Cfap90 (cilia and flagella associated protein 90) - Rat Genome Database

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Gene: Cfap90 (cilia and flagella associated protein 90) Rattus norvegicus
Analyze
Symbol: Cfap90
Name: cilia and flagella associated protein 90
RGD ID: 1308544
Description: Predicted to be involved in flagellated sperm motility. Predicted to be located in axoneme and ciliary basal body. Predicted to be active in axonemal B tubule inner sheath and sperm flagellum. Orthologous to human CFAP90 (cilia and flagella associated protein 90); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: cilia- and flagella-associated protein 90; LOC361192; RGD1308544; uncharacterized protein C5orf49 homolog
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8136,654,287 - 36,678,303 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl136,654,287 - 36,678,453 (-)EnsemblGRCr8
mRatBN7.2134,825,894 - 34,849,916 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl134,825,894 - 34,850,138 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx134,687,213 - 34,711,254 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0140,678,065 - 40,702,106 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0134,852,793 - 34,876,807 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0137,702,041 - 37,726,162 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl137,702,041 - 37,726,151 (-)Ensemblrn6Rnor6.0
Rnor_5.0139,083,665 - 39,107,716 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4175,044,084 - 5,069,032 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera133,395,288 - 33,419,581 (-)NCBICelera
RGSC_v3.1175,044,090 - 5,069,662 (-)NCBI
Cytogenetic Map1p11NCBI
JBrowse:




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

Biological Process

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

Genomics

Comparative Map Data
Cfap90
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8136,654,287 - 36,678,303 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl136,654,287 - 36,678,453 (-)EnsemblGRCr8
mRatBN7.2134,825,894 - 34,849,916 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl134,825,894 - 34,850,138 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx134,687,213 - 34,711,254 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0140,678,065 - 40,702,106 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0134,852,793 - 34,876,807 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0137,702,041 - 37,726,162 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl137,702,041 - 37,726,151 (-)Ensemblrn6Rnor6.0
Rnor_5.0139,083,665 - 39,107,716 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4175,044,084 - 5,069,032 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera133,395,288 - 33,419,581 (-)NCBICelera
RGSC_v3.1175,044,090 - 5,069,662 (-)NCBI
Cytogenetic Map1p11NCBI
CFAP90
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3857,830,378 - 7,851,133 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl57,830,378 - 7,851,512 (-)Ensemblhg38GRCh38
GRCh3757,830,491 - 7,851,246 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3657,884,511 - 7,904,264 (-)NCBIBuild 36Build 36hg18NCBI36
Celera57,872,579 - 7,892,308 (-)NCBICelera
Cytogenetic Map5p15.31NCBI
HuRef57,812,253 - 7,833,342 (-)NCBIHuRef
CHM1_157,830,570 - 7,851,693 (-)NCBICHM1_1
T2T-CHM13v2.057,769,514 - 7,790,256 (-)NCBIT2T-CHM13v2.0
Cfap90
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391368,745,558 - 68,762,350 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1368,745,540 - 68,762,350 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381368,597,439 - 68,614,231 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1368,597,421 - 68,614,231 (+)Ensemblmm10GRCm38
MGSCv371368,736,316 - 68,753,108 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361369,064,801 - 69,081,603 (+)NCBIMGSCv36mm8
Celera1370,957,259 - 70,973,445 (+)NCBICelera
Cytogenetic Map13B3NCBI
cM Map1335.55NCBI
Cfap90
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555045,380,575 - 5,395,166 (-)Ensembl
ChiLan1.0NW_0049555045,380,575 - 5,395,166 (-)NCBIChiLan1.0ChiLan1.0
CFAP90
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v248,085,098 - 8,106,587 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan156,236,535 - 6,260,196 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v058,156,838 - 8,178,329 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.157,978,684 - 7,999,876 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl57,978,684 - 7,999,876 (-)EnsemblpanPan2panpan1.1
CFAP90
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1346,132,731 - 6,136,340 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl346,133,267 - 6,136,301 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3410,628,123 - 10,644,465 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0346,025,559 - 6,041,883 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl346,025,601 - 6,041,844 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1346,075,303 - 6,091,642 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0346,056,069 - 6,072,370 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0346,268,962 - 6,285,310 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Cfap90
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213239,042,699 - 239,060,481 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936643342,561 - 359,902 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936643342,292 - 359,984 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CFAP90
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1674,288,049 - 74,302,047 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11674,288,038 - 74,302,052 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21680,340,678 - 80,355,084 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CFAP90
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.147,418,409 - 7,439,389 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl47,419,593 - 7,438,946 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366606421,177,185 - 21,198,839 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cfap90
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247515,413,401 - 5,428,093 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247515,409,850 - 5,428,096 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Cfap90
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v12199,918,667 - 199,947,013 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Cfap90
75 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:152
Count of miRNA genes:124
Interacting mature miRNAs:136
Transcripts:ENSRNOT00000071842
Prediction methods:Microtar, 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
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1774611852746118Rat
4889451Eae29Experimental allergic encephalomyelitis QTL 295.51nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1774612152746121Rat
1357397Bw41Body weight QTL 414.190.0001body mass (VT:0001259)body weight (CMO:0000012)12940927974409279Rat
70179Xhs2X-ray hypersensitivity QTL 23.2intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)1143965634Rat
1558642Prcr2Prostate cancer resistance QTL 24.3prostate integrity trait (VT:0010571)area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)11037949255379492Rat
7421626Bp360Blood pressure QTL 3600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1694102251941022Rat
1357401Bw43Body weight QTL 433.75body mass (VT:0001259)body weight (CMO:0000012)1690935351909353Rat
631494Bp95Blood pressure QTL 95400.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)11731537851816258Rat
5684998Bss101Bone structure and strength QTL 1013.6tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)1690935351909353Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134184556172281316Rat
5684999Bss102Bone structure and strength QTL 1025.57e-07tibia strength trait (VT:1000284)tibia stiffness (CMO:0001735)1690935351909353Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134565911208798288Rat
2302038Pia31Pristane induced arthritis QTL 315.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)11282049457820494Rat
634353Rends2Renal damage susceptibility QTL 20.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)12065642065656420Rat
1578756Iddm22Insulin dependent diabetes mellitus QTL 222.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)12050832665508326Rat
631508Sald1Serum aldosterone level QTL 13.7blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)11168446456684464Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)13070837587558729Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13456572679565726Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 10 42 116 19 28 6 16 6 1 107 66 112 12 57 22 13 13

