Tc2n (tandem C2 domains, nuclear) - Rat Genome Database
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Gene: Tc2n (tandem C2 domains, nuclear) Rattus norvegicus
Analyze
Symbol: Tc2n
Name: tandem C2 domains, nuclear
RGD ID: 1563876
Description: Predicted to localize to nucleus. Orthologous to human TC2N (tandem C2 domains, nuclear); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 3,3',4,4',5-pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: membrane targeting (tandem) C2 domain containing 1; Mtac2d1; Tac2-N
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
mRatBN7.26120,761,112 - 120,856,835 (-)NCBI
Rnor_6.0 Ensembl6125,437,775 - 125,590,049 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.06125,437,767 - 125,601,408 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06134,651,335 - 134,813,686 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46125,871,936 - 125,975,388 (-)NCBIRGSC3.4rn4RGSC3.4
Celera6118,263,473 - 118,355,476 (-)NCBICelera
Cytogenetic Map6q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IBA,ISO)

References

Additional References at PubMed
PMID:11526914   PMID:21810271  


Genomics

Comparative Map Data
Tc2n
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.26120,761,112 - 120,856,835 (-)NCBI
Rnor_6.0 Ensembl6125,437,775 - 125,590,049 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.06125,437,767 - 125,601,408 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06134,651,335 - 134,813,686 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46125,871,936 - 125,975,388 (-)NCBIRGSC3.4rn4RGSC3.4
Celera6118,263,473 - 118,355,476 (-)NCBICelera
Cytogenetic Map6q32NCBI
TC2N
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1491,779,746 - 91,867,536 (-)EnsemblGRCh38hg38GRCh38
GRCh381491,779,746 - 91,867,536 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371492,246,090 - 92,333,880 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361491,316,279 - 91,372,436 (-)NCBINCBI36hg18NCBI36
Build 341491,316,278 - 91,372,436NCBI
Celera1472,298,880 - 72,386,499 (-)NCBI
Cytogenetic Map14q32.12NCBI
HuRef1472,426,963 - 72,514,634 (-)NCBIHuRef
CHM1_11492,184,168 - 92,271,959 (-)NCBICHM1_1
Tc2n
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3912101,611,705 - 101,685,178 (-)NCBIGRCm39mm39
GRCm39 Ensembl12101,611,702 - 101,684,782 (-)Ensembl
GRCm3812101,645,446 - 101,718,919 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl12101,645,443 - 101,718,523 (-)EnsemblGRCm38mm10GRCm38
MGSCv3712102,886,812 - 102,956,712 (-)NCBIGRCm37mm9NCBIm37
MGSCv3612102,047,613 - 102,112,955 (-)NCBImm8
Celera12102,856,104 - 102,924,262 (-)NCBICelera
Cytogenetic Map12ENCBI
Tc2n
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543814,000,322 - 14,047,415 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543814,012,199 - 14,047,174 (-)NCBIChiLan1.0ChiLan1.0
TC2N
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11491,750,265 - 91,815,703 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1491,750,265 - 91,815,703 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01472,404,915 - 72,471,347 (-)NCBIMhudiblu_PPA_v0panPan3
TC2N
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl81,093,201 - 1,133,626 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.181,088,618 - 1,160,322 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Tc2n
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493673370,608 - 106,247 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TC2N
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl7113,337,035 - 113,389,588 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.17113,337,815 - 113,389,663 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.27119,945,860 - 119,997,695 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TC2N
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12469,538,975 - 69,624,868 (-)NCBI
ChlSab1.1 Ensembl2469,537,693 - 69,593,341 (-)Ensembl
Tc2n
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473410,877,974 - 10,912,859 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)675623277136143011Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)675623277136426962Rat
1581550Pur8Proteinuria QTL 8total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)675623393136142742Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)675623393136142742Rat
738034Anxrr5Anxiety related response QTL 55.9exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)688507712133507712Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)688996335139410483Rat
10054138Gmadr3Adrenal mass QTL 33.680.00045adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)689631358134631358Rat
10054123Srcrt6Stress Responsive Cort QTL 62.50.0043blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)689631358134631358Rat
1300076Glom8Glomerulus QTL 870.000000009kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)691703409136703409Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (VE) (CMO:0000132)692879510137879510Rat
1331725Bp212Blood pressure QTL 2123.52475arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)697949772133849286Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)699273921144273921Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)699273921144792678Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)6101207574147991367Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6104363890147991367Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6104381930138066274Rat
1331797Bp213Blood pressure QTL 2133.291arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)6108154445133849286Rat
4145118Mcs26Mammary carcinoma susceptibility QTL 260.0001mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6111134524138065254Rat
737976Pia24Pristane induced arthritis QTL 24joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)6117355600147991367Rat
1298087Iddm18Insulin dependent diabetes mellitus QTL 180.0001urine glucose amount (VT:0001758)percentage of study population developing diabetes mellitus during a period of time (CMO:0001114)6121224054135658578Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:135
Count of miRNA genes:102
Interacting mature miRNAs:123
Transcripts:ENSRNOT00000006371
Prediction methods:Microtar, Miranda, 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.


