Cyp4f39 (cytochrome P450, family 4, subfamily f, polypeptide 39) - Rat Genome Database

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Gene: Cyp4f39 (cytochrome P450, family 4, subfamily f, polypeptide 39) Rattus norvegicus
Analyze
Symbol: Cyp4f39
Name: cytochrome P450, family 4, subfamily f, polypeptide 39
RGD ID: 1308796
Description: Predicted to enable monooxygenase activity. Predicted to be involved in ceramide biosynthetic process. Predicted to be active in endoplasmic reticulum membrane. Human ortholog(s) of this gene implicated in autosomal recessive congenital ichthyosis 5. Orthologous to human CYP4F22 (cytochrome P450 family 4 subfamily F member 22); INTERACTS WITH (+)-schisandrin B; 1-naphthyl isothiocyanate; aflatoxin B1.
Type: protein-coding
RefSeq Status: MODEL
Also known as: cytochrome P450 4F22; LOC299566; RGD1308796; similar to RIKEN cDNA 4732474A20 gene
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
mRatBN7.2711,426,806 - 11,505,553 (+)NCBI
Rnor_6.0 Ensembl714,441,476 - 14,515,212 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0714,435,024 - 14,514,960 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0714,587,896 - 14,667,766 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4713,036,890 - 13,080,180 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1713,051,713 - 13,080,180 (+)NCBI
Celera79,536,310 - 9,614,458 (+)NCBICelera
Cytogenetic Map7q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

References

Additional References at PubMed
PMID:26056268  


Genomics

Comparative Map Data
Cyp4f39
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2711,426,806 - 11,505,553 (+)NCBI
Rnor_6.0 Ensembl714,441,476 - 14,515,212 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0714,435,024 - 14,514,960 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0714,587,896 - 14,667,766 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4713,036,890 - 13,080,180 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1713,051,713 - 13,080,180 (+)NCBI
Celera79,536,310 - 9,614,458 (+)NCBICelera
Cytogenetic Map7q11NCBI
CYP4F22
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1915,508,525 - 15,552,317 (+)EnsemblGRCh38hg38GRCh38
GRCh381915,508,487 - 15,552,317 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371915,619,336 - 15,663,128 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361915,480,336 - 15,524,128 (+)NCBINCBI36hg18NCBI36
Celera1915,516,166 - 15,559,962 (+)NCBI
Cytogenetic Map19p13.12NCBI
HuRef1915,187,100 - 15,231,018 (+)NCBIHuRef
CHM1_11915,618,891 - 15,662,706 (+)NCBICHM1_1
Cyp4f39
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391732,671,670 - 32,712,294 (+)NCBIGRCm39mm39
GRCm39 Ensembl1732,671,697 - 32,712,294 (+)Ensembl
GRCm381732,452,697 - 32,493,320 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1732,452,723 - 32,493,320 (+)EnsemblGRCm38mm10GRCm38
MGSCv371732,589,668 - 32,630,265 (+)NCBIGRCm37mm9NCBIm37
MGSCv361732,186,858 - 32,228,975 (+)NCBImm8
Celera1733,365,223 - 33,405,906 (+)NCBICelera
Cytogenetic Map17B1NCBI
LOC102004294
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554957,730,826 - 7,763,684 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554957,730,881 - 7,763,684 (-)NCBIChiLan1.0ChiLan1.0
CYP4F22
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11916,024,339 - 16,068,490 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1916,041,583 - 16,068,490 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01915,039,212 - 15,083,771 (+)NCBIMhudiblu_PPA_v0panPan3
CYP4F22
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12046,674,580 - 46,743,183 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2046,458,620 - 46,705,789 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2046,522,329 - 46,590,674 (-)NCBI
ROS_Cfam_1.02047,161,362 - 47,229,749 (-)NCBI
UMICH_Zoey_3.12046,396,281 - 46,464,620 (-)NCBI
UNSW_CanFamBas_1.02046,812,935 - 46,881,278 (-)NCBI
UU_Cfam_GSD_1.02047,085,714 - 47,154,773 (-)NCBI
LOC101977389
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118205,438,437 - 205,469,009 (-)NCBI
SpeTri2.0NW_0049365964,987,577 - 5,006,459 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CYP4F22
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl262,081,471 - 62,103,971 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1262,078,403 - 62,110,891 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2261,596,927 - 61,626,506 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CYP4F22
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1614,111,406 - 14,153,617 (+)NCBI
ChlSab1.1 Ensembl614,126,086 - 14,152,447 (+)Ensembl
Vero_WHO_p1.0NW_0236660745,345,276 - 5,393,850 (-)NCBI
LOC101706763
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249012,596,387 - 2,619,965 (+)NCBI

