Ctcfl (CCCTC-binding factor like) - Rat Genome Database

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Gene: Ctcfl (CCCTC-binding factor like) Rattus norvegicus
Analyze
Symbol: Ctcfl
Name: CCCTC-binding factor like
RGD ID: 2321501
Description: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and histone binding activity. Predicted to be involved in macromolecule methylation; regulation of gene expression; and regulation of histone H3-K4 methylation. Predicted to be located in cytosol and nuclear body. Predicted to be active in nucleus. Orthologous to human CTCFL (CCCTC-binding factor like); INTERACTS WITH Cuprizon; fipronil; thioacetamide.
Type: protein-coding
RefSeq Status: INFERRED
Previously known as: CCCTC-binding factor (zinc finger protein)-like; LOC100360757; LOC296420; transcriptional repressor CTCFL
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23161,868,306 - 161,890,949 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl3161,868,306 - 161,890,949 (-)Ensembl
Rnor_6.03171,145,203 - 171,168,375 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3171,145,584 - 171,166,454 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03177,211,373 - 177,233,853 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43163,952,971 - 163,973,834 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13163,857,327 - 163,914,593 (-)NCBI
Celera3161,061,586 - 161,084,222 (-)NCBICelera
Cytogenetic Map3q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12011441   PMID:16140944   PMID:17048991   PMID:18413740   PMID:18765639  


