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LOC111188152 CSF1R promoter E1 [ Homo sapiens (human) ]

Gene ID: 111188152, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111188152
Gene description
CSF1R promoter E1
Gene type
biological region
Feature type(s)
protein_bind
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 region represents an alternative promoter of the colony stimulating factor 1 receptor (CSF1R) gene, also known as FMS. This promoter is stimulated by glucorticoids and retinoic acid though a response element that overlaps with a binding site for AP-1 family transcription factors. A 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 H3K27ac and H3K4me1 histone modifications. [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC111188152 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (150112609..150114048)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (150649201..150650640)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (149492833..149493611)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene HMG-box containing 3 Neighboring gene small nucleolar RNA U13 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 LTR-CSF1R promoter Neighboring gene Sharpr-MPRA regulatory region 12786 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149490949-149491461 Neighboring gene ribosomal protein L7 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149497723-149498310 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149499971-149500878 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149507353-149507854 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149509491-149510101 Neighboring gene platelet derived growth factor receptor beta 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 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149537326-149538114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23399 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149540489-149541398 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:149565453-149566393 Neighboring gene caudal type homeobox 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149585404-149586030 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:149587985-149589184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149589159-149589702 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149590543-149591114 Neighboring gene solute carrier family 6 member 7

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. Repression of the c-fms gene in fibroblast cells by c-Myc-MM-1-TIF1beta complex. Satou A, et al. FEBS Lett, 2004 Aug 13. PMID 15304350
  2. Hormonal regulation of the c-fms proto-oncogene in breast cancer cells is mediated by a composite glucocorticoid response element. Flick MB, et al. J Cell Biochem, 2002. PMID 11891846
  3. Effect of all-trans-retinoic acid on c-fms proto-oncogene [colony-stimulating factor 1 (CSF-1) receptor] expression and CSF-1-induced invasion and anchorage-independent growth of human breast carcinoma cells. Sapi E, et al. Cancer Res, 1999 Nov 1. PMID 10554038
  4. Transcriptional regulation of the c-fms (CSF-1R) proto-oncogene in human breast carcinoma cells by glucocorticoids. Sapi E, et al. Oncogene, 1995 Feb 2. PMID 7845678
  5. Differential transcription of exon 1 of the human c-fms gene in placental trophoblasts and monocytes. Visvader J, et al. Mol Cell Biol, 1989 Mar. PMID 2524648, Free PMC Article

See all (8) citations in PubMed

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

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149492172-149492921

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_055555.2 

    Range
    101..1540
    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
    150112609..150114048
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    150649201..150650640
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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