Frg1 (FSHD region gene 1) - Rat Genome Database

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Gene: Frg1 (FSHD region gene 1) Rattus norvegicus
Analyze
Symbol: Frg1
Name: FSHD region gene 1
RGD ID: 1585495
Description: Predicted to enable actin filament binding activity. Predicted to be located in membrane. Predicted to be part of catalytic step 2 spliceosome. Predicted to be active in nucleolus and striated muscle dense body. Orthologous to human FRG1 (FSHD region gene 1); INTERACTS WITH 4,4'-sulfonyldiphenol; bisphenol A; bisphenol F.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC686103; similar to FRG1 protein (FSHD region gene 1 protein)
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Related Pseudogenes: Frg1-ps1  
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81657,629,221 - 57,650,188 (+)NCBIGRCr8
mRatBN7.21650,925,783 - 50,946,661 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1650,925,803 - 50,946,661 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1656,245,194 - 56,266,193 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01659,644,817 - 59,665,672 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01654,879,132 - 54,900,128 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01653,957,858 - 53,978,865 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1653,957,858 - 53,978,865 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01653,671,547 - 53,692,902 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41654,237,736 - 54,259,311 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1648,821,020 - 48,841,877 (+)NCBICelera
Cytogenetic Map16q12.1NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11991638   PMID:22658674  


Genomics

Comparative Map Data
Frg1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81657,629,221 - 57,650,188 (+)NCBIGRCr8
mRatBN7.21650,925,783 - 50,946,661 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1650,925,803 - 50,946,661 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1656,245,194 - 56,266,193 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01659,644,817 - 59,665,672 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01654,879,132 - 54,900,128 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01653,957,858 - 53,978,865 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1653,957,858 - 53,978,865 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01653,671,547 - 53,692,902 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41654,237,736 - 54,259,311 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1648,821,020 - 48,841,877 (+)NCBICelera
Cytogenetic Map16q12.1NCBI
FRG1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh384189,940,872 - 189,963,192 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl4189,940,855 - 189,963,202 (+)EnsemblGRCh38hg38GRCh38
GRCh374190,862,027 - 190,884,347 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 364191,098,968 - 191,121,353 (+)NCBINCBI36Build 36hg18NCBI36
Build 344191,237,122 - 191,259,507NCBI
Celera4188,156,485 - 188,178,883 (+)NCBICelera
Cytogenetic Map4q35.2NCBI
HuRef4186,602,905 - 186,625,302 (+)NCBIHuRef
CHM1_14190,846,305 - 190,868,690 (+)NCBICHM1_1
T2T-CHM13v2.04193,305,857 - 193,328,177 (+)NCBIT2T-CHM13v2.0
Frg1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39841,842,218 - 41,870,179 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl841,850,496 - 41,870,111 (-)EnsemblGRCm39 Ensembl
GRCm38841,389,181 - 41,417,138 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl841,397,459 - 41,417,074 (-)EnsemblGRCm38mm10GRCm38
MGSCv37842,482,808 - 42,502,472 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36842,896,282 - 42,923,664 (-)NCBIMGSCv36mm8
Celera844,019,679 - 44,039,444 (-)NCBICelera
Cytogenetic Map8A4NCBI
cM Map823.89NCBI
FRG1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v23187,646,975 - 187,669,239 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan14188,007,498 - 188,029,762 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v04182,084,087 - 182,106,472 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.14195,265,251 - 195,308,282 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4195,265,473 - 195,314,040 (+)Ensemblpanpan1.1panPan2
FRG1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11641,361,347 - 41,381,088 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1641,361,436 - 41,401,007 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1641,871,756 - 41,893,673 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01643,421,520 - 43,441,269 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1643,421,610 - 43,547,410 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11641,512,765 - 41,568,347 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01642,059,190 - 42,109,246 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01642,251,297 - 42,271,061 (-)NCBIUU_Cfam_GSD_1.0
Frg1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494337,933,546 - 37,947,412 (+)NCBIHiC_Itri_2
SpeTri2.0NW_004936554160,360 - 176,442 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FRG1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl175,780,866 - 5,800,464 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1175,780,847 - 5,800,503 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2176,401,206 - 6,420,868 (+)NCBISscrofa10.2Sscrofa10.2susScr3
FRG1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.17135,697,624 - 135,720,664 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl7135,697,640 - 135,723,963 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037116,112,263 - 116,135,445 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Frg1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476921,068,814 - 21,088,728 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476921,068,817 - 21,088,723 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Frg1
94 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:225
Count of miRNA genes:172
Interacting mature miRNAs:193
Transcripts:ENSRNOT00000013078
Prediction methods:Microtar, Miranda, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)163775215682752156Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)161900443575226532Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163528887080288870Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760960252231Rat
2302057Pia29Pristane induced arthritis QTL 293.60.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)162173597566735975Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164239634584729064Rat
8694453Bw172Body weight QTL 1728.330.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)162432551369325513Rat
1298529Arunc1Aerobic running capacity QTL 14exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)163195152060148445Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
6903294Stl30Serum triglyceride level QTL 302.60.0013blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)162515279370152793Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)163775215682752156Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000013078   ⟹   ENSRNOP00000013078
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1650,925,803 - 50,946,661 (+)Ensembl
Rnor_6.0 Ensembl1653,957,858 - 53,978,865 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000097848   ⟹   ENSRNOP00000096320
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1650,925,803 - 50,944,754 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000104619   ⟹   ENSRNOP00000091267
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1650,925,803 - 50,946,312 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000115611   ⟹   ENSRNOP00000077749
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1650,925,803 - 50,945,834 (+)Ensembl
RefSeq Acc Id: NM_001290133   ⟹   NP_001277062
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81657,629,331 - 57,650,188 (+)NCBI
mRatBN7.21650,925,803 - 50,946,661 (+)NCBI
Rnor_6.01653,957,858 - 53,978,865 (+)NCBI
Celera1648,821,020 - 48,841,877 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039094827   ⟹   XP_038950755
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81657,629,221 - 57,650,083 (+)NCBI
mRatBN7.21650,925,783 - 50,946,557 (+)NCBI
RefSeq Acc Id: XM_039094828   ⟹   XP_038950756
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81657,630,365 - 57,650,083 (+)NCBI
mRatBN7.21650,926,891 - 50,946,557 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001277062 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950755 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950756 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000013078.7
  ENSRNOP00000077749.1
  ENSRNOP00000091267.1
  ENSRNOP00000096320.1
RefSeq Acc Id: NP_001277062   ⟸   NM_001290133
- UniProtKB: D3ZZK8 (UniProtKB/TrEMBL),   A0A8I6AIP8 (UniProtKB/TrEMBL),   A6J0V5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000013078   ⟸   ENSRNOT00000013078
RefSeq Acc Id: XP_038950755   ⟸   XM_039094827
- Peptide Label: isoform X1
- UniProtKB: A0A8I6AIP8 (UniProtKB/TrEMBL),   A6J0V5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038950756   ⟸   XM_039094828
- Peptide Label: isoform X2
Ensembl Acc Id: ENSRNOP00000077749   ⟸   ENSRNOT00000115611
Ensembl Acc Id: ENSRNOP00000096320   ⟸   ENSRNOT00000097848
Ensembl Acc Id: ENSRNOP00000091267   ⟸   ENSRNOT00000104619