Genomics

Comparative Map Data
Ctcfl
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23161,868,306 - 161,890,949 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl3161,868,306 - 161,890,949 (-)Ensembl
Rnor_6.03171,145,203 - 171,168,375 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3171,145,584 - 171,166,454 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03177,211,373 - 177,233,853 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43163,952,971 - 163,973,834 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13163,857,327 - 163,914,593 (-)NCBI
Celera3161,061,586 - 161,084,222 (-)NCBICelera
Cytogenetic Map3q42NCBI
CTCFL
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382057,495,965 - 57,525,652 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2057,495,966 - 57,525,652 (-)EnsemblGRCh38hg38GRCh38
GRCh372056,071,021 - 56,100,708 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362055,505,630 - 55,533,560 (-)NCBINCBI36hg18NCBI36
Build 342055,505,629 - 55,533,560NCBI
Celera2052,812,617 - 52,840,546 (-)NCBI
Cytogenetic Map20q13.31NCBI
HuRef2052,852,627 - 52,882,314 (-)NCBIHuRef
CHM1_12055,972,071 - 56,001,746 (-)NCBICHM1_1
T2T-CHM13v2.02059,273,778 - 59,303,467 (-)NCBI
Ctcfl
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392172,935,402 - 172,961,318 (-)NCBIGRCm39mm39
GRCm39 Ensembl2172,935,402 - 172,961,318 (-)Ensembl
GRCm382173,093,609 - 173,119,525 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2173,093,609 - 173,119,525 (-)EnsemblGRCm38mm10GRCm38
MGSCv372172,919,110 - 172,945,026 (-)NCBIGRCm37mm9NCBIm37
MGSCv362172,736,548 - 172,762,464 (-)NCBImm8
Celera2179,059,119 - 179,084,765 (-)NCBICelera
Cytogenetic Map2H3NCBI
Ctcfl
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554451,944,789 - 1,970,484 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554451,944,845 - 1,969,502 (+)NCBIChiLan1.0ChiLan1.0
CTCFL
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12055,115,325 - 55,143,717 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2055,114,405 - 55,143,717 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02053,836,295 - 53,865,974 (-)NCBIMhudiblu_PPA_v0panPan3
CTCFL
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12442,477,029 - 42,507,217 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2442,477,342 - 42,507,225 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2441,724,185 - 41,754,347 (-)NCBI
ROS_Cfam_1.02443,342,428 - 43,372,548 (-)NCBI
ROS_Cfam_1.0 Ensembl2443,342,729 - 43,372,545 (-)Ensembl
UMICH_Zoey_3.12442,426,987 - 42,457,178 (-)NCBI
UNSW_CanFamBas_1.02442,566,848 - 42,596,982 (-)NCBI
UU_Cfam_GSD_1.02443,225,081 - 43,255,079 (-)NCBI
Ctcfl
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640182,970,292 - 182,993,625 (+)NCBI
SpeTri2.0NW_004936530312,630 - 335,929 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CTCFL
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1757,860,787 - 57,891,924 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11757,860,231 - 57,891,094 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21765,024,460 - 65,055,353 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CTCFL
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.126,592,924 - 6,623,787 (+)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605054,651,624 - 54,682,401 (+)NCBIVero_WHO_p1.0
Ctcfl
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474123,925,326 - 23,948,819 (-)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462474123,924,124 - 23,948,849 (-)NCBIHetGla_female_1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3118839124163839124Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3120538241165538241Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3122438700167438700Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3127162703168026850Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3137398739169034231Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3138799500169034231Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141074471169034231Rat
1331726Bp208Blood pressure QTL 2083.129arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3141339013162184794Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3145526770169034231Rat
12879871Am7Aortic mass QTL 70.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)3145925360166177555Rat
12879872Cm97Cardiac mass QTL 970.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3145925360166177555Rat
12879873Cm96Cardiac mass QTL 960.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)3145925360166177555Rat
12879874Cm98Cardiac mass QTL 980.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)3145925360166177555Rat
12879875Kidm64Kidney mass QTL 640.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3145925360166177555Rat
12879876Bw182Body weight QTL 1820.003body mass (VT:0001259)body weight (CMO:0000012)3145925360166177555Rat
2301411Bp320Blood pressure QTL 3200.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3145925360166177555Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3145956084169034231Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3149040888168026850Rat
1300161Rf10Renal function QTL 103.57renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)3161192952169034231Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:57
Count of miRNA genes:54
Interacting mature miRNAs:56
Transcripts:ENSRNOT00000034131
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 endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1
Low 2 1 3 1 10 12
Below cutoff 2 26 15 14 15 2 2 3 13 12 8 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000034131   ⟹   ENSRNOP00000034635
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3161,868,306 - 161,890,949 (-)Ensembl
Rnor_6.0 Ensembl3171,145,584 - 171,166,454 (-)Ensembl
RefSeq Acc Id: NM_001322486   ⟹   NP_001309415
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23161,868,306 - 161,890,949 (-)NCBI
Rnor_6.03171,145,204 - 171,167,845 (-)NCBI
Celera3161,061,586 - 161,084,222 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001309415 (Get FASTA)   NCBI Sequence Viewer  
  XP_230900 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001309415   ⟸   NM_001322486
- Sequence:
RefSeq Acc Id: ENSRNOP00000034635   ⟸   ENSRNOT00000034131

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZQ48-F1-model_v2 AlphaFold D3ZQ48 1-635 view protein structure