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 10 10 10 19 24 11
Low 37 47 31 19 31 8 9 74 16 17 8
Below cutoff 6 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001025152 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008764836 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112744 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112745 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112746 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112747 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112749 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112750 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112751 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112752 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112753 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112754 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC088432 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC168677 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473982 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211170 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000168 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KU240047 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000006371   ⟹   ENSRNOP00000006371
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6125,437,775 - 125,590,049 (-)Ensembl
RefSeq Acc Id: NM_001025152   ⟹   NP_001020323
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26120,761,116 - 120,856,750 (-)NCBI
Rnor_6.06125,437,767 - 125,601,316 (-)NCBI
Rnor_5.06134,651,335 - 134,813,686 (-)NCBI
RGSC_v3.46125,871,936 - 125,975,388 (-)RGD
Celera6118,263,473 - 118,355,476 (-)RGD
Sequence:
RefSeq Acc Id: XM_008764831   ⟹   XP_008763053
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.06125,437,767 - 125,601,408 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008764836   ⟹   XP_008763058
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26120,761,116 - 120,856,835 (-)NCBI
Rnor_6.06125,437,767 - 125,601,408 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039112744   ⟹   XP_038968672
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26120,761,112 - 120,856,835 (-)NCBI
RefSeq Acc Id: XM_039112745   ⟹   XP_038968673
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26120,761,112 - 120,856,835 (-)NCBI
RefSeq Acc Id: XM_039112746   ⟹   XP_038968674
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26120,761,112 - 120,849,045 (-)NCBI
RefSeq Acc Id: XM_039112747   ⟹   XP_038968675
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26120,761,112 - 120,856,835 (-)NCBI
RefSeq Acc Id: XM_039112749   ⟹   XP_038968677
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26120,761,112 - 120,849,188 (-)NCBI
RefSeq Acc Id: XM_039112750   ⟹   XP_038968678
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26120,761,112 - 120,856,835 (-)NCBI
RefSeq Acc Id: XM_039112751   ⟹   XP_038968679
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26120,777,273 - 120,849,094 (-)NCBI
RefSeq Acc Id: XM_039112752   ⟹   XP_038968680
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26120,761,112 - 120,849,094 (-)NCBI
RefSeq Acc Id: XM_039112753   ⟹   XP_038968681
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26120,761,112 - 120,842,931 (-)NCBI
RefSeq Acc Id: XM_039112754   ⟹   XP_038968682
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26120,761,112 - 120,822,508 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001020323   ⟸   NM_001025152
- UniProtKB: Q5M7U8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008763058   ⟸   XM_008764836
- Peptide Label: isoform X1
- UniProtKB: Q5M7U8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008763053   ⟸   XM_008764831
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000006371   ⟸   ENSRNOT00000006371
RefSeq Acc Id: XP_038968678   ⟸   XM_039112750
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038968672   ⟸   XM_039112744
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038968675   ⟸   XM_039112747
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038968673   ⟸   XM_039112745
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038968677   ⟸   XM_039112749
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038968680   ⟸   XM_039112752
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038968674   ⟸   XM_039112746
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038968681   ⟸   XM_039112753
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038968682   ⟸   XM_039112754
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038968679   ⟸   XM_039112751
- Peptide Label: isoform X2
Protein Domains
C2

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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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
6 134781191 134781192 C G snv LE/OrlBarth (UDEL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563876 AgrOrtholog
Ensembl Genes ENSRNOG00000004754 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000006371 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006371 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.150 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7124658 IMAGE-MGC_LOAD
InterPro C2_Ca-dep UniProtKB/TrEMBL
  C2_domain_sf UniProtKB/TrEMBL
  C2A_Tac2-N UniProtKB/TrEMBL
  C2B_Tac2-N UniProtKB/TrEMBL
  Tac2-N UniProtKB/TrEMBL
KEGG Report rno:500707 UniProtKB/TrEMBL
MGC_CLONE MGC:95063 IMAGE-MGC_LOAD
NCBI Gene 500707 ENTREZGENE
PANTHER PTHR46887 UniProtKB/TrEMBL
Pfam PF00168 UniProtKB/TrEMBL
PhenoGen Tc2n PhenoGen
PROSITE PS50004 UniProtKB/TrEMBL
SMART SM00239 UniProtKB/TrEMBL
UniProt Q5M7U8 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary E9PTC2 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-06 Tc2n  tandem C2 domains, nuclear  Mtac2d1  membrane targeting (tandem) C2 domain containing 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 Mtac2d1  membrane targeting (tandem) C2 domain containing 1      Symbol and Name status set to provisional 70820 PROVISIONAL