Cbfa2t3 (CBFA2/RUNX1 partner transcriptional co-repressor 3) - Rat Genome Database

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Gene: Cbfa2t3 (CBFA2/RUNX1 partner transcriptional co-repressor 3) Rattus norvegicus
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Symbol: Cbfa2t3
Name: CBFA2/RUNX1 partner transcriptional co-repressor 3
RGD ID: 1310547
Description: Predicted to have chromatin binding activity and transcription corepressor activity. Predicted to be involved in several processes, including granulocyte differentiation; positive regulation of proteasomal ubiquitin-dependent protein catabolic process; and regulation of generation of precursor metabolites and energy. Predicted to localize to nucleoplasm. Orthologous to human CBFA2T3 (CBFA2/RUNX1 partner transcriptional co-repressor 3); INTERACTS WITH 17alpha-ethynylestradiol; acetamide; amphetamine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: CBFA2/RUNX1 translocation partner 3; core-binding factor, runt domain, alpha subunit 2; core-binding factor, runt domain, alpha subunit 2, translocated to, 3; core-binding factor, runt domain, alpha subunit 2, translocated to, 3 (human); core-binding factor, runt domain, alpha subunit 2; translocated to, 3; LOC361431; translocated to, 3
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
mRatBN7.21950,679,897 - 50,750,028 (-)NCBI
Rnor_6.0 Ensembl1955,441,572 - 55,510,460 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01955,438,409 - 55,510,652 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01966,145,151 - 66,218,784 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41952,908,942 - 52,980,399 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11952,913,754 - 53,012,742 (-)NCBI
Celera1949,920,125 - 49,988,577 (-)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

Additional References at PubMed
PMID:15231665   PMID:19799863   PMID:22871113   PMID:23251453   PMID:23840896   PMID:25974097  


Genomics

Comparative Map Data
Cbfa2t3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21950,679,897 - 50,750,028 (-)NCBI
Rnor_6.0 Ensembl1955,441,572 - 55,510,460 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01955,438,409 - 55,510,652 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01966,145,151 - 66,218,784 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41952,908,942 - 52,980,399 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11952,913,754 - 53,012,742 (-)NCBI
Celera1949,920,125 - 49,988,577 (-)NCBICelera
Cytogenetic Map19q12NCBI
CBFA2T3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1688,874,858 - 88,977,207 (-)EnsemblGRCh38hg38GRCh38
GRCh381688,874,858 - 88,977,207 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371688,941,266 - 89,043,615 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361687,468,768 - 87,570,902 (-)NCBINCBI36hg18NCBI36
Build 341687,468,767 - 87,535,109NCBI
Celera1674,009,858 - 74,110,779 (-)NCBI
Cytogenetic Map16q24.3NCBI
HuRef1674,638,423 - 74,739,781 (-)NCBIHuRef
CHM1_11690,352,535 - 90,454,228 (-)NCBICHM1_1
Cbfa2t3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398123,351,875 - 123,426,069 (-)NCBIGRCm39mm39
GRCm39 Ensembl8123,351,880 - 123,425,848 (-)Ensembl
GRCm388122,625,136 - 122,699,332 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8122,625,141 - 122,699,109 (-)EnsemblGRCm38mm10GRCm38
MGSCv378125,149,036 - 125,223,009 (-)NCBIGRCm37mm9NCBIm37
MGSCv368125,516,082 - 125,585,069 (-)NCBImm8
Celera8126,854,512 - 126,929,272 (-)NCBICelera
Cytogenetic Map8E1NCBI
Cbfa2t3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555412,724,312 - 2,777,592 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555412,724,369 - 2,777,540 (-)NCBIChiLan1.0ChiLan1.0
CBFA2T3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11689,246,545 - 89,347,435 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1689,246,545 - 89,347,435 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01669,592,293 - 69,662,321 (-)NCBIMhudiblu_PPA_v0panPan3
CBFA2T3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1564,432,291 - 64,518,905 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl564,431,843 - 64,519,528 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha564,443,579 - 64,529,331 (+)NCBI
ROS_Cfam_1.0564,652,241 - 64,738,015 (+)NCBI
UMICH_Zoey_3.1564,678,376 - 64,764,153 (+)NCBI
UNSW_CanFamBas_1.0564,510,060 - 64,595,977 (+)NCBI
UU_Cfam_GSD_1.0564,915,902 - 65,001,888 (+)NCBI
Cbfa2t3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934925,056,311 - 25,121,988 (+)NCBI
SpeTri2.0NW_004936641857,483 - 875,527 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CBFA2T3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6778,967 - 852,821 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16779,164 - 854,449 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.261,022,699 - 1,044,424 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CBFA2T3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1574,260,516 - 74,361,268 (-)NCBI
ChlSab1.1 Ensembl574,263,375 - 74,289,875 (-)Ensembl
Vero_WHO_p1.0NW_0236660471,300,151 - 1,364,549 (+)NCBI
Cbfa2t3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624746716,848 - 773,169 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)193299439262275575Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19243296362275575Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19650676160220581Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)192140778762275575Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191899398262275575Rat
2313395Anxrr26Anxiety related response QTL 26aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)195473521758072143Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193791679960220451Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193791679960220451Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192481825762275575Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)194883071260220581Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191917749562275575Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:448
Count of miRNA genes:209
Interacting mature miRNAs:241
Transcripts:ENSRNOT00000019820
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


