Tcn2 (transcobalamin 2) - Rat Genome Database
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Gene: Tcn2 (transcobalamin 2) Rattus norvegicus
Analyze
Symbol: Tcn2
Name: transcobalamin 2
RGD ID: 620681
Description: Exhibits cobalamin binding activity. Predicted to be involved in cobalamin transport. Localizes to extracellular space. Human ortholog(s) of this gene implicated in Parkinson's disease; megaloblastic anemia; and transcobalamin II deficiency. Orthologous to human TCN2 (transcobalamin 2); INTERACTS WITH 1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: TC II; TC-2; Tc2; TCII; Tcn2p; transcobalamin II; transcobalamin II precursor; transcobalamin-2
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
mRatBN7.21478,813,343 - 78,828,549 (-)NCBI
Rnor_6.0 Ensembl1484,174,138 - 84,189,266 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01484,173,992 - 84,189,299 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01484,857,864 - 84,873,021 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41484,579,191 - 84,593,641 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11484,598,335 - 84,612,786 (-)NCBI
Celera1477,725,351 - 77,739,968 (-)NCBICelera
Cytogenetic Map14q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cobalamin transport  (IBA,IEA,ISO,ISS,TAS)
cobalt ion transport  (IEA)

Cellular Component
extracellular space  (IBA,IDA,IEA,ISO)

Molecular Function
cobalamin binding  (IBA,IDA,IEA,ISO)
metal ion binding  (IEA)
protein binding  (ISO)

References

Additional References at PubMed
PMID:8443384   PMID:15488467   PMID:16537422   PMID:23376485   PMID:24006456   PMID:27411955  


Genomics

Comparative Map Data
Tcn2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21478,813,343 - 78,828,549 (-)NCBI
Rnor_6.0 Ensembl1484,174,138 - 84,189,266 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01484,173,992 - 84,189,299 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01484,857,864 - 84,873,021 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41484,579,191 - 84,593,641 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11484,598,335 - 84,612,786 (-)NCBI
Celera1477,725,351 - 77,739,968 (-)NCBICelera
Cytogenetic Map14q21NCBI
TCN2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2230,607,003 - 30,627,271 (+)EnsemblGRCh38hg38GRCh38
GRCh382230,607,174 - 30,627,271 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372231,003,161 - 31,023,258 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362229,333,161 - 29,353,047 (+)NCBINCBI36hg18NCBI36
Build 342229,327,714 - 29,347,601NCBI
Celera2214,802,947 - 14,823,211 (+)NCBI
Cytogenetic Map22q12.2NCBI
HuRef2213,965,286 - 13,985,550 (+)NCBIHuRef
CHM1_12230,962,510 - 30,982,925 (+)NCBICHM1_1
Tcn2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39113,867,077 - 3,882,078 (-)NCBIGRCm39mm39
GRCm39 Ensembl113,867,192 - 3,882,159 (-)Ensembl
GRCm38113,917,077 - 3,932,078 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl113,917,192 - 3,932,159 (-)EnsemblGRCm38mm10GRCm38
MGSCv37113,817,080 - 3,832,081 (-)NCBIGRCm37mm9NCBIm37
MGSCv36113,817,193 - 3,831,586 (-)NCBImm8
Celera114,411,604 - 4,426,160 (-)NCBICelera
Cytogenetic Map11A1NCBI
cM Map112.76NCBI
Tcn2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554554,826,694 - 4,849,613 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554554,827,030 - 4,849,810 (+)NCBIChiLan1.0ChiLan1.0
TCN2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12229,435,506 - 29,455,494 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2229,435,517 - 29,455,494 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02211,635,107 - 11,655,137 (+)NCBIMhudiblu_PPA_v0panPan3
TCN2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2623,693,773 - 23,709,832 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12623,693,664 - 23,710,342 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Tcn2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493690497,535 - 113,886 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TCN2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1447,496,323 - 47,515,965 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11447,496,245 - 47,515,966 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21450,598,159 - 50,627,102 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TCN2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11913,489,849 - 13,511,360 (+)NCBI
ChlSab1.1 Ensembl1913,490,645 - 13,511,810 (+)Ensembl
Tcn2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247476,970,707 - 6,987,946 (+)NCBI

