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LOC109115964 FGF3 5' regulatory region [ Homo sapiens (human) ]

Gene ID: 109115964, updated on 14-Mar-2024

Summary

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Gene symbol
LOC109115964
Gene description
FGF3 5' regulatory region
Gene type
biological region
Feature type(s)
regulatory: DNase_I_hypersensitive_site, 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 contains multiple DNase I hypersensitive sites and includes the proximal promoter and putative upstream promoter of the fibroblast growth factor 3 (FGF3) gene. 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 H3K4me1 histone modification. [provided by RefSeq, Jan 2023]
Orthologs
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Genomic context

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Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (69817540..69825634)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (69834448..69842543)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (69632308..69640347)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69555555-69556140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69556141-69556725 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69565172-69565761 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69565762-69566352 Neighboring gene DNAJB6 pseudogene 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69579027-69580027 Neighboring gene FGF4 3' enhancer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69588083-69589008 Neighboring gene FGF4 promoter region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69596435-69596972 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69596973-69597508 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69604158-69604702 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69603612-69604157 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69605134-69605838 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69605839-69606541 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69612316-69613027 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69613028-69613738 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69615738-69616268 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69631724-69632244 Neighboring gene uncharacterized LOC107984368 Neighboring gene fibroblast growth factor 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69640403-69641083 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69647091-69647682 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69649493-69650298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69651106-69651911 Neighboring gene MPRA-validated peak1329 silencer Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:69657667-69658333 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:69661705-69662302 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_21658 Neighboring gene fibroblast growth factor 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69679525-69680082 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69680083-69680640 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69680641-69681198 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69693599-69694230 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69698210-69698710 Neighboring gene Sharpr-MPRA regulatory region 8845 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69705859-69706454 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69720311-69720812 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69724011-69724512 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:69778215-69779191 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69789289-69790190 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:69794428-69795627 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69810871-69811654 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69812439-69813222 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69823537-69824036 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69827276-69827998 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69827999-69828721 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69832189-69833006 Neighboring gene anoctamin 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:69871617-69872015 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69881245-69881784 Neighboring gene uncharacterized LOC105369371 Neighboring gene long intergenic non-protein coding RNA 2753

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. Sequence analysis of the transcription control region upstream of the human FGF-3 gene. Djenabi S, et al. DNA Seq, 1999. PMID 10727086
  2. Regulation of FGF-3 gene expression in tumorigenic and non-tumorigenic clones of a human colon carcinoma cell line. Galdemard C, et al. J Biol Chem, 2000 Jun 9. PMID 10749884
  3. Sequence organization of the human int-2 gene and its expression in teratocarcinoma cells. Brookes S, et al. Oncogene, 1989 Apr. PMID 2470007
  4. 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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Homology

Other Names

  • H3K4me1 hESC enhancer GRCh37_chr11:69639722-69640402

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_052068.2 

    Range
    101..8195
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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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    69817540..69825634
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    69834448..69842543
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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