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LOC108228201 CIR1P1-LARP1 intergenic CAGE-defined high expression enhancer [ Homo sapiens (human) ]

Gene ID: 108228201, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108228201
Gene description
CIR1P1-LARP1 intergenic CAGE-defined high expression enhancer
Gene type
biological region
Feature type(s)
misc_feature: CAGE_cluster
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 element is located in the intergenic region between the CIR1P1 (corepressor interacting with RBPJ, 1 pseudogene 1) pseudogene and the LARP1 (La ribonucleoprotein domain family member 1) gene. A subregion was defined as a high expression actively transcribed enhancer based on the presence of balanced bidirectional capped transcripts by cap analysis of gene expression (CAGE), and was validated as an enhancer by reporter assays in HeLa cells. Another subregion was also validated as an enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC108228201 in Genome Data Viewer
Location:
5q33.2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (154583345..154584192)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (155117322..155118164)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (153963201..153963752)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene VPS37A, ESCRT-I subunit pseudogene Neighboring gene myotubularin related protein 7 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23478 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23479 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:153898879-153899379 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:153900569-153901172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:153920920-153921422 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_83489 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:153962321-153962904 Neighboring gene CIR1 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:153983238-153983756 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:153983757-153984274 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16544 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:153990742-153991511 Neighboring gene microRNA 3141 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:154026765-154027427 Neighboring gene CRISPRi-validated cis-regulatory element chr5.4044 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16545 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16546 Neighboring gene microRNA 1303 Neighboring gene La ribonucleoprotein 1, translational regulator

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. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

  • CIR1P1-LARP1 interval high CAGE FANTOM5 enhancer
  • H3K4me1 hESC enhancer GRCh37_chr5:153962905-153963488

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_050974.2 

    Range
    101..948
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    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
    154583345..154584192
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    155117322..155118164
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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