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LOC108281162 SLC26A11-RNF213 intergenic CAGE-defined mid-level expression enhancer [ Homo sapiens (human) ]

Gene ID: 108281162, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108281162
Gene description
SLC26A11-RNF213 intergenic CAGE-defined mid-level expression enhancer
Gene type
biological region
Feature type(s)
regulatory: enhancer, transcriptional_cis_regulatory_region
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic element is located in the intergenic region between the SLC26A11 (solute carrier family 26 member 11) and RNF213 (ring finger protein 213) genes. A subregion was defined as a mid-level expression actively transcribed enhancer based on the presence of balanced bidirectional capped transcripts by cap analysis of gene expression (CAGE). It was validated as a functional enhancer by reporter assays in HeLa cells. In addition, an overlapping subregion was validated as a high-confidence cis-regulatory element for the RNF213 (ring finger protein 213) gene on chromosome 17, and with lower confidence for the SLC26A11 (solute carrier family 26 member 11) gene, based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. 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:
17q25.3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (80254661..80255234)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (81155058..81155631)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (78228460..78229033)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene caspase recruitment domain family member 14 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:78178385-78179584 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:78183891-78184046 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12929 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9102 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9103 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78195951-78196788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78196789-78197626 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78200105-78200606 Neighboring gene N-sulfoglucosamine sulfohydrolase Neighboring gene solute carrier family 26 member 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78209849-78210638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78210639-78211426 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78227308-78228024 Neighboring gene CRISPRi-validated cis-regulatory element chr17.5742 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9104 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9106 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78237270-78237826 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12934 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9107 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78247837-78248435 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78251821-78252439 Neighboring gene ring finger protein 213 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78258533-78259093 Neighboring gene RNF213 antisense RNA 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:78345568-78346767 Neighboring gene MPRA-validated peak3024 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78354122-78354622 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:78359110-78360309 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78369069-78369570 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78371216-78371723 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78371724-78372230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12935 Neighboring gene microRNA 4730 Neighboring gene endonuclease V

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. An atlas of active enhancers across human cell types and tissues. Andersson R, et al. Nature, 2014 Mar 27. PMID 24670763, Free PMC Article
  2. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Gasperini M, et al. Cell, 2019 Jan 10. PMID 30612741, Free PMC Article
  3. An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium. Nature, 2012 Sep 6. PMID 22955616, Free PMC Article
  4. The accessible chromatin landscape of the human genome. Thurman RE, et al. Nature, 2012 Sep 6. PMID 22955617, Free PMC Article
  5. 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 12930
  • ATAC-STARR-seq lymphoblastoid active region 12931
  • CRISPRi-validated cis-regulatory element chr17.5742
  • SLC26A11-RNF213 interval mid CAGE FANTOM5 enhancer

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_051122.2 

    Range
    101..674
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    80254661..80255234
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    81155058..81155631
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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