Cyp4f40 (cytochrome P450, family 4, subfamily f, polypeptide 40) - Rat Genome Database

Send us a Message



 Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes QTLs Strains Markers Community Projects Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap)  (beta) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease COVID-19 Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Cyp4f40 (cytochrome P450, family 4, subfamily f, polypeptide 40) Rattus norvegicus
Analyze
Symbol: Cyp4f40
Name: cytochrome P450, family 4, subfamily f, polypeptide 40
RGD ID: 1559596
Description: Predicted to enable fatty acid binding activity and monooxygenase activity. Predicted to be involved in icosanoid metabolic process and quinone catabolic process. Orthologous to human CYP4F11 (cytochrome P450 family 4 subfamily F member 11); PARTICIPATES IN arachidonic acid metabolic pathway; INTERACTS WITH bisphenol A; 17beta-estradiol (ortholog); 9-cis-retinoic acid (ortholog).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC503122; RGD1559596; similar to Cyp4f15 protein
RGD Orthologs
Human
Bonobo
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2711,691,648 - 11,707,437 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl711,692,086 - 11,706,229 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx714,501,836 - 14,515,977 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0716,379,277 - 16,393,416 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0714,259,460 - 14,273,608 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0714,865,941 - 14,880,084 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl714,865,941 - 14,880,084 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0715,019,492 - 15,035,347 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4713,268,030 - 13,282,102 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera79,791,839 - 9,805,981 (+)NCBICelera
Cytogenetic Map7q11NCBI
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

Molecular Pathway Annotations     Click to see Annotation Detail View
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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Cyp4f40
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2711,691,648 - 11,707,437 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl711,692,086 - 11,706,229 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx714,501,836 - 14,515,977 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0716,379,277 - 16,393,416 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0714,259,460 - 14,273,608 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0714,865,941 - 14,880,084 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl714,865,941 - 14,880,084 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0715,019,492 - 15,035,347 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4713,268,030 - 13,282,102 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera79,791,839 - 9,805,981 (+)NCBICelera
Cytogenetic Map7q11NCBI
CYP4F11
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381915,912,377 - 15,934,867 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1915,912,367 - 15,934,867 (-)EnsemblGRCh38hg38GRCh38
GRCh371916,023,187 - 16,045,677 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361915,884,181 - 15,906,326 (-)NCBINCBI36Build 36hg18NCBI36
Build 341915,885,486 - 15,906,326NCBI
Celera1915,921,026 - 15,945,078 (-)NCBICelera
Cytogenetic Map19p13.12NCBI
HuRef1915,594,445 - 15,615,786 (-)NCBIHuRef
CHM1_11916,022,955 - 16,045,451 (-)NCBICHM1_1
T2T-CHM13v2.01916,043,606 - 16,068,596 (-)NCBIT2T-CHM13v2.0
CYP4F11
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan11919,788,197 - 19,807,053 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01915,403,595 - 15,422,428 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11916,383,898 - 16,402,720 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1916,383,898 - 16,402,720 (-)Ensemblpanpan1.1panPan2
CYP4F11
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1614,460,588 - 14,482,294 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl614,426,592 - 14,481,523 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660745,011,652 - 5,033,060 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Cyp4f40
34 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:50
Count of miRNA genes:49
Interacting mature miRNAs:50
Transcripts:ENSRNOT00000066654
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.


QTLs in Region (mRatBN7.2)
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)7127829089Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat

Markers in Region
D10Rat157  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2711,695,965 - 11,696,078 (+)MAPPERmRatBN7.2
Rnor_6.0714,869,821 - 14,869,933NCBIRnor6.0
Rnor_5.0715,023,843 - 15,023,955UniSTSRnor5.0
RGSC_v3.4713,271,838 - 13,271,951RGDRGSC3.4
RGSC_v3.4713,271,839 - 13,271,951UniSTSRGSC3.4
RGSC_v3.1713,271,838 - 13,271,951RGD
Celera79,795,718 - 9,795,830UniSTS
SHRSP x BN Map1046.5699UniSTS
SHRSP x BN Map1046.5699RGD
Cytogenetic Map7q11UniSTS


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 renal system reproductive system
High
Medium 2
Low 1 1
Below cutoff 7 3 1 3 1 14

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000066654   ⟹   ENSRNOP00000059676
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl711,692,086 - 11,706,229 (+)Ensembl
Rnor_6.0 Ensembl714,865,941 - 14,880,084 (+)Ensembl
RefSeq Acc Id: NM_001109360   ⟹   NP_001102830
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2711,692,086 - 11,706,229 (+)NCBI
Rnor_6.0714,865,941 - 14,880,084 (+)NCBI
Rnor_5.0715,019,492 - 15,035,347 (+)NCBI
RGSC_v3.4713,268,030 - 13,282,102 (+)RGD
Celera79,791,839 - 9,805,981 (+)RGD
Sequence:
RefSeq Acc Id: XM_039079773   ⟹   XP_038935701
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2711,691,648 - 11,707,437 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001102830 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935701 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL89476 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000059676
  ENSRNOP00000059676.1
Reference Protein Sequences
RefSeq Acc Id: NP_001102830   ⟸   NM_001109360
- UniProtKB: D3ZTC9 (UniProtKB/TrEMBL),   A6K956 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000059676   ⟸   ENSRNOT00000066654
RefSeq Acc Id: XP_038935701   ⟸   XM_039079773
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZTC9-F1-model_v2 AlphaFold D3ZTC9 1-523 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1559596 AgrOrtholog
BioCyc Gene G2FUF-34816 BioCyc
Ensembl Genes ENSRNOG00000043344 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066654 ENTREZGENE
  ENSRNOT00000066654.2 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:503122 UniProtKB/TrEMBL
NCBI Gene 503122 ENTREZGENE
PANTHER CYTOCHROME P450 FAMILY 4 UniProtKB/TrEMBL
  CYTOCHROME P450, FAMILY 4, SUBFAMILY F, POLYPEPTIDE 40 UniProtKB/TrEMBL
Pfam p450 UniProtKB/TrEMBL
PhenoGen Cyp4f40 PhenoGen
PRINTS EP450I UniProtKB/TrEMBL
  P450 UniProtKB/TrEMBL
PROSITE CYTOCHROME_P450 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000043344 RatGTEx
Superfamily-SCOP Cytochrome_P450 UniProtKB/TrEMBL
UniProt A6K956 ENTREZGENE, UniProtKB/TrEMBL
  D3ZTC9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Cyp4f40  cytochrome P450, family 4, subfamily f, polypeptide 40   Cyp4f40_predicted  cytochrome P450, family 4, subfamily f, polypeptide 40 (predicted)  'predicted' is removed 2292626 APPROVED
2007-07-06 Cyp4f40_predicted  cytochrome P450, family 4, subfamily f, polypeptide 40 (predicted)  RGD1559596_predicted  similar to Cyp4f15 protein (predicted)  Name updated 1299863 APPROVED
2006-03-07 RGD1559596_predicted  similar to Cyp4f15 protein (predicted)  LOC503122  similar to Cyp4f15 protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC503122  similar to Cyp4f15 protein      Symbol and Name status set to provisional 70820 PROVISIONAL