Position Markers
D7Mit17  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2711,500,212 - 11,500,307 (+)MAPPER
Rnor_6.0714,509,626 - 14,509,720NCBIRnor6.0
Rnor_5.0714,662,432 - 14,662,526UniSTSRnor5.0
RGSC_v3.4713,075,572 - 13,075,667RGDRGSC3.4
RGSC_v3.4713,075,573 - 13,075,667UniSTSRGSC3.4
RGSC_v3.1713,075,573 - 13,075,667RGD
RH 3.4 Map759.3UniSTS
RH 3.4 Map759.3RGD
RH 2.0 Map70.0RGD
Cytogenetic Map7q11UniSTS
BF411316  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2711,505,030 - 11,505,153 (+)MAPPER
Rnor_6.0714,514,438 - 14,514,560NCBIRnor6.0
Rnor_5.0714,667,244 - 14,667,366UniSTSRnor5.0
RGSC_v3.4713,080,503 - 13,080,625UniSTSRGSC3.4
Celera79,613,936 - 9,614,058UniSTS
RH 3.4 Map764.4UniSTS
Cytogenetic Map7q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7134147172Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7134828535Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7134828535Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7137009673Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7138119654Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)7265313832258115Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7591147750911477Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7595196950951969Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7975804554758045Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)71164710256647102Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)71232846767193263Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)712328467106995532Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)71268785067801690Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71395217958952179Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)71444568559445685Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:89
Count of miRNA genes:77
Interacting mature miRNAs:83
Transcripts:ENSRNOT00000007548
Prediction methods:Miranda, Rnahybrid
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 24 24 24 1
Low 2 28 17 15 17 6 8 17 14 11 6
Below cutoff 3 16 5 4 2 3 48 35 26 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000007548   ⟹   ENSRNOP00000007548
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl714,486,638 - 14,515,212 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093687   ⟹   ENSRNOP00000076248
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl714,441,476 - 14,514,974 (+)Ensembl
RefSeq Acc Id: XM_006241090   ⟹   XP_006241152
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2711,433,039 - 11,505,553 (+)NCBI
Rnor_6.0714,441,481 - 14,514,960 (+)NCBI
Rnor_5.0714,587,896 - 14,667,766 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006241091   ⟹   XP_006241153
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2711,426,806 - 11,505,415 (+)NCBI
Rnor_6.0714,435,024 - 14,514,960 (+)NCBI
Rnor_5.0714,587,896 - 14,667,766 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006241092   ⟹   XP_006241154
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2711,433,038 - 11,505,415 (+)NCBI
Rnor_6.0714,441,466 - 14,514,960 (+)NCBI
Rnor_5.0714,587,896 - 14,667,766 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008765183   ⟹   XP_008763405
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2711,462,404 - 11,505,415 (+)NCBI
Rnor_6.0714,470,584 - 14,514,960 (+)NCBI
Sequence:
RefSeq Acc Id: XM_234837   ⟹   XP_234837
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2711,462,634 - 11,505,415 (+)NCBI
Rnor_6.0714,470,814 - 14,514,960 (+)NCBI
Rnor_5.0714,587,896 - 14,667,766 (+)NCBI
RGSC_v3.4713,036,890 - 13,080,180 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: XP_234837   ⟸   XM_234837
- UniProtKB: D4A1H9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006241153   ⟸   XM_006241091
- UniProtKB: D4A1H9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006241154   ⟸   XM_006241092
- UniProtKB: D4A1H9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006241152   ⟸   XM_006241090
- UniProtKB: D4A1H9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008763405   ⟸   XM_008765183
- UniProtKB: D4A1H9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000076248   ⟸   ENSRNOT00000093687
RefSeq Acc Id: ENSRNOP00000007548   ⟸   ENSRNOT00000007548

Transcriptome

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

Promoters
RGD ID:13695072
Promoter ID:EPDNEW_R5595
Type:initiation region
Name:Cyp4f39_1
Description:cytochrome P450, family 4, subfamily f, polypeptide 39
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_6.0714,441,489 - 14,441,549EPDNEW

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)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308796 AgrOrtholog
Ensembl Genes ENSRNOG00000029478 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000007548 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000076248 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000007548 UniProtKB/TrEMBL
  ENSRNOT00000093687 UniProtKB/TrEMBL
Gene3D-CATH 1.10.630.10 UniProtKB/TrEMBL
InterPro Cyt_P450 UniProtKB/TrEMBL
  Cyt_P450_CS UniProtKB/TrEMBL
  Cyt_P450_E_grp-I UniProtKB/TrEMBL
  Cyt_P450_sf UniProtKB/TrEMBL
KEGG Report rno:299566 UniProtKB/TrEMBL
NCBI Gene 299566 ENTREZGENE
Pfam p450 UniProtKB/TrEMBL
PhenoGen Cyp4f39 PhenoGen
PRINTS EP450I UniProtKB/TrEMBL
  P450 UniProtKB/TrEMBL
PROSITE CYTOCHROME_P450 UniProtKB/TrEMBL
Superfamily-SCOP Cytochrome_P450 UniProtKB/TrEMBL
UniProt D4A1H9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Cyp4f39  cytochrome P450, family 4, subfamily f, polypeptide 39   Cyp4f39_predicted  cytochrome P450, family 4, subfamily f, polypeptide 39 (predicted)  'predicted' is removed 2292626 APPROVED
2007-07-06 Cyp4f39_predicted  cytochrome P450, family 4, subfamily f, polypeptide 39 (predicted)  RGD1308796_predicted  similar to RIKEN cDNA 4732474A20 gene (predicted)  Name updated 1299863 APPROVED
2005-01-20 RGD1308796_predicted  similar to RIKEN cDNA 4732474A20 gene (predicted)  LOC299566_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC299566_predicted  similar to RIKEN cDNA 4732474A20 gene (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL