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LOC112577531 Sharpr-MPRA regulatory region 5904 [ Homo sapiens (human) ]

Gene ID: 112577531, updated on 10-Dec-2024

Summary

Gene symbol
LOC112577531
Gene description
Sharpr-MPRA regulatory region 5904
Gene type
biological region
Feature type(s)
regulatory: enhancer
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. A subregion was validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss). This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate 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

See LOC112577531 in Genome Data Viewer
Location:
1q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (203861381..203861743)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (203125332..203125694)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (203830509..203830871)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene zinc finger CCCH-type containing 11A Neighboring gene charged multivesicular body protein 5 pseudogene Neighboring gene zinc finger BED-type containing 6 Neighboring gene MPRA-validated peak661 silencer Neighboring gene ribosomal protein L35a pseudogene 5 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:203810670-203811170 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:203831257-203831832 Neighboring gene small nuclear ribonucleoprotein polypeptide E Neighboring gene keratin 8 pseudogene 29 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:203857413-203858612 Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 6

Genomic regions, transcripts, and products

General gene information

Other Names

  • ATAC-STARR-seq lymphoblastoid active region 2358

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_060451.2 

    Range
    101..463
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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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    203861381..203861743
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    203125332..203125694
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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