Fndc3c1 (fibronectin type III domain containing 3C1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Fndc3c1 (fibronectin type III domain containing 3C1) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Fndc3c1
Name: fibronectin type III domain containing 3C1
RGD ID: 1563846
Description: Predicted to be located in membrane; INTERACTS WITH 17beta-estradiol; 2,3,7,8-Tetrachlorodibenzofuran; 2-methoxyethanol.
Type: protein-coding
RefSeq Status: INFERRED
Previously known as: fibronectin type III domain containing protein 3C1; LOC103694494; LOC317224; LOC501597; RGD1561693; RGD1563846; similar to Gene model 784; uncharacterized LOC103694494
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X75,562,242 - 75,630,812 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX75,562,242 - 75,630,500 (-)EnsemblGRCr8
mRatBN7.2X71,489,374 - 71,547,160 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX71,448,420 - 71,547,010 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX73,005,706 - 73,062,659 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X76,505,568 - 76,562,527 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X74,068,429 - 74,125,382 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X77,416,959 - 77,559,348 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX77,416,959 - 77,570,825 (-)Ensemblrn6Rnor6.0
Rnor_5.0X77,614,445 - 77,633,945 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X94,616,949 - 94,674,730 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX72,805,504 - 72,864,454 (-)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse:




Gene-Chemical Interaction 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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in Fndc3c1
194 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:54
Count of miRNA genes:49
Interacting mature miRNAs:49
Transcripts:ENSRNOT00000047823
Prediction methods:Microtar, Miranda, Pita, Rnahybrid
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
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX45182909117740458Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between duration of physical contact or close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X4493088389930883Rat

Markers in Region
RH130415  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X71,489,631 - 71,489,823 (+)MAPPERmRatBN7.2
Rnor_6.0X77,417,217 - 77,417,408NCBIRnor6.0
Rnor_5.0X77,614,703 - 77,614,894UniSTSRnor5.0
RGSC_v3.4X94,617,207 - 94,617,398UniSTSRGSC3.4
CeleraX72,805,762 - 72,805,953UniSTS
Cytogenetic MapXq31UniSTS


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
8 11 56 110 72 71 40 24 40 6 203 108 5 90 39 75 31 4 4

Sequence


Ensembl Acc Id: ENSRNOT00000047823   ⟹   ENSRNOP00000045822
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX75,562,242 - 75,619,924 (-)Ensembl
mRatBN7.2 EnsemblX71,448,420 - 71,546,327 (-)Ensembl
Rnor_6.0 EnsemblX77,507,871 - 77,559,348 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000078213   ⟹   ENSRNOP00000071362
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX77,507,814 - 77,529,374 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000092303   ⟹   ENSRNOP00000075746
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX77,416,959 - 77,418,525 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000092498
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX77,507,779 - 77,529,712 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000092505   ⟹   ENSRNOP00000075748
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX75,562,242 - 75,619,924 (-)Ensembl
mRatBN7.2 EnsemblX71,489,374 - 71,547,010 (-)Ensembl
Rnor_6.0 EnsemblX77,431,005 - 77,570,825 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000173384   ⟹   ENSRNOP00000108182
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX75,562,242 - 75,630,500 (-)Ensembl
RefSeq Acc Id: NM_001191722   ⟹   NP_001178651
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X75,562,242 - 75,619,193 (-)NCBI
mRatBN7.2X71,489,374 - 71,546,327 (-)NCBI
Rnor_6.0X77,416,959 - 77,559,348 (-)NCBI
Rnor_5.0X77,614,445 - 77,633,945 (-)NCBI
CeleraX72,805,504 - 72,864,454 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099738   ⟹   XP_038955666
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X75,562,242 - 75,620,025 (-)NCBI
mRatBN7.2X71,489,374 - 71,547,160 (-)NCBI
RefSeq Acc Id: XM_039099739   ⟹   XP_038955667
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X75,562,242 - 75,620,025 (-)NCBI
mRatBN7.2X71,489,374 - 71,547,160 (-)NCBI
RefSeq Acc Id: XM_063280022   ⟹   XP_063136092
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X75,562,242 - 75,630,812 (-)NCBI
RefSeq Acc Id: XM_063280023   ⟹   XP_063136093
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X75,562,242 - 75,630,745 (-)NCBI
RefSeq Acc Id: NP_001178651   ⟸   NM_001191722
- UniProtKB: A0A0U1RRN5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000075746   ⟸   ENSRNOT00000092303
Ensembl Acc Id: ENSRNOP00000075748   ⟸   ENSRNOT00000092505
Ensembl Acc Id: ENSRNOP00000045822   ⟸   ENSRNOT00000047823
Ensembl Acc Id: ENSRNOP00000071362   ⟸   ENSRNOT00000078213
RefSeq Acc Id: XP_038955667   ⟸   XM_039099739
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038955666   ⟸   XM_039099738
- Peptide Label: isoform X1
- UniProtKB: A0A0U1RRN5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063136092   ⟸   XM_063280022
- Peptide Label: isoform X1
- UniProtKB: A0A0U1RRN5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063136093   ⟸   XM_063280023
- Peptide Label: isoform X1
- UniProtKB: A0A0U1RRN5 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000108182   ⟸   ENSRNOT00000173384

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M6T0-F1-model_v2 AlphaFold F1M6T0 1-1329 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:1563846 AgrOrtholog
BioCyc Gene G2FUF-1912 BioCyc
Ensembl Genes ENSRNOG00000002451 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000047823.7 UniProtKB/TrEMBL
  ENSRNOT00000092505 ENTREZGENE
  ENSRNOT00000092505.3 UniProtKB/TrEMBL
  ENSRNOT00000173384 ENTREZGENE
  ENSRNOT00000173384.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
InterPro E3_ligase_FN3/SPRY UniProtKB/TrEMBL
  FN3_dom UniProtKB/TrEMBL
  FN3_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
KEGG Report rno:317224 UniProtKB/TrEMBL
NCBI Gene 317224 ENTREZGENE
PANTHER E3 UBIQUITIN-PROTEIN LIGASE TRIM36-RELATED UniProtKB/TrEMBL
  FIBRONECTIN TYPE III DOMAIN-CONTAINING 3BA-RELATED UniProtKB/TrEMBL
Pfam fn3 UniProtKB/TrEMBL
PhenoGen Fndc3c1 PhenoGen
PRINTS FNTYPEIII UniProtKB/TrEMBL
PROSITE FN3 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000002451 RatGTEx
SMART FN3 UniProtKB/TrEMBL
Superfamily-SCOP SSF49265 UniProtKB/TrEMBL
UniProt A0A0U1RRN5 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0LZY0_RAT UniProtKB/TrEMBL
  F1M6T0_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Fndc3c1  fibronectin type III domain containing 3C1  LOC103694494  uncharacterized LOC103694494  Data merged from RGD:9390416 737654 PROVISIONAL
2015-07-29 Fndc3c1  fibronectin type III domain containing 3C1  RGD1561693  similar to Gene model 784  Data merged from RGD:1561693 737654 PROVISIONAL
2014-08-25 LOC103694494  uncharacterized LOC103694494      Symbol and Name status set to provisional 70820 PROVISIONAL
2009-06-12 Fndc3c1  fibronectin type III domain containing 3C1  RGD1563846  similar to Gene model 784   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1563846  similar to Gene model 784   RGD1563846_predicted  similar to Gene model 784 (predicted)  'predicted' is removed 2292626 APPROVED
2008-04-30 RGD1561693  similar to Gene model 784   RGD1561693_predicted  similar to Gene model 784 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1563846_predicted  similar to Gene model 784 (predicted)  LOC317224  similar to Gene model 784  Symbol and Name status set to approved 1299863 APPROVED
2006-03-07 RGD1561693_predicted  similar to Gene model 784 (predicted)  LOC501597  similar to Gene model 784  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC317224  similar to Gene model 784      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-02-09 LOC501597  similar to Gene model 784      Symbol and Name status set to provisional 70820 PROVISIONAL