Sequence


Ensembl Acc Id: ENSRNOT00000071842   ⟹   ENSRNOP00000064743
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl136,654,287 - 36,678,453 (-)Ensembl
mRatBN7.2 Ensembl134,825,894 - 34,850,138 (-)Ensembl
Rnor_6.0 Ensembl137,702,041 - 37,726,151 (-)Ensembl
RefSeq Acc Id: NM_001400836   ⟹   NP_001387765
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8136,654,287 - 36,678,303 (-)NCBI
mRatBN7.2134,825,894 - 34,849,916 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001387765 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL87603 (Get FASTA)   NCBI Sequence Viewer  
  EDL87604 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000064743
  ENSRNOP00000064743.2
Ensembl Acc Id: ENSRNOP00000064743   ⟸   ENSRNOT00000071842
RefSeq Acc Id: NP_001387765   ⟸   NM_001400836
- UniProtKB: M0R5R5 (UniProtKB/TrEMBL),   A6JV26 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R5R5-F1-model_v2 AlphaFold M0R5R5 1-180 view protein structure

Transcriptome

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

Promoters
RGD ID:13689586
Promoter ID:EPDNEW_R101
Type:initiation region
Name:RGD1308544_1
Description:LOC361192
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_6.0137,725,969 - 37,726,029EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308544 AgrOrtholog
BioCyc Gene G2FUF-61853 BioCyc
Ensembl Genes ENSRNOG00000047406 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000071842 ENTREZGENE
  ENSRNOT00000071842.4 UniProtKB/TrEMBL
InterPro DUF4541 UniProtKB/TrEMBL
NCBI Gene 361192 ENTREZGENE
PANTHER LOC361192 UniProtKB/TrEMBL
  PTHR34444 UniProtKB/TrEMBL
Pfam DUF4541 UniProtKB/TrEMBL
PhenoGen Cfap90 PhenoGen
RatGTEx ENSRNOG00000047406 RatGTEx
UniProt A6JV26 ENTREZGENE, UniProtKB/TrEMBL
  M0R5R5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-10-27 Cfap90  cilia and flagella associated protein 90  RGD1308544  LOC361192  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1308544  LOC361192   RGD1308544_predicted  LOC361192 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1308544_predicted  LOC361192 (predicted)  LOC361192_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC361192_predicted  LOC361192 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL