Cfap300 (cilia and flagella associated protein 300) - 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 Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) 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 Coronavirus Disease 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 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: Cfap300 (cilia and flagella associated protein 300) Rattus norvegicus
Analyze
Symbol: Cfap300
Name: cilia and flagella associated protein 300
RGD ID: 1591894
Description: Predicted to be located in cytoplasm and motile cilium. Human ortholog(s) of this gene implicated in primary ciliary dyskinesia 38. Orthologous to human CFAP300 (cilia and flagella associated protein 300); INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; bisphenol A; endosulfan.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: cilia- and flagella-associated protein 300; hypothetical protein LOC654482; LOC654482; uncharacterized protein C11orf70 homolog
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8813,465,016 - 13,483,679 (-)NCBIGRCr8
mRatBN7.285,180,180 - 5,198,840 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl85,180,675 - 5,198,807 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx89,134,759 - 9,152,057 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.087,432,428 - 7,449,704 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.085,440,897 - 5,458,480 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.086,218,391 - 6,236,438 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl86,218,393 - 6,235,967 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.086,217,030 - 6,234,756 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.484,863,693 - 4,881,270 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera86,738,387 - 6,755,957 (-)NCBICelera
Cytogenetic Map8q11NCBI
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

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15489334  


Genomics

Comparative Map Data
Cfap300
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8813,465,016 - 13,483,679 (-)NCBIGRCr8
mRatBN7.285,180,180 - 5,198,840 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl85,180,675 - 5,198,807 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx89,134,759 - 9,152,057 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.087,432,428 - 7,449,704 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.085,440,897 - 5,458,480 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.086,218,391 - 6,236,438 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl86,218,393 - 6,235,967 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.086,217,030 - 6,234,756 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.484,863,693 - 4,881,270 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera86,738,387 - 6,755,957 (-)NCBICelera
Cytogenetic Map8q11NCBI
CFAP300
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3811102,047,437 - 102,084,554 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl11102,047,437 - 102,084,554 (+)EnsemblGRCh38hg38GRCh38
GRCh3711101,918,168 - 101,955,285 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3611101,423,409 - 101,459,360 (+)NCBINCBI36Build 36hg18NCBI36
Celera1199,079,748 - 99,116,853 (+)NCBICelera
Cytogenetic Map11q22.1NCBI
HuRef1197,844,750 - 97,881,818 (+)NCBIHuRef
CHM1_111101,801,177 - 101,838,287 (+)NCBICHM1_1
T2T-CHM13v2.011102,049,520 - 102,086,624 (+)NCBIT2T-CHM13v2.0
Cfap300
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3998,021,673 - 8,042,876 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl98,021,673 - 8,042,824 (-)EnsemblGRCm39 Ensembl
GRCm3898,021,672 - 8,042,875 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl98,021,672 - 8,042,823 (-)EnsemblGRCm38mm10GRCm38
MGSCv3798,021,672 - 8,042,823 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3698,022,193 - 8,043,344 (-)NCBIMGSCv36mm8
Celera95,413,955 - 5,435,063 (-)NCBICelera
Cytogenetic Map9A1NCBI
cM Map92.46NCBI
Cfap300
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554125,368,495 - 5,400,305 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554125,368,983 - 5,399,406 (+)NCBIChiLan1.0ChiLan1.0
CFAP300
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v29102,850,602 - 102,888,109 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan111103,938,151 - 103,975,681 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01196,997,736 - 97,034,422 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.111100,495,365 - 100,530,644 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11100,495,360 - 100,530,638 (+)Ensemblpanpan1.1panPan2
CFAP300
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1529,511,852 - 29,532,684 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl529,512,182 - 29,527,849 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha529,460,110 - 29,481,957 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0529,565,046 - 29,586,902 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl529,565,570 - 29,586,866 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1529,621,372 - 29,643,220 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0529,478,316 - 29,500,138 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0529,653,163 - 29,674,987 (-)NCBIUU_Cfam_GSD_1.0
Cfap300
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494785,731,368 - 85,769,843 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365515,766,610 - 5,797,531 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365515,766,757 - 5,797,491 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CFAP300
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl932,765,880 - 32,795,297 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1932,753,274 - 32,795,303 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2936,714,818 - 36,744,705 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CFAP300
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1193,414,720 - 93,453,964 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl193,414,766 - 93,454,729 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604332,408,477 - 32,444,774 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cfap300
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624878801,132 - 830,574 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624878801,173 - 830,479 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cfap300
78 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:88
Count of miRNA genes:71
Interacting mature miRNAs:83
Transcripts:ENSRNOT00000068290
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)8470581049705810Rat
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8124597739Rat
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125902202Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8209764047097640Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8209764047097640Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8209764047097640Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8209764047097640Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)8470581049705810Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)8470581049705810Rat

