Fgf16 (fibroblast growth factor 16) - Rat Genome Database

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Gene: Fgf16 (fibroblast growth factor 16) Rattus norvegicus
Analyze
Symbol: Fgf16
Name: fibroblast growth factor 16
RGD ID: 71052
Description: Enables fibroblast growth factor receptor binding activity. Acts upstream of or within fibroblast growth factor receptor signaling pathway and positive regulation of brown fat cell proliferation. Predicted to be active in cytoplasm and extracellular space. Human ortholog(s) of this gene implicated in syndactyly type 8. Orthologous to human FGF16 (fibroblast growth factor 16); PARTICIPATES IN melanoma pathway; mitogen activated protein kinase signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; ammonium chloride; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: FGF-16
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X74,882,863 - 74,893,598 (+)NCBIGRCr8
mRatBN7.2X70,816,658 - 70,828,028 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX70,817,433 - 70,878,717 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX72,326,620 - 72,336,209 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X75,826,927 - 75,836,512 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X73,390,086 - 73,399,673 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X76,786,728 - 76,796,311 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX76,786,466 - 76,797,069 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X55,910,573 - 55,920,156 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X93,870,484 - 93,880,067 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1X93,943,654 - 93,954,254 (+)NCBI
CeleraX72,132,220 - 72,141,534 (+)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Fibroblast growth factor-16 is a growth factor for embryonic brown adipocytes. Konishi M, etal., J Biol Chem. 2000 Apr 21;275(16):12119-22.
4. Gene Data Set MGD Curation, June 12, 2002
5. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
6. Structure and expression of a novel member, FGF-16, on the fibroblast growth factor family. Miyake A, etal., Biochem Biophys Res Commun 1998 Feb 4;243(1):148-52.
7. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
8. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
9. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
10. GOA pipeline RGD automated data pipeline
11. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
12. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:12851399   PMID:15489334   PMID:16756958   PMID:18337564   PMID:30230915  


Genomics

Comparative Map Data
Fgf16
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X74,882,863 - 74,893,598 (+)NCBIGRCr8
mRatBN7.2X70,816,658 - 70,828,028 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX70,817,433 - 70,878,717 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX72,326,620 - 72,336,209 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X75,826,927 - 75,836,512 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X73,390,086 - 73,399,673 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X76,786,728 - 76,796,311 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX76,786,466 - 76,797,069 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X55,910,573 - 55,920,156 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X93,870,484 - 93,880,067 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1X93,943,654 - 93,954,254 (+)NCBI
CeleraX72,132,220 - 72,141,534 (+)NCBICelera
Cytogenetic MapXq22NCBI
FGF16
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X77,447,389 - 77,457,278 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX77,447,389 - 77,457,278 (+)EnsemblGRCh38hg38GRCh38
GRCh37X76,709,643 - 76,712,769 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X76,596,304 - 76,598,669 (+)NCBINCBI36Build 36hg18NCBI36
Build 34X76,515,791 - 76,518,158NCBI
CeleraX76,943,778 - 76,952,520 (+)NCBICelera
Cytogenetic MapXq21.1NCBI
HuRefX70,299,289 - 70,300,827 (+)NCBIHuRef
CHM1_1X76,602,327 - 76,604,695 (+)NCBICHM1_1
T2T-CHM13v2.0X75,884,945 - 75,894,834 (+)NCBIT2T-CHM13v2.0
Fgf16
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X104,808,083 - 104,820,138 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX104,807,885 - 104,818,545 (+)EnsemblGRCm39 Ensembl
GRCm38X105,764,477 - 105,776,532 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX105,764,279 - 105,774,939 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X102,959,816 - 102,971,871 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X101,967,260 - 101,976,899 (+)NCBIMGSCv36mm8
CeleraX92,618,588 - 92,630,442 (+)NCBICelera
Cytogenetic MapXDNCBI
cM MapX47.2NCBI
Fgf16
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955557905,576 - 919,415 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955557906,361 - 915,590 (+)NCBIChiLan1.0ChiLan1.0
FGF16
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X77,023,718 - 77,033,339 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X77,027,329 - 77,036,950 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X66,623,050 - 66,634,325 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X76,737,733 - 76,746,816 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX76,737,733 - 76,749,731 (+)Ensemblpanpan1.1panPan2
FGF16
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X59,738,512 - 59,748,188 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX59,739,398 - 59,748,204 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX50,753,734 - 50,762,935 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X60,977,750 - 60,986,950 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX60,977,988 - 60,986,988 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X58,685,639 - 58,694,838 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X60,291,788 - 60,301,024 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X59,883,445 - 59,892,646 (+)NCBIUU_Cfam_GSD_1.0
Fgf16
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X42,484,065 - 42,493,677 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366832,454,067 - 2,463,635 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366832,454,067 - 2,463,653 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FGF16
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX61,552,460 - 61,561,954 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X61,551,487 - 61,561,807 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X70,358,080 - 70,368,401 (+)NCBISscrofa10.2Sscrofa10.2susScr3
FGF16
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X66,389,983 - 66,401,562 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606715,117,006 - 15,126,908 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Fgf16
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248363,521,243 - 3,541,824 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248363,521,170 - 3,541,844 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Fgf16
35 total Variants
miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
Mir99arno-miR-99a-5pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830
Mir331rno-miR-331-3pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830

Predicted Target Of
Summary Value
Count of predictions:437
Count of miRNA genes:225
Interacting mature miRNAs:285
Transcripts:ENSRNOT00000003463
Prediction methods:Microtar, Miranda, Pita, Pita,Microtar, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 63
Low 7 42 54 15 21 16 53 6 48 44 9
Below cutoff 14 24 57 36 34 36 15 29 104 95 56 13 15

Sequence


Ensembl Acc Id: ENSRNOT00000090665   ⟹   ENSRNOP00000071308
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX70,817,433 - 70,828,022 (+)Ensembl
Rnor_6.0 EnsemblX76,786,466 - 76,797,069 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000097872   ⟹   ENSRNOP00000092162
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX70,817,433 - 70,878,717 (+)Ensembl
RefSeq Acc Id: NM_021867   ⟹   NP_068639
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X74,882,995 - 74,893,598 (+)NCBI
mRatBN7.2X70,817,425 - 70,828,028 (+)NCBI
Rnor_6.0X76,786,728 - 76,796,311 (+)NCBI
Rnor_5.0X55,910,573 - 55,920,156 (+)NCBI
RGSC_v3.4X93,870,484 - 93,880,067 (+)RGD
CeleraX72,132,220 - 72,141,534 (+)RGD
Sequence:
RefSeq Acc Id: XM_039100003   ⟹   XP_038955931
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X74,882,863 - 74,892,648 (+)NCBI
mRatBN7.2X70,816,658 - 70,827,078 (+)NCBI
RefSeq Acc Id: NP_068639   ⟸   NM_021867
- UniProtKB: O54769 (UniProtKB/Swiss-Prot),   A6IV34 (UniProtKB/TrEMBL),   A0A8I6AHM0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000071308   ⟸   ENSRNOT00000090665
RefSeq Acc Id: XP_038955931   ⟸   XM_039100003
- Peptide Label: isoform X1
Ensembl Acc Id: ENSRNOP00000092162   ⟸   ENSRNOT00000097872

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O54769-F1-model_v2 AlphaFold O54769 1-207 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:71052 AgrOrtholog
BioCyc Gene G2FUF-1934 BioCyc
Ensembl Genes ENSRNOG00000061530 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00055027080 UniProtKB/Swiss-Prot
  ENSRNOG00060021416 UniProtKB/Swiss-Prot
  ENSRNOG00065024912 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000090665.2 UniProtKB/Swiss-Prot
  ENSRNOT00000097872.1 UniProtKB/TrEMBL
  ENSRNOT00055046800 UniProtKB/Swiss-Prot
  ENSRNOT00060037079 UniProtKB/Swiss-Prot
  ENSRNOT00065042795 UniProtKB/Swiss-Prot
Gene3D-CATH 2.80.10.50 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7189721 IMAGE-MGC_LOAD
InterPro Fibroblast_GF_fam UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IL1/FGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:60464 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:93457 IMAGE-MGC_LOAD
NCBI Gene 60464 ENTREZGENE
PANTHER PTHR11486 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR11486:SF27 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam FGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Fgf16 PhenoGen
PRINTS HBGFFGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IL1HBGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE HBGF_FGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000061530 RatGTEx
  ENSRNOG00055027080 RatGTEx
  ENSRNOG00060021416 RatGTEx
  ENSRNOG00065024912 RatGTEx
SMART FGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF50353 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6AHM0 ENTREZGENE, UniProtKB/TrEMBL
  A6IV34 ENTREZGENE, UniProtKB/TrEMBL
  FGF16_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-07-09 Fgf16  fibroblast growth factor 16      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression mRNA predominantly expressed in heart in adult; predominantly expressed in brown adipose tissue in embryo 70737
gene_homology shares 98.6% aa sequence identity with human FGF16 70737