Cfhr2 (complement factor H-related 2) - Rat Genome Database

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Gene: Cfhr2 (complement factor H-related 2) Rattus norvegicus
Analyze
Symbol: Cfhr2
Name: complement factor H-related 2
RGD ID: 1584079
Description: Predicted to have complement component C3b binding activity and heparin binding activity. Predicted to localize to extracellular space. Orthologous to human CFHR4 (complement factor H related 4); INTERACTS WITH benzo[a]pyrene (ortholog); bisphenol A (ortholog); MeIQx (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Also known as: complement factor H-related protein 3; complement factor H-related protein 4; LOC688887; LOC688901; similar to complement component factor H
RGD Orthologs
Human
Mouse
Bonobo
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21351,175,824 - 51,247,924 (-)NCBI
Rnor_6.0 Ensembl1356,642,365 - 56,693,968 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01356,641,657 - 56,713,305 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01361,659,797 - 61,731,674 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41352,909,017 - 52,924,436 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1351,439,040 - 51,508,049 (-)NCBICelera
Cytogenetic Map13q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References


Genomics

Comparative Map Data
Cfhr2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21351,175,824 - 51,247,924 (-)NCBI
Rnor_6.0 Ensembl1356,642,365 - 56,693,968 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01356,641,657 - 56,713,305 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01361,659,797 - 61,731,674 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41352,909,017 - 52,924,436 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1351,439,040 - 51,508,049 (-)NCBICelera
Cytogenetic Map13q13NCBI
CFHR4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1196,888,014 - 196,918,713 (+)EnsemblGRCh38hg38GRCh38
GRCh381196,888,051 - 196,918,911 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371196,857,182 - 196,887,763 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361195,123,835 - 195,154,386 (+)NCBINCBI36hg18NCBI36
Build 341193,588,868 - 193,619,419NCBI
Celera1169,971,227 - 170,001,824 (+)NCBI
Cytogenetic Map1q31.3NCBI
HuRef1168,014,575 - 168,045,285 (+)NCBIHuRef
CHM1_11198,279,376 - 198,310,085 (+)NCBICHM1_1
Cfhr4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391139,625,657 - 139,708,977 (-)NCBIGRCm39mm39
GRCm39 Ensembl1139,625,361 - 139,708,981 (-)Ensembl
GRCm381139,697,919 - 139,781,239 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1139,697,623 - 139,781,243 (-)EnsemblGRCm38mm10GRCm38
MGSCv371141,594,496 - 141,677,816 (-)NCBIGRCm37mm9NCBIm37
MGSCv361141,514,046 - 141,597,647 (-)NCBImm8
Celera1142,332,928 - 142,428,269 (-)NCBICelera
Cytogenetic Map1FNCBI
CFHR4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Mhudiblu_PPA_v01172,392,804 - 172,454,153 (+)NCBIMhudiblu_PPA_v0panPan3
LOC103230383
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12532,488,314 - 32,609,868 (-)NCBI
ChlSab1.1 Ensembl2532,487,816 - 32,507,705 (-)Ensembl


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131107975663Rat
1581554Pur11Proteinuria QTL 11urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13901690682995569Rat
1581573Uae36Urinary albumin excretion QTL 36urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13901690682995569Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1312193394108478121Rat
9589141Insul28Insulin level QTL 2810.820.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)131409633059096330Rat
7411662Foco29Food consumption QTL 2920.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)131409633059096330Rat
2317040Aia21Adjuvant induced arthritis QTL 212.75joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)131462463159624631Rat
2317046Aia8Adjuvant induced arthritis QTL 83.9700000286102295joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)131462463159624631Rat
631645Bp121Blood pressure QTL 1213.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131981081464810814Rat
9589164Gluco66Glucose level QTL 666.670.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)132005247765052477Rat
1331784Bp222Blood pressure QTL 2222.944arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)132148248158537177Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1324502279108770533Rat
61391Bp5Blood pressure QTL 55.6arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)132800833873008338Rat
70170Eae14Experimental allergic encephalomyelitis QTL 140.0024nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)132858445273584452Rat
1558644Cm45Cardiac mass QTL 453.60.002heart mass (VT:0007028)heart wet weight (CMO:0000069)132907693474076934Rat
6893338Cm76Cardiac mass QTL 7600.99heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)132907693474076934Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1335301263107975663Rat
2301962Cm72Cardiac mass QTL 724.12heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)133614753364868393Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133614753399968921Rat
2303563Bw89Body weight QTL 896body mass (VT:0001259)body weight (CMO:0000012)133734634882346348Rat
61340Bp25Blood pressure QTL 254.20.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133937292784372927Rat
10755495Bp387Blood pressure QTL 3873.78arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133950130093652524Rat
4889861Pur29Proteinuria QTL 2913.80.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)134231074486833540Rat
1331750Bp220Blood pressure QTL 2202.98arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)134231074487310744Rat
70220Bp55Blood pressure QTL 555.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)134250834587508345Rat
61349Bp31Blood pressure QTL 315.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)134250834587508345Rat
1549897Stresp12Stress response QTL 123.35stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)134357571788575717Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134567662990676629Rat
6893344Cm79Cardiac mass QTL 791.50.04heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)134905850767207219Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)135108098996080989Rat
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135156924896569248Rat
71119Thym2Thymus enlargement QTL 23.8thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)135157782490675199Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:584
Count of miRNA genes:164
Interacting mature miRNAs:178
Transcripts:ENSRNOT00000029281, ENSRNOT00000029294, ENSRNOT00000060160
Prediction methods:Microtar, Miranda
Result types:miRGate_prediction

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

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


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 29 29 29
Low 1 12 10 10 1 2
Below cutoff 1 1 9 2 7 2 4 4 5 8 11 6 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000060160   ⟹   ENSRNOP00000056904
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1356,642,365 - 56,693,968 (-)Ensembl
RefSeq Acc Id: XM_001068704   ⟹   XP_001068704
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21351,175,824 - 51,247,669 (-)NCBI
Rnor_6.01356,641,657 - 56,713,304 (-)NCBI
Rnor_5.01361,659,797 - 61,731,674 (-)NCBI
RGSC_v3.41352,909,017 - 52,924,436 (-)RGD
Sequence:
RefSeq Acc Id: XM_006249947   ⟹   XP_006250009
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21351,175,824 - 51,247,671 (-)NCBI
Rnor_6.01356,641,657 - 56,713,305 (-)NCBI
Rnor_5.01361,659,797 - 61,731,674 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006249948   ⟹   XP_006250010
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21351,175,824 - 51,247,672 (-)NCBI
Rnor_6.01356,641,657 - 56,713,304 (-)NCBI
Rnor_5.01361,659,797 - 61,731,674 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006249949   ⟹   XP_006250011
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21351,175,824 - 51,247,672 (-)NCBI
Rnor_6.01356,641,657 - 56,713,303 (-)NCBI
Rnor_5.01361,659,797 - 61,731,674 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006249950   ⟹   XP_006250012
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21351,175,824 - 51,247,670 (-)NCBI
Rnor_6.01356,641,657 - 56,713,302 (-)NCBI
Rnor_5.01361,659,797 - 61,731,674 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006249951   ⟹   XP_006250013
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21351,175,824 - 51,247,675 (-)NCBI
Rnor_6.01356,641,657 - 56,713,305 (-)NCBI
Rnor_5.01361,659,797 - 61,731,674 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017604627   ⟹   XP_017460116
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1351,439,040 - 51,508,049 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039091339   ⟹   XP_038947267
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21351,175,824 - 51,247,667 (-)NCBI
RefSeq Acc Id: XM_039091340   ⟹   XP_038947268
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21351,191,208 - 51,247,924 (-)NCBI
Reference Sequences
RefSeq Acc Id: XP_001068704   ⟸   XM_001068704
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006250013   ⟸   XM_006249951
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_006250009   ⟸   XM_006249947
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006250010   ⟸   XM_006249948
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006250012   ⟸   XM_006249950
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006250011   ⟸   XM_006249949
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017460116   ⟸   XM_017604627
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: ENSRNOP00000056904   ⟸   ENSRNOT00000060160
RefSeq Acc Id: XP_038947267   ⟸   XM_039091339
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038947268   ⟸   XM_039091340
- Peptide Label: isoform X8
Protein Domains
Sushi

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)
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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
13 61679148 61679149 C T snv FHH/EurMcwi (MCW), ZFDM (KyushuU), SBN/Ygl (MCW), SR/JrHsd (MCW), LH/MavRrrc (KNAW), LL/MavRrrc (KNAW), SR/JrHsd (KNAW), SBN/Ygl (KNAW), F344/NRrrc (Illumina) (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), BUF/N (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), MNS/Gib (KNAW), WN/N (KNAW), SDLEF7/Barth (UDEL), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), F344/DuCrlCrlj (KyushuU), LE/Stm (KyushuU), F344/NSlc (KyushuU), F344/Stm (KyushuU), LEC/Tj (KyushuU), F344/Jcl (KyushuU), KFRS3B/Kyo (KyushuU), FHL/EurMcwi (MCW)
13 61723104 61723105 A T snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), LH/MavRrrc (KNAW), LL/MavRrrc (KNAW), LN/MavRrrc (KNAW), SR/JrHsd (KNAW), SS/Jr (KNAW), SS/JrHsdMcwi (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), BBDP/WorN (KNAW), SBH/Ygl (KNAW), SBN/Ygl (KNAW), SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), SHRSP/Gcrc (KNAW), F344/NRrrc (Illumina) (KNAW), WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), BUF/N (KNAW), DA/BklArbNsi (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), M520/N (KNAW), MNS/Gib (KNAW), WN/N (KNAW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), Crl:SD (UDEL)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
13 56660766 56660767 C T snv LE/Stm (RGD), LH/MavRrrc (RGD), CDS, FHH/EurMcwi (RGD), WKY/NHsd (RGD), SR/JrHsd (RGD), SBN/Ygl (MCW), F344/NCrl (RGD), FHL/EurMcwi (MCW), SBN/Ygl (RGD), FHH/EurMcwi (MCW), SR/JrHsd (MCW), MNS/Gib (RGD), WN/N (MCW), WKY/N (MCW), LL/MavRrrc (RGD), F344/NRrrc (MCW), Buf/N (MCW), WKY/NCrl (RGD)
13 56704722 56704723 A T snv MNS/Gib (RGD), SBH/Ygl (RGD), SBN/Ygl (RGD), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), SR/JrHsd (RGD), SS/Jr (RGD), SS/JrHsdMcwi (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), LL/MavRrrc (RGD), LN/MavRrrc (RGD), LH/MavRrrc (RGD), LE/Stm (RGD), FHH/EurMcwi (RGD), F344/NCrl (RGD), BBDP/Wor (RGD), ACI/EurMcwi (RGD), FHL/EurMcwi (RGD), CDS, CDR, SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), SBN/Ygl (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), SBH/Ygl (MCW), GH/OmrMcwi (MCW), ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1584079 AgrOrtholog
Ensembl Genes ENSRNOG00000021575 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000056904 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000060160 UniProtKB/TrEMBL
InterPro Sushi/SCR/CCP_sf UniProtKB/TrEMBL
  Sushi_SCR_CCP_dom UniProtKB/TrEMBL
NCBI Gene 688887 ENTREZGENE
Pfam Sushi UniProtKB/TrEMBL
PhenoGen Cfhr2 PhenoGen
PROSITE SUSHI UniProtKB/TrEMBL
SMART CCP UniProtKB/TrEMBL
Superfamily-SCOP SSF57535 UniProtKB/TrEMBL
UniProt F1LWS4_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-29 Cfhr2  complement factor H-related 2  LOC688901  similar to complement component factor H  Data Merged 737654 PROVISIONAL
2013-10-17 Cfhr2  complement factor H-related 2  LOC688887  similar to complement component factor H  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC688887  similar to complement component factor H      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC688901  similar to complement component factor H      Symbol and Name status set to provisional 70820 PROVISIONAL