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LOC111188153 LTR-CSF1R promoter [ Homo sapiens (human) ]

Gene ID: 111188153, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111188153
Gene description
LTR-CSF1R promoter
Gene type
biological region
Feature type(s)
mobile_element
regulatory: DNase_I_hypersensitive_site, promoter
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This region represents an alternate promoter of the colony stimulating factor 1 receptor (CSF1R) gene that derives from endogenous retroviral long terminal repeat (LTR) sequence. This promoter may be stimulated in lymphoma cells such as Hodgkin/Reed-Sternberg (HRS) cells and is epigenetically repressed in other contexts. This region corresponds to a DNaseI hypersensitive site and may be regulated through putative binding sites for Ap-1 family transcription factors, Sp1, and nuclear factor kappa B. [provided by RefSeq, Sep 2017]
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Genomic context

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Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (150092453..150093086)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (150629027..150629660)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (149472016..149472649)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene HMG-box containing 3 Neighboring gene small nucleolar RNA U13 Neighboring gene ribosomal protein S20 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23395 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23396 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:149439174-149439376 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:149444398-149444573 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23397 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149447500-149448210 Neighboring gene colony stimulating factor 1 receptor Neighboring gene RORalpha allelically-responsive CSF1R enhancer Neighboring gene CSF1R promoter/intronic regulatory region Neighboring gene ribosomal protein L7 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 12786 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149490949-149491461 Neighboring gene CSF1R promoter E1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149497723-149498310 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149499971-149500878 Neighboring gene platelet derived growth factor receptor beta Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149507353-149507854 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149509491-149510101 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82275 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149515109-149515620 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149515621-149516130 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149516131-149516642 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149517153-149517664 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149526270-149526796 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149532128-149532648 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149532649-149533168

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. Derepression of an endogenous long terminal repeat activates the CSF1R proto-oncogene in human lymphoma. Lamprecht B, et al. Nat Med, 2010 May. PMID 20436485

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_055556.1 

    Range
    101..734
    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
    150092453..150093086
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    150629027..150629660
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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