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LOC119407423 HARS1 and HARS2 bidirectional promoter region [ Homo sapiens (human) ]

Gene ID: 119407423, updated on 10-Oct-2023

Summary

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Gene symbol
LOC119407423
Gene description
HARS1 and HARS2 bidirectional promoter region
Gene type
biological region
Feature type(s)
regulatory: enhancer, promoter
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region represents the 5' regulatory region of both the HARS1 (histidyl-tRNA synthetase 1) and HARS2 (histidyl-tRNA synthetase 2, mitochondrial) genes, which exist in head-to-head orientation and are transcribed from opposite strands of chromosome 5. This region functions as a bidirectional promoter that can drive transcription in either orientation in reporter assays in transfected HeLa cells. A minimal 27 bp fragment within this region was found to be sufficient for bidirectional promoter activity, where increased activity was seen with increased copies of that fragment. This locus also includes two accessible chromatin subregions that were validated as enhancers based on their 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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Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (140691305..140691805)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (141216692..141217192)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (140070890..140071390)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901088 Neighboring gene IK cytokine Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140043900-140044566 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140052035-140052830 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140052831-140053626 Neighboring gene WD repeat domain 55 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23284 Neighboring gene DND microRNA-mediated repression inhibitor 1 Neighboring gene histidyl-tRNA synthetase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23285 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23288 Neighboring gene histidyl-tRNA synthetase 2, mitochondrial Neighboring gene NANOG hESC enhancer GRCh37_chr5:140082322-140082864 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:140090124-140091323 Neighboring gene zinc finger matrin-type 2 Neighboring gene uncharacterized LOC105378198 Neighboring gene vault RNA 1-1

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. Genomic organization, transcriptional mapping, and evolutionary implications of the human bi-directional histidyl-tRNA synthetase locus (HARS/HARSL). O'Hanlon TP, et al. Biochem Biophys Res Commun, 2002 Jun 14. PMID 12056811
  2. Transcriptional analyses of the gene region that encodes human histidyl-tRNA synthetase: identification of a novel bidirectional regulatory element. Tsui HW, et al. Gene, 1993 Sep 15. PMID 8406012
  3. A novel gene oriented in a head-to-head configuration with the human histidyl-tRNA synthetase (HRS) gene encodes an mRNA that predicts a polypeptide homologous to HRS. O'Hanlon TP, et al. Biochem Biophys Res Commun, 1995 May 16. PMID 7755634
  4. 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 active region 23286
  • ATAC-STARR-seq lymphoblastoid active region 23287
  • HRS bidirectional regulatory element

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_070993.1 

    Range
    101..601
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    140691305..140691805
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    141216692..141217192
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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