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LOC129992625 ATAC-STARR-seq lymphoblastoid active region 21580 [ Homo sapiens (human) ]

Gene ID: 129992625, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129992625
Gene description
ATAC-STARR-seq lymphoblastoid active region 21580
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 LOC129992625 in Genome Data Viewer
Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (56467462..56467671)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (59955468..59955677)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (57333628..57333837)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene aminoadipate-semialdehyde dehydrogenase Neighboring gene ribosomal protein L7a pseudogene 31 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:57253075-57253582 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:57253583-57254089 Neighboring gene phosphoribosyl pyrophosphate amidotransferase Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:57291569-57292254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21579 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15449 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15450 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:57302513-57303396 Neighboring gene phosphoribosylaminoimidazole carboxylase and phosphoribosylaminoimidazolesuccinocarboxamide synthase Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:57325164-57326363 Neighboring gene uncharacterized LOC124900706 Neighboring gene signal recognition particle 72 Neighboring gene uncharacterized LOC105377665 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:57397246-57397779 Neighboring gene ARF like GTPase 9 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15451 Neighboring gene sperm microtubule associated protein 2 like Neighboring gene ReSE screen-validated silencer GRCh37_chr4:57424181-57424393 Neighboring gene glycine decarboxylase pseudogene 1

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_172071.1 

    Range
    101..310
    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    56467462..56467671
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    59955468..59955677
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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