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LOC129993747 ATAC-STARR-seq lymphoblastoid active region 22433 [ Homo sapiens (human) ]

Gene ID: 129993747, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129993747
Gene description
ATAC-STARR-seq lymphoblastoid active region 22433
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 represents an accessible chromatin region 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) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC129993747 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (31532473..31532522)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (31646184..31646233)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (31532580..31532629)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene cadherin 6 Neighboring gene double homeobox 4 like 51 (pseudogene) Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:31342590-31343789 Neighboring gene NANOG hESC enhancer GRCh37_chr5:31427117-31427643 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:31452968-31453512 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_84469 Neighboring gene drosha ribonuclease III Neighboring gene Sharpr-MPRA regulatory region 6191 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:31493720-31494220 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_84483 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22431 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22432 Neighboring gene chromosome 5 open reading frame 22 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:31618177-31618357 Neighboring gene RNA, U6 small nuclear 363, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:31680333-31680851 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:31680852-31681369 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:31716787-31717309 Neighboring gene PDZ domain containing 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:31753742-31754275 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22434 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:31780232-31780511 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:31798873-31799374 Neighboring gene RNA, U6 small nuclear 358, pseudogene

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)

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_173193.1 

    Range
    101..150
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    31532473..31532522
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    31646184..31646233
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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