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZZK8-F1-model_v2 AlphaFold D3ZZK8 1-258 view protein structure

Transcriptome

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

Promoters
RGD ID:13700113
Promoter ID:EPDNEW_R10637
Type:initiation region
Name:Frg1_1
Description:FSHD region gene 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01653,957,924 - 53,957,984EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1585495 AgrOrtholog
BioCyc Gene G2FUF-11272 BioCyc
Ensembl Genes ENSRNOG00000009846 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000013078.8 UniProtKB/TrEMBL
  ENSRNOT00000097848.1 UniProtKB/TrEMBL
  ENSRNOT00000104619.1 UniProtKB/TrEMBL
  ENSRNOT00000115611.1 UniProtKB/TrEMBL
Gene3D-CATH 2.80.10.50 UniProtKB/TrEMBL
InterPro Actin_cross-linking UniProtKB/TrEMBL
  FRG1 UniProtKB/TrEMBL
KEGG Report rno:686103 UniProtKB/TrEMBL
NCBI Gene 686103 ENTREZGENE
PANTHER FRG1 UniProtKB/TrEMBL
  PROTEIN FRG1 UniProtKB/TrEMBL
Pfam FRG1 UniProtKB/TrEMBL
PhenoGen Frg1 PhenoGen
RatGTEx ENSRNOG00000009846 RatGTEx
Superfamily-SCOP Actin_crosslink UniProtKB/TrEMBL
UniProt A0A8I5Y7V3_RAT UniProtKB/TrEMBL
  A0A8I6ABR2_RAT UniProtKB/TrEMBL
  A0A8I6AIP8 ENTREZGENE
  A0A8I6AQH1_RAT UniProtKB/TrEMBL
  A6J0V5 ENTREZGENE
  D3ZZK8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-10-01 Frg1  FSHD region gene 1  LOC686103  similar to FRG1 protein (FSHD region gene 1 protein)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC686103  similar to FRG1 protein (FSHD region gene 1 protein)      Symbol and Name status set to provisional 70820 PROVISIONAL