Transcriptome

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


Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 171146276 171146277 G A snv SBH/Ygl (MCW), F344/NRrrc (MCW), M520/N (MCW), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), BXH3/CubMcwi (2020), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), HXB2/IpcvMcwi (2019), HXB31/IpcvMcwi (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), M520/N (2020), MR/N (2020), MWF/Hsd (2019), PVG/Seac (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), WAG/RijCrl (2020), WN/N (2020), CDR, CDS, FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), GH/OmrMcwi (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), Buf/N (MCW), WN/N (MCW), FHL/EurMcwi (RGD), LEW/Crl (RGD), LEW/NCrlBR (RGD), MNS/Gib (RGD), SBN/Ygl (RGD), SR/JrHsd (RGD), WAG/Rij (RGD), WKY/Gcrc (RGD), BUF/N (2020), BXH2/CubMcwi (2020), FHH/EurMcwi (2019), LEW/Crl (2019), SR/JrHsd (2020)
3 171146331 171146332 C T snv SBH/Ygl (MCW), SHR/OlalpcvMcwi (2019), M520/N (MCW), WAG/RijCrl (2020), SBH/Ygl (RGD), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), BXH2/CubMcwi (2020), BXH3/CubMcwi (2020), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), HXB2/IpcvMcwi (2019), HXB31/IpcvMcwi (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), M520/N (2020), MR/N (2020), MWF/Hsd (2019), PVG/Seac (2019), SHRSP/A3NCrl (2019), F344/NRrrc (MCW)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 161869378 161869379 G A snv BXH3/CubMcwi (2020), WAG/RijCrl (2020), SR/JrHsd (2020), SHR/OlalpcvMcwi (2019), SHRSP/A3NCrl (2019), PVG/Seac (2019), MWF/Hsd (2019), MR/N (2020), M520/N (2020), M520/NRrrcMcwi (2019), LEXF10A/StmMcwi (2020), LE/Stm (2019), LEXF4/Stm (2020), LEXF3/Stm (2020), LEXF2B/Stm (2019), LEXF1C/Stm (2019), LEXF1A/Stm (2019), LEXF11/Stm (2020), LEW/Crl (2019), HXB31/IpcvMcwi (2019), HXB2/IpcvMcwi (2019), FXLE18/Stm (2020), FXLE16/Stm (2020), FHH/EurMcwi (2019), F344/Stm (2019), F344/N (2020), BUF/N (2020), BXH2/CubMcwi (2020), WN/N (2020), F344/DuCrl (2019), F344/NCrl (2019)
3 161869433 161869434 C T snv WAG/RijCrl (2020), BXH2/CubMcwi (2020), SHRSP/A3NCrl (2019), PVG/Seac (2019), MWF/Hsd (2019), MR/N (2020), M520/N (2020), M520/NRrrcMcwi (2019), LEXF10A/StmMcwi (2020), LE/Stm (2019), LEXF4/Stm (2020), LEXF3/Stm (2020), LEXF2B/Stm (2019), LEXF1C/Stm (2019), LEXF1A/Stm (2019), LEXF11/Stm (2020), HXB31/IpcvMcwi (2019), HXB2/IpcvMcwi (2019), FXLE18/Stm (2020), FXLE16/Stm (2020), F344/Stm (2019), F344/N (2020), F344/NCrl (2019), F344/DuCrl (2019), BXH3/CubMcwi (2020), SHR/OlalpcvMcwi (2019)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2321501 AgrOrtholog
BioCyc Gene G2FUF-46517 BioCyc
Ensembl Genes ENSRNOG00000028661 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000034635 ENTREZGENE
  ENSRNOP00000034635.7 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000034131 ENTREZGENE
  ENSRNOT00000034131.7 UniProtKB/TrEMBL
InterPro Znf_C2H2/integrase_DNA-bd UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/TrEMBL
NCBI Gene 100360757 ENTREZGENE
Pfam zf-C2H2 UniProtKB/TrEMBL
PhenoGen Ctcfl PhenoGen
PROSITE ZINC_FINGER_C2H2_1 UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/TrEMBL
SMART ZnF_C2H2 UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/TrEMBL
UniProt D3ZQ48_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Ctcfl  CCCTC-binding factor like  Ctcfl  CCCTC-binding factor (zinc finger protein)-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-08-09 LOC100360757  CCCTC-binding factor (zinc finger protein)-like  Ctcfl  CCCTC-binding factor (zinc finger protein)-like  Data Merged 737654 APPROVED
2012-08-09 Ctcfl  CCCTC-binding factor (zinc finger protein)-like  LOC100360757  CCCTC-binding factor (zinc finger protein)-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-06 LOC100360757  CCCTC-binding factor (zinc finger protein)-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 Ctcfl  CCCTC-binding factor (zinc finger protein)-like   Ctcfl_predicted  CCCTC-binding factor (zinc finger protein)-like (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Ctcfl_predicted  CCCTC-binding factor (zinc finger protein)-like (predicted)      Symbol and Name status set to approved 70820 APPROVED