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LOC121392956 Sharpr-MPRA regulatory region 13344 [ Homo sapiens (human) ]

Gene ID: 121392956, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121392956
Gene description
Sharpr-MPRA regulatory region 13344
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. It 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 K562 erythroleukemia cells (group: K562 Activating DNase matched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). 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 LOC121392956 in Genome Data Viewer
Location:
12p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (3073443..3073737)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (3079570..3079864)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (3182609..3182903)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902859 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:3068733-3069468 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:3073099-3073924 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:3075837-3076336 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:3090196-3090815 Neighboring gene TEA domain transcription factor 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3100825-3101326 Neighboring gene Sharpr-MPRA regulatory region 741 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3112529-3113410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3122802-3123643 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3141331-3141892 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4138 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4139 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:3193518-3194192 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:3192842-3193517 Neighboring gene ribosomal protein L13a pseudogene 24 Neighboring gene Sharpr-MPRA regulatory region 10584 Neighboring gene tetraspanin 9 Neighboring gene Sharpr-MPRA regulatory region 6988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3244823-3245324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3245325-3245824 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3245886-3246736 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3257812-3258357 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:3260221-3261034 Neighboring gene TSPAN9 intronic transcript 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:3271635-3272136 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:3277658-3278241 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:3278242-3278824 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3281002-3281760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3281761-3282518 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3297721-3298231 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:3306798-3307336 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:3307337-3307874 Neighboring gene ribosomal protein S27 pseudogene 3

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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 4137

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_074614.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    3073443..3073737
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    3079570..3079864
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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