Position Markers
AW208754  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01484,174,317 - 84,174,405NCBIRnor6.0
Rnor_5.01484,858,042 - 84,858,130UniSTSRnor5.0
RGSC_v3.41484,579,367 - 84,579,455UniSTSRGSC3.4
Celera1477,725,676 - 77,725,764UniSTS
Cytogenetic Map14q21UniSTS
BE099486  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01484,184,671 - 84,184,825NCBIRnor6.0
Rnor_5.01484,868,396 - 84,868,550UniSTSRnor5.0
RGSC_v3.41484,589,575 - 84,589,729UniSTSRGSC3.4
Celera1477,735,884 - 77,736,038UniSTS
RH 3.4 Map14543.6UniSTS
Cytogenetic Map14q21UniSTS
RH127671  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01484,174,272 - 84,174,488NCBIRnor6.0
Rnor_5.01484,857,997 - 84,858,213UniSTSRnor5.0
RGSC_v3.41484,579,322 - 84,579,538UniSTSRGSC3.4
Celera1477,725,631 - 77,725,847UniSTS
RH 3.4 Map14545.2UniSTS
Cytogenetic Map14q21UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1412680424106641756Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143259392686191589Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)144031561085315610Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)144031561085315610Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)144031561085315610Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)144031561085315610Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1442442731108833671Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1443910761105074364Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1451818462105074364Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1460980905105980905Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1460980905105980905Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)146187332388870994Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1461993178106993178Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1463548095108548095Rat
70153Bp59Blood pressure QTL 593.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)147339146788870994Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1478172765102549388Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)1478172765102549388Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1478172765102549388Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1478172765102549388Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1478172765106641756Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1478446303110402569Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1480049285115493446Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1480049285115493446Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:48
Count of miRNA genes:42
Interacting mature miRNAs:45
Transcripts:ENSRNOT00000005934
Prediction methods: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.


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 40 52 41 14 41 2 3 74 35 36 11 2
Low 3 5 5 6 8 5 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000005934   ⟹   ENSRNOP00000005934
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1484,174,138 - 84,189,266 (-)Ensembl
RefSeq Acc Id: NM_022534   ⟹   NP_071979
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21478,813,343 - 78,827,960 (-)NCBI
Rnor_6.01484,173,992 - 84,188,755 (-)NCBI
Rnor_5.01484,857,864 - 84,873,021 (-)NCBI
RGSC_v3.41484,579,191 - 84,593,641 (-)RGD
Celera1477,725,351 - 77,739,968 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251366   ⟹   XP_006251428
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21478,813,490 - 78,828,531 (-)NCBI
Rnor_6.01484,174,139 - 84,189,299 (-)NCBI
Rnor_5.01484,857,864 - 84,873,021 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251367   ⟹   XP_006251429
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21478,813,490 - 78,828,492 (-)NCBI
Rnor_6.01484,174,139 - 84,189,297 (-)NCBI
Rnor_5.01484,857,864 - 84,873,021 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251368   ⟹   XP_006251430
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21478,813,490 - 78,828,549 (-)NCBI
Rnor_6.01484,174,139 - 84,189,295 (-)NCBI
Rnor_5.01484,857,864 - 84,873,021 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251370   ⟹   XP_006251432
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21478,813,490 - 78,828,510 (-)NCBI
Rnor_6.01484,174,139 - 84,189,290 (-)NCBI
Rnor_5.01484,857,864 - 84,873,021 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599370   ⟹   XP_017454859
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21478,813,490 - 78,828,448 (-)NCBI
Rnor_6.01484,174,139 - 84,189,288 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599371   ⟹   XP_017454860
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01484,174,139 - 84,188,612 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_071979   ⟸   NM_022534
- Peptide Label: precursor
- UniProtKB: G3V6K1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006251428   ⟸   XM_006251366
- Peptide Label: isoform X1
- UniProtKB: G3V6K1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006251430   ⟸   XM_006251368
- Peptide Label: isoform X1
- UniProtKB: G3V6K1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006251429   ⟸   XM_006251367
- Peptide Label: isoform X1
- UniProtKB: G3V6K1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006251432   ⟸   XM_006251370
- Peptide Label: isoform X1
- UniProtKB: G3V6K1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017454859   ⟸   XM_017599370
- Peptide Label: isoform X1
- UniProtKB: G3V6K1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017454860   ⟸   XM_017599371
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000005934   ⟸   ENSRNOT00000005934
Protein Domains
DUF4430

Transcriptome

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

Promoters
RGD ID:13699434
Promoter ID:EPDNEW_R9958
Type:initiation region
Name:Tcn2_1
Description:transcobalamin 2
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_6.01484,189,248 - 84,189,308EPDNEW

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
14 84863258 84863259 G A snv LEC/Tj (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 84179533 84179534 G A snv MR/N (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 84584437 84584438 G A snv MR/N (KNAW), HCR/2Mco (UMich), LCR/1Mco (UMich), HCR/1Mco (UMich)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620681 AgrOrtholog
Ensembl Genes ENSRNOG00000004280 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000005934 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000005934 UniProtKB/TrEMBL
InterPro Cbl-bd_prot UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DUF4430 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:64365 UniProtKB/TrEMBL
NCBI Gene 64365 ENTREZGENE
Pfam Cobalamin_bind UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DUF4430 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Tcn2 PhenoGen
PROSITE COBALAMIN_BINDING UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt G3V6K1 ENTREZGENE, UniProtKB/TrEMBL
  Q9R0D6 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-04-22 Tcn2  transcobalamin 2  Tcn2p  transcobalamin II precursor  Symbol and Name updated to reflect Human and Mouse nomenclature 625702 APPROVED
2002-08-07 Tcn2p  transcobalamin II precursor      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_protein mature product is a nonglycoprotein secretory protein of molecular mass 43 kDa 724784