (human) ]

Gene ID: 125146428, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125146428
Gene description
Sharpr-MPRA regulatory region 3906
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 25:Art, potential CNV or repetitive artifacts) and K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 25:Art). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125146428 in Genome Data Viewer
Location:
16p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (22300488..22300782)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (21916430..21916724, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (22311809..22312103)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7264 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7265 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:22221261-22221761 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_43156 Neighboring gene GATA motif-containing MPRA enhancer 198 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:22229709-22230208 Neighboring gene eukaryotic elongation factor 2 kinase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:22237029-22237652 Neighboring gene Sharpr-MPRA regulatory region 4253 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:22308474-22309018 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10570 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7267 Neighboring gene tRNA-Leu (anticodon AAG) 2-4 Neighboring gene RNA polymerase III subunit E Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:22333033-22333580 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:22333581-22334130 Neighboring gene uncharacterized LOC124903664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:22358198-22358698 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10571 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7268 Neighboring gene cerebellar degeneration related protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7269

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_080354.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    22300488..22300782
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_017852933.1 Reference GRCh38.p14 PATCHES

    Range
    804248..804542 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    21916430..21916724 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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