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 1 4 2 8 2 3 58 5 3
Low 42 46 32 11 32 8 8 16 35 34 8 8
Below cutoff 7 7 7 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000019820   ⟹   ENSRNOP00000019820
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1955,441,572 - 55,510,460 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000081800   ⟹   ENSRNOP00000069430
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1955,442,107 - 55,490,426 (-)Ensembl
RefSeq Acc Id: NM_001108453   ⟹   NP_001101923
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21950,680,729 - 50,749,610 (-)NCBI
Rnor_6.01955,441,572 - 55,510,460 (-)NCBI
Rnor_5.01966,145,151 - 66,218,784 (-)NCBI
RGSC_v3.41952,908,942 - 52,980,399 (-)RGD
Celera1949,920,125 - 49,988,577 (-)RGD
Sequence:
RefSeq Acc Id: XM_006255770   ⟹   XP_006255832
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21950,679,897 - 50,750,011 (-)NCBI
Rnor_6.01955,438,409 - 55,510,652 (-)NCBI
Rnor_5.01966,145,151 - 66,218,784 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006255772   ⟹   XP_006255834
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21950,679,897 - 50,729,554 (-)NCBI
Rnor_6.01955,438,409 - 55,490,575 (-)NCBI
Rnor_5.01966,145,151 - 66,218,784 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601326   ⟹   XP_017456815
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01955,438,409 - 55,491,283 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039097877   ⟹   XP_038953805
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21950,679,897 - 50,697,412 (-)NCBI
RefSeq Acc Id: XM_039097878   ⟹   XP_038953806
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21950,684,991 - 50,750,028 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001101923   ⟸   NM_001108453
- UniProtKB: D4A303 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006255832   ⟸   XM_006255770
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006255834   ⟸   XM_006255772
- Peptide Label: isoform X3
- UniProtKB: A0A0G2JVC6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456815   ⟸   XM_017601326
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000069430   ⟸   ENSRNOT00000081800
RefSeq Acc Id: ENSRNOP00000019820   ⟸   ENSRNOT00000019820
RefSeq Acc Id: XP_038953805   ⟸   XM_039097877
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038953806   ⟸   XM_039097878
- Peptide Label: isoform X4
Protein Domains
MYND-type   TAFH

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)
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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
19 66169583 66169584 C T snv ACI/N (KNAW), WKY/Gcrc (KNAW), WKY/NHsd (KNAW), WKY/NCrl (KNAW), WKY/N (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
19 55461069 55461070 C T snv WKY/NCrl (RGD), WKY/NHsd (RGD), WKY/Gcrc (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310547 AgrOrtholog
Ensembl Genes ENSRNOG00000014723 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000019820 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000069430 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000019820 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000081800 UniProtKB/TrEMBL
Gene3D-CATH 1.20.120.1110 UniProtKB/TrEMBL
InterPro ETO UniProtKB/TrEMBL
  MTG16 UniProtKB/TrEMBL
  NHR2 UniProtKB/TrEMBL
  TAFH/NHR1_dom_sf UniProtKB/TrEMBL
  TAFH_NHR1 UniProtKB/TrEMBL
  Znf_MYND UniProtKB/TrEMBL
KEGG Report rno:361431 UniProtKB/TrEMBL
NCBI Gene 361431 ENTREZGENE
PANTHER PTHR10379 UniProtKB/TrEMBL
Pfam NHR2 UniProtKB/TrEMBL
  TAFH UniProtKB/TrEMBL
  zf-MYND UniProtKB/TrEMBL
PhenoGen Cbfa2t3 PhenoGen
PRINTS ETOFAMILY UniProtKB/TrEMBL
  MTG16PROTEIN UniProtKB/TrEMBL
PROSITE TAFH UniProtKB/TrEMBL
  ZF_MYND_1 UniProtKB/TrEMBL
  ZF_MYND_2 UniProtKB/TrEMBL
SMART TAFH UniProtKB/TrEMBL
Superfamily-SCOP SSF158553 UniProtKB/TrEMBL
UniProt A0A0G2JVC6 ENTREZGENE, UniProtKB/TrEMBL
  D4A303 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-07-01 Cbfa2t3  CBFA2/RUNX1 partner transcriptional co-repressor 3  Cbfa2t3  CBFA2/RUNX1 translocation partner 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-03-29 Cbfa2t3  CBFA2/RUNX1 translocation partner 3  Cbfa2t3  core-binding factor, runt domain, alpha subunit 2; translocated to, 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-11-05 Cbfa2t3  core-binding factor, runt domain, alpha subunit 2; translocated to, 3  Cbfa2t3  core-binding factor, runt domain, alpha subunit 2, translocated to, 3 (human)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-05-15 Cbfa2t3  core-binding factor, runt domain, alpha subunit 2, translocated to, 3 (human)  Cbfa2t3  core-binding factor, runt domain, alpha subunit 2, translocated to, 3   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-10 Cbfa2t3  core-binding factor, runt domain, alpha subunit 2, translocated to, 3   Cbfa2t3  core-binding factor, runt domain, alpha subunit 2, translocated to, 3 (human)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-03 Cbfa2t3  core-binding factor, runt domain, alpha subunit 2, translocated to, 3 (human)  Cbfa2t3_predicted  core-binding factor, runt domain, alpha subunit 2; translocated to, 3 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Cbfa2t3_predicted  core-binding factor, runt domain, alpha subunit 2; translocated to, 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED