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LOC123464477 Sharpr-MPRA regulatory region 11729 [ Homo sapiens (human) ]

Gene ID: 123464477, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123464477
Gene description
Sharpr-MPRA regulatory region 11729
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 HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, Nov 2021]
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Genomic context

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Location:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (186990841..186991135)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (189808581..189808875)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (186708629..186708923)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:186626722-186627417 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:186627418-186628112 Neighboring gene ribosomal protein S20 pseudogene 14 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:186647930-186648538 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14990 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20946 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20947 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:186659211-186659712 Neighboring gene ribosomal protein L29 pseudogene 9 Neighboring gene ST6 beta-galactoside alpha-2,6-sialyltransferase 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:186673829-186674071 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:186674568-186675068 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20948 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:186681641-186682220 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:186693287-186694168 Neighboring gene uncharacterized LOC124906314 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20949 Neighboring gene Sharpr-MPRA regulatory region 4195 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14991 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20951 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:186716158-186717048 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:186717049-186717939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20952 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20953 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20955 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20957 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20958 Neighboring gene ST6GAL1 promoter P2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14992 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20959 Neighboring gene ST6GAL1 promoter P1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20960 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20961 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20962 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20963 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14993 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:186789896-186790855 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20964 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20966 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:186854800-186855300 Neighboring gene ribosomal protein L39 pseudogene 19 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:186856490-186856996 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20968 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14994 Neighboring gene ribosomal protein L39 like Neighboring gene NANOG hESC enhancer GRCh37_chr3:186888631-186889132 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:186892851-186893682 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:186893683-186894513 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:186894725-186895400 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:186898085-186898586 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:186898587-186899086 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:186899087-186899588 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:186900591-186901090 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:186901091-186901592 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:186903095-186904094 Neighboring gene uncharacterized LOC101929106 Neighboring gene receptor transporter protein 1

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_077462.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    186990841..186991135
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    189808581..189808875
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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