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LOC122819166 Sharpr-MPRA regulatory region 9639 [ Homo sapiens (human) ]

Gene ID: 122819166, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122819166
Gene description
Sharpr-MPRA regulatory region 9639
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 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations). [provided by RefSeq, Oct 2021]
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Genomic context

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Location:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (148967035..148967329)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (149417392..149417686)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (149823549..149823843)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12001 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:149633462-149634040 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:149634041-149634620 Neighboring gene KIF5C antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:149645774-149646369 Neighboring gene kinesin family member 5C Neighboring gene Sharpr-MPRA regulatory region 1843 Neighboring gene uncharacterized LOC101928553 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:149683568-149684192 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:149830455-149831291 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:149855785-149856718 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:149856719-149857650 Neighboring gene NANOG hESC enhancer GRCh37_chr2:149883850-149884499 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16622 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12002 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12003 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16623 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16624 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16625 Neighboring gene LY6/PLAUR domain containing 6B Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:149937379-149937971 Neighboring gene thioredoxin pseudogene 5 Neighboring gene uncharacterized LOC105373677

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_077026.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    148967035..148967329
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NW_003571033.2 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    39051..39345
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    149417392..149417686
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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