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LOC121740667 Sharpr-MPRA regulatory region 12009 [ Homo sapiens (human) ]

Gene ID: 121740667, updated on 12-Sep-2024

Summary

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Gene symbol
LOC121740667
Gene description
Sharpr-MPRA regulatory region 12009
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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. The major subregion includes an enhancer that was validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. Another subregion was validated as an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase matched - State 4:PromP, inactive/poised promoter, highly conserved). Another subregion includes an accessible chromatin region used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in K562 cells. This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC121740667 in Genome Data Viewer
Location:
6q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (139029329..139030528)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (140217858..140219057)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (139350466..139351665)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene epithelial cell transforming 2 like Neighboring gene uncharacterized LOC107986650 Neighboring gene RALBP1 associated Eps domain containing 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:139298793-139299367 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17601 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17602 Neighboring gene NANOG hESC enhancer GRCh37_chr6:139331747-139332499 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17603 Neighboring gene ABRA C-terminal like Neighboring gene Sharpr-MPRA regulatory region 5517 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:139447769-139448270 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25165 Neighboring gene Sharpr-MPRA regulatory region 4168 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17606 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25166 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:139484703-139485202 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17608 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25167 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25168 Neighboring gene hdc homolog, cell cycle regulator Neighboring gene taxilin beta Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:139563281-139563806 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:139563807-139564332 Neighboring gene Sharpr-MPRA regulatory region 11439 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:139583345-139584544 Neighboring gene uncharacterized LOC102723690

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)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 17604
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:139350846-139351665
  • ReSE screen-validated silencer GRCh37_chr6:139350885-139351075

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_075729.3 

    Range
    101..1300
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    139029329..139030528
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    140217858..140219057
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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