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

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Gene: Cyp4f40 (cytochrome P450, family 4, subfamily f, polypeptide 40) Rattus norvegicus
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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 ketone catabolic process. Predicted to be located in endoplasmic reticulum membrane. Orthologous to human CYP4F11 (cytochrome P450 family 4 subfamily F member 11); PARTICIPATES IN arachidonic acid metabolic pathway; INTERACTS WITH oxybenzone.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC503122; RGD1559596; similar to Cyp4f15 protein
RGD Orthologs
Human
Bonobo
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8712,342,121 - 12,357,974 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl712,342,590 - 12,356,733 (+)EnsemblGRCr8
mRatBN7.2711,691,648 - 11,707,437 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl711,692,086 - 11,706,229 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx714,501,836 - 14,515,977 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0716,379,277 - 16,393,416 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0714,259,460 - 14,273,608 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0714,865,941 - 14,880,084 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl714,865,941 - 14,880,084 (+)Ensemblrn6Rnor6.0
Rnor_5.0715,019,492 - 15,035,347 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4713,268,030 - 13,282,102 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera79,791,839 - 9,805,981 (+)NCBICelera
Cytogenetic Map7q11NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
oxybenzone  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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
GRCr8712,342,121 - 12,357,974 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl712,342,590 - 12,356,733 (+)EnsemblGRCr8
mRatBN7.2711,691,648 - 11,707,437 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl711,692,086 - 11,706,229 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx714,501,836 - 14,515,977 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0716,379,277 - 16,393,416 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0714,259,460 - 14,273,608 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0714,865,941 - 14,880,084 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl714,865,941 - 14,880,084 (+)Ensemblrn6Rnor6.0
Rnor_5.0715,019,492 - 15,035,347 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4713,268,030 - 13,282,102 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
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 - 15,934,933 (-)Ensemblhg38GRCh38
GRCh371916,023,187 - 16,045,677 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361915,884,181 - 15,906,326 (-)NCBIBuild 36Build 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_mPanPan1-v22020,785,557 - 20,804,435 (-)NCBINHGRI_mPanPan1-v2
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 (-)EnsemblpanPan2panpan1.1
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 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660745,011,652 - 5,033,060 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Cyp4f40
181 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7166965846669658Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)7123748937Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7721609752216097Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)71051708662346019Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)71011291699900612Rat
2290372Gluco33Glucose level QTL 332.71blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)7131777942Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)71104117804Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7170952746709527Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)71509236116977875Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7132612984Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)71011291660150541Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7946087754460877Rat
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7129716167Rat
1300138Hrtrt9Heart rate QTL 94.72heart pumping trait (VT:2000009)heart rate (CMO:0000002)71049882055498820Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134650782Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7132612984Rat

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
Celera79,795,718 - 9,795,830UniSTS
RGSC_v3.1713,271,838 - 13,271,951RGD
SHRSP x BN Map1046.5699UniSTS
SHRSP x BN Map1046.5699RGD
Cytogenetic Map7q11UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 6 34 35 28 15 10 15 6 71 32 1 18 8 42 13 5 5

Sequence


Ensembl Acc Id: ENSRNOT00000066654   ⟹   ENSRNOP00000059676
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl712,342,590 - 12,356,733 (+)Ensembl
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: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8712,342,590 - 12,356,733 (+)NCBI
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_063264148   ⟹   XP_063120218
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8712,342,121 - 12,357,974 (+)NCBI
RefSeq Acc Id: XM_063264149   ⟹   XP_063120219
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8712,342,127 - 12,357,974 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001102830 (Get FASTA)   NCBI Sequence Viewer  
  NP_001426776 (Get FASTA)   NCBI Sequence Viewer  
  XP_063120218 (Get FASTA)   NCBI Sequence Viewer  
  XP_063120219 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL89476 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000059676
  ENSRNOP00000059676.1
RefSeq Acc Id: NP_001102830   ⟸   NM_001109360
- UniProtKB: D3ZTC9 (UniProtKB/TrEMBL),   A6K956 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000059676   ⟸   ENSRNOT00000066654
RefSeq Acc Id: XP_063120218   ⟸   XM_063264148
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063120219   ⟸   XM_063264149
- 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
  ENSRNOT00000066654.3 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
  Cytochrome_P450_Monoox 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