Markers in Region
RH136987  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.285,181,279 - 5,181,461 (+)MAPPERmRatBN7.2
Rnor_6.086,218,471 - 6,218,652NCBIRnor6.0
Rnor_5.086,217,110 - 6,217,291UniSTSRnor5.0
RGSC_v3.484,863,773 - 4,863,954UniSTSRGSC3.4
Celera86,738,467 - 6,738,648UniSTS
Cytogenetic Map8q11UniSTS


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 18 4 4 4 53 20 39 9
Low 3 25 36 20 19 20 5 5 21 15 2 2 5
Below cutoff 17 17 17 3 6 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000068290   ⟹   ENSRNOP00000061520
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl85,180,675 - 5,198,807 (-)Ensembl
Rnor_6.0 Ensembl86,218,393 - 6,235,967 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107963   ⟹   ENSRNOP00000092820
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl85,181,801 - 5,198,807 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000116063   ⟹   ENSRNOP00000077604
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl85,180,808 - 5,198,807 (-)Ensembl
RefSeq Acc Id: NM_001039174   ⟹   NP_001034263
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8813,466,036 - 13,483,608 (-)NCBI
mRatBN7.285,181,200 - 5,198,752 (-)NCBI
Rnor_6.086,218,391 - 6,235,967 (-)NCBI
Rnor_5.086,217,030 - 6,234,756 (-)NCBI
RGSC_v3.484,863,693 - 4,881,270 (-)RGD
Celera86,738,387 - 6,755,957 (-)RGD
Sequence:
RefSeq Acc Id: XM_006242497   ⟹   XP_006242559
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8813,465,016 - 13,483,679 (-)NCBI
mRatBN7.285,180,180 - 5,198,840 (-)NCBI
Rnor_6.086,218,395 - 6,236,050 (-)NCBI
Rnor_5.086,217,030 - 6,234,756 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039082122   ⟹   XP_038938050
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8813,466,587 - 13,483,679 (-)NCBI
mRatBN7.285,180,180 - 5,198,839 (-)NCBI
RefSeq Acc Id: XM_039082123   ⟹   XP_038938051
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8813,465,016 - 13,483,673 (-)NCBI
mRatBN7.285,180,180 - 5,198,833 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001034263   ⟸   NM_001039174
- UniProtKB: Q68FQ4 (UniProtKB/Swiss-Prot),   A0A8L2QTY4 (UniProtKB/TrEMBL),   A6JN50 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242559   ⟸   XM_006242497
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000061520   ⟸   ENSRNOT00000068290
RefSeq Acc Id: XP_038938050   ⟸   XM_039082122
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038938051   ⟸   XM_039082123
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000077604   ⟸   ENSRNOT00000116063
RefSeq Acc Id: ENSRNOP00000092820   ⟸   ENSRNOT00000107963

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q68FQ4-F1-model_v2 AlphaFold Q68FQ4 1-267 view protein structure

Transcriptome

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

Promoters
RGD ID:13695739
Promoter ID:EPDNEW_R6263
Type:initiation region
Name:LOC654482_1
Description:hypothetical protein LOC654482
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_6.086,235,991 - 6,236,051EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1591894 AgrOrtholog
BioCyc Gene G2FUF-31760 BioCyc
Ensembl Genes ENSRNOG00000043410 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000068290 ENTREZGENE
  ENSRNOT00000068290.2 UniProtKB/TrEMBL
  ENSRNOT00000107963.1 UniProtKB/TrEMBL
  ENSRNOT00000116063.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7114230 IMAGE-MGC_LOAD
InterPro CFAP300 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:654482 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94966 IMAGE-MGC_LOAD
NCBI Gene 654482 ENTREZGENE
PANTHER CILIA- AND FLAGELLA-ASSOCIATED PROTEIN 300 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR31078 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam DUF4498 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cfap300 PhenoGen
RatGTEx ENSRNOG00000043410 RatGTEx
UniProt A0A8I5Y6J4_RAT UniProtKB/TrEMBL
  A0A8I6AIA2_RAT UniProtKB/TrEMBL
  A0A8L2QTY4 ENTREZGENE, UniProtKB/TrEMBL
  A6JN50 ENTREZGENE, UniProtKB/TrEMBL
  CF300_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-03-01 Cfap300  cilia and flagella associated protein 300  LOC654482  hypothetical protein LOC654482  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC654482  hypothetical protein LOC654482      Symbol and Name status set to provisional 70820 PROVISIONAL