Cfap20 (cilia and flagella associated protein 20) - Rat Genome Database

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Gene: Cfap20 (cilia and flagella associated protein 20) Rattus norvegicus
Analyze
Symbol: Cfap20
Name: cilia and flagella associated protein 20
RGD ID: 1308493
Description: Predicted to be involved in several processes, including cilium assembly; positive regulation of feeding behavior; and regulation of cilium beat frequency involved in ciliary motility. Predicted to be located in axonemal microtubule; centriole; and nucleoplasm. Predicted to be active in axonemal B tubule inner sheath; ciliary basal body; and motile cilium. Orthologous to human CFAP20 (cilia and flagella associated protein 20); INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: cilia- and flagella-associated protein 20; gene trap locus 3; gene trap locus 3 protein homolog; Gtl3; LOC307642; MGC124689; transcription factor IIB-like; UPF0468 protein C16orf80 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
GRCr8199,614,265 - 9,628,612 (+)NCBIGRCr8
mRatBN7.2199,608,867 - 9,622,558 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl199,608,859 - 9,622,558 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx199,573,964 - 9,587,384 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01910,340,790 - 10,354,212 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0199,627,120 - 9,640,542 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01910,024,938 - 10,038,838 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1910,024,947 - 10,038,784 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01910,009,188 - 10,022,985 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41910,067,502 - 10,081,452 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11910,072,290 - 10,086,278 (+)NCBI
Celera199,500,482 - 9,514,062 (+)NCBICelera
Cytogenetic Map19p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
axonemal B tubule inner sheath  (ISO)
axonemal microtubule  (IEA,ISO,ISS)
centriole  (IEA,ISO,ISS)
ciliary basal body  (IBA,IEA,ISO,ISS)
cilium  (IEA,ISO,ISS)
cytoplasm  (IEA)
microtubule  (IEA)
motile cilium  (IBA)
nucleoplasm  (IEA,ISO)
nucleus  (IEA)
sperm flagellum  (ISS)

Molecular Function

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:19056867   PMID:20118210   PMID:22326026   PMID:22681889   PMID:24414207  


Genomics

Comparative Map Data
Cfap20
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8199,614,265 - 9,628,612 (+)NCBIGRCr8
mRatBN7.2199,608,867 - 9,622,558 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl199,608,859 - 9,622,558 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx199,573,964 - 9,587,384 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01910,340,790 - 10,354,212 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0199,627,120 - 9,640,542 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01910,024,938 - 10,038,838 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1910,024,947 - 10,038,784 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01910,009,188 - 10,022,985 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41910,067,502 - 10,081,452 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11910,072,290 - 10,086,278 (+)NCBI
Celera199,500,482 - 9,514,062 (+)NCBICelera
Cytogenetic Map19p13NCBI
CFAP20
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381658,113,592 - 58,129,381 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1658,113,592 - 58,129,381 (-)EnsemblGRCh38hg38GRCh38
GRCh371658,147,496 - 58,163,285 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361656,704,997 - 56,720,797 (-)NCBINCBI36Build 36hg18NCBI36
Celera1642,644,770 - 42,662,761 (-)NCBICelera
Cytogenetic Map16q21NCBI
HuRef1644,014,719 - 44,031,168 (-)NCBIHuRef
CHM1_11659,554,542 - 59,570,329 (-)NCBICHM1_1
T2T-CHM13v2.01663,908,917 - 63,925,035 (-)NCBIT2T-CHM13v2.0
Cfap20
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39896,146,867 - 96,161,716 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl896,146,877 - 96,161,497 (-)EnsemblGRCm39 Ensembl
GRCm38895,420,249 - 95,434,869 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl895,420,249 - 95,434,869 (-)EnsemblGRCm38mm10GRCm38
MGSCv37897,944,149 - 97,958,769 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36898,309,381 - 98,323,921 (-)NCBIMGSCv36mm8
Celera899,735,109 - 99,749,735 (-)NCBICelera
Cytogenetic Map8C5NCBI
cM Map847.12NCBI
Cfap20
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543315,648,099 - 15,663,502 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543315,648,529 - 15,663,308 (-)NCBIChiLan1.0ChiLan1.0
CFAP20
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21867,587,278 - 67,602,717 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11673,508,168 - 73,523,603 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01638,392,912 - 38,408,320 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11657,524,195 - 57,539,638 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1657,524,195 - 57,539,638 (-)Ensemblpanpan1.1panPan2
CFAP20
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1258,445,932 - 58,459,437 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl258,445,927 - 58,459,779 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha255,075,887 - 55,089,744 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0258,984,422 - 58,998,257 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl258,984,403 - 58,998,253 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1255,815,965 - 55,829,801 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0256,823,530 - 56,837,397 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0257,716,352 - 57,730,234 (+)NCBIUU_Cfam_GSD_1.0
Cfap20
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934949,565,422 - 49,577,404 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647510,011,616 - 10,023,756 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647510,011,671 - 10,023,643 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CFAP20
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl619,954,925 - 19,969,347 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1619,954,698 - 19,969,383 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2617,978,593 - 17,993,262 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CFAP20
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1544,047,860 - 44,063,605 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl544,047,464 - 44,063,738 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604732,114,936 - 32,130,731 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cfap20
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474628,071,519 - 28,085,231 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474628,071,502 - 28,085,040 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cfap20
80 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:255
Count of miRNA genes:175
Interacting mature miRNAs:205
Transcripts:ENSRNOT00000061392
Prediction methods:Microtar, 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
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19131963836Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19136824771Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19128982497Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19136824771Rat
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127355345Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
7411590Foco7Food consumption QTL 76.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)19124688055Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19128982497Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19136824771Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19136824771Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat

Markers in Region
RH125490  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2199,622,331 - 9,622,452 (+)MAPPERmRatBN7.2
Rnor_6.01910,038,608 - 10,038,728NCBIRnor6.0
Rnor_5.01910,022,755 - 10,022,875UniSTSRnor5.0
RGSC_v3.41910,081,222 - 10,081,342UniSTSRGSC3.4
Celera199,513,832 - 9,513,952UniSTS
Cytogenetic Map19p13UniSTS


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
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000061392   ⟹   ENSRNOP00000058109
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl199,608,859 - 9,622,540 (+)Ensembl
Rnor_6.0 Ensembl1910,024,947 - 10,038,784 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000111543   ⟹   ENSRNOP00000082405
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl199,608,859 - 9,620,942 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000113232   ⟹   ENSRNOP00000086249
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl199,608,933 - 9,622,558 (+)Ensembl
RefSeq Acc Id: NM_001037978   ⟹   NP_001033067
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8199,614,978 - 9,628,612 (+)NCBI
mRatBN7.2199,608,923 - 9,622,558 (+)NCBI
Rnor_6.01910,025,024 - 10,038,838 (+)NCBI
Rnor_5.01910,009,188 - 10,022,985 (+)NCBI
RGSC_v3.41910,067,502 - 10,081,452 (+)RGD
Celera199,500,482 - 9,514,062 (+)RGD
Sequence:
RefSeq Acc Id: NM_001399181   ⟹   NP_001386110
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8199,614,978 - 9,628,612 (+)NCBI
mRatBN7.2199,608,923 - 9,622,558 (+)NCBI
RefSeq Acc Id: XM_039097696   ⟹   XP_038953624
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8199,614,265 - 9,628,274 (+)NCBI
mRatBN7.2199,608,867 - 9,621,752 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001033067 (Get FASTA)   NCBI Sequence Viewer  
  NP_001386110 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953624 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH99768 (Get FASTA)   NCBI Sequence Viewer  
  EDL87284 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000058109.4
  ENSRNOP00000082405.1
  ENSRNOP00000086249.1
GenBank Protein Q499T7 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001033067   ⟸   NM_001037978
- Peptide Label: isoform 2
- UniProtKB: Q499T7 (UniProtKB/Swiss-Prot),   A0A8I5ZUW3 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000058109   ⟸   ENSRNOT00000061392
RefSeq Acc Id: XP_038953624   ⟸   XM_039097696
- Peptide Label: isoform X1
Ensembl Acc Id: ENSRNOP00000082405   ⟸   ENSRNOT00000111543
Ensembl Acc Id: ENSRNOP00000086249   ⟸   ENSRNOT00000113232
RefSeq Acc Id: NP_001386110   ⟸   NM_001399181
- Peptide Label: isoform 1
- UniProtKB: A0A0H2UI05 (UniProtKB/TrEMBL),   A0A8I5ZUW3 (UniProtKB/TrEMBL),   A6JY06 (UniProtKB/TrEMBL)
Protein Domains
CFA20

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q499T7-F1-model_v2 AlphaFold Q499T7 1-164 view protein structure

Transcriptome

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

Promoters
RGD ID:13700928
Promoter ID:EPDNEW_R11452
Type:initiation region
Name:Cfap20_1
Description:cilia and flagella associated protein 20
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_6.01910,025,008 - 10,025,068EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308493 AgrOrtholog
BioCyc Gene G2FUF-6532 BioCyc
Ensembl Genes ENSRNOG00000042179 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000061392.5 UniProtKB/TrEMBL
  ENSRNOT00000111543.1 UniProtKB/TrEMBL
  ENSRNOT00000113232.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7932140 IMAGE-MGC_LOAD
InterPro CFA20/C3orf67 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CFA20_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:307642 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124689 IMAGE-MGC_LOAD
NCBI Gene 307642 ENTREZGENE
PANTHER CILIA- AND FLAGELLA-ASSOCIATED PROTEIN 20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR12458 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam DUF667 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cfap20 PhenoGen
RatGTEx ENSRNOG00000042179 RatGTEx
UniProt A0A0H2UI05 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZUW3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6A0V5_RAT UniProtKB/TrEMBL
  A6JY06 ENTREZGENE, UniProtKB/TrEMBL
  CFA20_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-07-09 Cfap20  cilia and flagella associated protein 20  Gtl3  gene trap locus 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Gtl3  gene trap locus 3  Gtl3_predicted  gene trap locus 3 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Gtl3_predicted  gene trap locus 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED