Fndc3a (fibronectin type III domain containing 3a) - Rat Genome Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Fndc3a (fibronectin type III domain containing 3a) Rattus norvegicus
Analyze
Symbol: Fndc3a
Name: fibronectin type III domain containing 3a
RGD ID: 1304736
Description: Predicted to be involved in several processes, including Sertoli cell development; fertilization; and spermatid development. Predicted to localize to several cellular components, including Golgi apparatus; acrosomal vesicle; and vesicle membrane. Orthologous to human FNDC3A (fibronectin type III domain containing 3A); INTERACTS WITH 17alpha-ethynylestradiol; acetamide; benzo[a]pyrene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: fibronectin type III domain containing 3; fibronectin type-III domain-containing protein 3A; Fndc3; LOC306022
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21547,689,909 - 47,867,354 (-)NCBI
Rnor_6.0 Ensembl1554,381,044 - 54,528,480 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01554,378,865 - 54,582,954 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01558,102,190 - 58,306,554 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41553,124,740 - 53,312,367 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11553,140,516 - 53,328,793 (-)NCBI
Celera1547,348,000 - 47,488,015 (-)NCBICelera
Cytogenetic Map15p11NCBI
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

Biological Process

Cellular Component

References

Additional References at PubMed
PMID:1759682   PMID:2164218   PMID:16904100   PMID:18218838   PMID:19946888   PMID:22658674  


Genomics

Comparative Map Data
Fndc3a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21547,689,909 - 47,867,354 (-)NCBI
Rnor_6.0 Ensembl1554,381,044 - 54,528,480 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01554,378,865 - 54,582,954 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01558,102,190 - 58,306,554 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41553,124,740 - 53,312,367 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11553,140,516 - 53,328,793 (-)NCBI
Celera1547,348,000 - 47,488,015 (-)NCBICelera
Cytogenetic Map15p11NCBI
FNDC3A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1348,975,912 - 49,209,779 (+)EnsemblGRCh38hg38GRCh38
GRCh381348,975,241 - 49,209,779 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371349,550,048 - 49,783,915 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361348,448,049 - 48,681,916 (+)NCBINCBI36hg18NCBI36
Build 341348,448,939 - 48,681,729NCBI
Celera1330,605,901 - 30,839,799 (+)NCBI
Cytogenetic Map13q14.2NCBI
HuRef1330,344,082 - 30,577,725 (+)NCBIHuRef
CHM1_11349,517,625 - 49,751,465 (+)NCBICHM1_1
Fndc3a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391472,775,393 - 72,948,141 (-)NCBIGRCm39mm39
GRCm39 Ensembl1472,775,386 - 72,947,443 (-)Ensembl
GRCm381472,537,948 - 72,710,701 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1472,537,946 - 72,710,003 (-)EnsemblGRCm38mm10GRCm38
MGSCv371472,937,760 - 73,109,810 (-)NCBIGRCm37mm9NCBIm37
MGSCv361471,273,033 - 71,445,085 (-)NCBImm8
Celera1470,075,554 - 70,248,633 (-)NCBICelera
Cytogenetic Map14D2NCBI
cM Map1437.62NCBI
Fndc3a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554312,553,892 - 2,696,744 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554312,553,311 - 2,696,596 (+)NCBIChiLan1.0ChiLan1.0
FNDC3A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11348,820,120 - 49,047,770 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1348,820,018 - 49,049,274 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01330,119,740 - 30,347,544 (+)NCBIMhudiblu_PPA_v0panPan3
FNDC3A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl222,526,381 - 2,700,780 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1222,524,173 - 2,700,223 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Fndc3a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365652,154,672 - 2,312,670 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FNDC3A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1118,564,280 - 18,757,869 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11118,564,280 - 18,757,742 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21118,971,020 - 19,002,968 (+)NCBISscrofa10.2Sscrofa10.2susScr3
FNDC3A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1326,902,353 - 27,121,248 (+)NCBI
ChlSab1.1 Ensembl326,902,353 - 27,121,008 (+)Ensembl
Fndc3a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247485,503,053 - 5,716,734 (-)NCBI

Position Markers
D15Rat16  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01554,439,669 - 54,439,793NCBIRnor6.0
Rnor_5.01558,162,994 - 58,163,118UniSTSRnor5.0
RGSC_v3.41553,185,540 - 53,185,665RGDRGSC3.4
RGSC_v3.41553,185,541 - 53,185,665UniSTSRGSC3.4
RGSC_v3.11553,201,320 - 53,201,445RGD
Celera1547,406,298 - 47,406,422UniSTS
SHRSP x BN Map1533.4699UniSTS
SHRSP x BN Map1533.4699RGD
FHH x ACI Map1546.36RGD
Cytogenetic Map15p11UniSTS
D15Got110  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01554,554,814 - 54,555,018NCBIRnor6.0
Rnor_6.01554,569,662 - 54,569,866NCBIRnor6.0
Rnor_5.01558,293,473 - 58,293,677UniSTSRnor5.0
Rnor_5.01558,278,625 - 58,278,829UniSTSRnor5.0
RGSC_v3.41553,300,389 - 53,300,594RGDRGSC3.4
RGSC_v3.41553,300,390 - 53,300,594UniSTSRGSC3.4
RGSC_v3.11553,316,169 - 53,316,374RGD
Celera1547,509,094 - 47,509,298UniSTS
Cytogenetic Map15p11UniSTS
RH138547  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01554,381,926 - 54,382,074NCBIRnor6.0
Rnor_5.01558,105,251 - 58,105,399UniSTSRnor5.0
RGSC_v3.41553,127,798 - 53,127,946UniSTSRGSC3.4
Celera1547,348,882 - 47,349,030UniSTS
Cytogenetic Map15p11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15162301382Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151071919155719191Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151549236072568189Rat
9590272Scort14Serum corticosterone level QTL 142.780.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)151698090761980907Rat
8694427Bw163Body weight QTL 1634.820.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)151698090761980907Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151724964162249641Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151809320881255430Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151851391388036354Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1526381041106550657Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1526381041106550657Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1526381041106550657Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152870974173709741Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)153321910189640841Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)153321910189640841Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)153321910189640841Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)153948079762596410Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153974955779033707Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153974955779033707Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)154106809486068094Rat
7411725Strs7Sensitivity to stroke QTL 73.8cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)154275724156027084Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1543097470106550657Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:307
Count of miRNA genes:196
Interacting mature miRNAs:231
Transcripts:ENSRNOT00000066888
Prediction methods:Microtar, Miranda
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.


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 3 28 57 41 19 41 1 1 74 35 41 11 1
Low 15 7 10 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000066888   ⟹   ENSRNOP00000062773
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1554,381,044 - 54,528,480 (-)Ensembl
RefSeq Acc Id: NM_001107278   ⟹   NP_001100748
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21547,692,088 - 47,832,580 (-)NCBI
Rnor_6.01554,381,044 - 54,528,480 (-)NCBI
Rnor_5.01558,102,190 - 58,306,554 (-)NCBI
RGSC_v3.41553,124,740 - 53,312,367 (-)RGD
Celera1547,348,000 - 47,488,015 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006252296   ⟹   XP_006252358
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21547,689,909 - 47,846,054 (-)NCBI
Rnor_6.01554,378,865 - 54,542,524 (-)NCBI
Rnor_5.01558,102,190 - 58,306,554 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006252297   ⟹   XP_006252359
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21547,689,909 - 47,866,408 (-)NCBI
Rnor_6.01554,378,865 - 54,566,481 (-)NCBI
Rnor_5.01558,102,190 - 58,306,554 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006252298   ⟹   XP_006252360
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21547,689,909 - 47,867,354 (-)NCBI
Rnor_6.01554,378,865 - 54,582,954 (-)NCBI
Rnor_5.01558,102,190 - 58,306,554 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006252299   ⟹   XP_006252361
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21547,689,909 - 47,821,615 (-)NCBI
Rnor_6.01554,378,865 - 54,518,427 (-)NCBI
Rnor_5.01558,102,190 - 58,306,554 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006252300   ⟹   XP_006252362
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21547,689,909 - 47,802,969 (-)NCBI
Rnor_6.01554,378,865 - 54,494,188 (-)NCBI
Rnor_5.01558,102,190 - 58,306,554 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006252301   ⟹   XP_006252363
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21547,689,909 - 47,759,991 (-)NCBI
Rnor_6.01554,378,865 - 54,450,715 (-)NCBI
Rnor_5.01558,102,190 - 58,306,554 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006252302   ⟹   XP_006252364
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21547,689,909 - 47,867,028 (-)NCBI
Rnor_6.01554,378,865 - 54,566,785 (-)NCBI
Rnor_5.01558,102,190 - 58,306,554 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039093358   ⟹   XP_038949286
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21547,689,909 - 47,824,369 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001100748   ⟸   NM_001107278
- UniProtKB: D3ZEA0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252360   ⟸   XM_006252298
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006252364   ⟸   XM_006252302
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006252359   ⟸   XM_006252297
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006252358   ⟸   XM_006252296
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006252361   ⟸   XM_006252299
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006252362   ⟸   XM_006252300
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006252363   ⟸   XM_006252301
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000062773   ⟸   ENSRNOT00000066888
RefSeq Acc Id: XP_038949286   ⟸   XM_039093358
- Peptide Label: isoform X4
Protein Domains
Fibronectin type-III

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
15 58122097 58122098 T C snv FHH/EurMcwi (MCW), SR/JrHsd (MCW)
15 58138234 58138235 T G snv ACI/EurMcwi (MCW), FHH/EurMcwi (MCW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
15 54398772 54398773 T C snv FHH/EurMcwi (MCW), LEW/Crl (RGD), SR/JrHsd (RGD)
15 54414909 54414910 T G snv FHH/EurMcwi (MCW), ACI/EurMcwi (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
15 53144644 53144645 T C snv SR/JrHsd (MCW), FHH/EurMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304736 AgrOrtholog
Ensembl Genes ENSRNOG00000014478 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000062773 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066888 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
InterPro FN3_sf UniProtKB/TrEMBL
  FN_III UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
KEGG Report rno:306022 UniProtKB/TrEMBL
NCBI Gene 306022 ENTREZGENE
Pfam fn3 UniProtKB/TrEMBL
PhenoGen Fndc3a PhenoGen
PROSITE FN3 UniProtKB/TrEMBL
SMART FN3 UniProtKB/TrEMBL
Superfamily-SCOP FN_III-like UniProtKB/TrEMBL
UniProt D3ZEA0 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary D3ZUE6 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Fndc3a  fibronectin type III domain containing 3a   Fndc3a_predicted  fibronectin type III domain containing 3a (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Fndc3a_predicted  fibronectin type III domain containing 3a (predicted)  Fndc3_predicted  fibronectin type III domain containing 3 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-12 Fndc3_predicted  fibronectin type III domain containing 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED