Cfap96 (cilia and flagella associated protein 96) - Rat Genome Database

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Gene: Cfap96 (cilia and flagella associated protein 96) Rattus norvegicus
Analyze
Symbol: Cfap96
Name: cilia and flagella associated protein 96
RGD ID: 1564308
Description: Predicted to be located in 9+0 non-motile cilium. Predicted to be active in centrosome and cytoplasmic microtubule. Orthologous to human CFAP96 (cilia and flagella associated protein 96); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: C16h4orf47; cilia-and flagella-associated protein 96; LOC100911106; LOC502086; RGD1564308; similar to human chromosome 4 open reading frame 47; similar to LOC495042 protein; uncharacterized protein LOC502086; UPF0602 protein C4orf47 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
GRCr81653,023,623 - 53,048,176 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1653,023,878 - 53,048,965 (+)EnsemblGRCr8
mRatBN7.21646,291,075 - 46,315,616 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1646,291,311 - 46,315,625 (+)EnsemblmRatBN7.2
Rnor_6.01649,485,022 - 49,509,756 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1649,485,256 - 49,509,767 (+)Ensemblrn6Rnor6.0
Rnor_5.01649,211,727 - 49,236,305 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41649,573,429 - 49,596,596 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1644,289,273 - 44,313,879 (+)NCBICelera
Cytogenetic Map16q11NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
9+0 non-motile cilium  (IEA,ISO)
centrosome  (IBA,IEA,ISO)
cytoplasmic microtubule  (IBA,IEA,ISO)

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:25074808  


Genomics

Comparative Map Data
Cfap96
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81653,023,623 - 53,048,176 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1653,023,878 - 53,048,965 (+)EnsemblGRCr8
mRatBN7.21646,291,075 - 46,315,616 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1646,291,311 - 46,315,625 (+)EnsemblmRatBN7.2
Rnor_6.01649,485,022 - 49,509,756 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1649,485,256 - 49,509,767 (+)Ensemblrn6Rnor6.0
Rnor_5.01649,211,727 - 49,236,305 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41649,573,429 - 49,596,596 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1644,289,273 - 44,313,879 (+)NCBICelera
Cytogenetic Map16q11NCBI
CFAP96
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh384185,408,434 - 185,449,826 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl4185,426,014 - 185,449,828 (+)Ensemblhg38GRCh38
GRCh374186,347,408 - 186,370,980 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 364186,584,397 - 186,607,976 (+)NCBIBuild 36Build 36hg18NCBI36
Celera4183,676,735 - 183,698,471 (+)NCBICelera
Cytogenetic Map4q35.1NCBI
HuRef4182,103,998 - 182,124,561 (+)NCBIHuRef
CHM1_14186,326,952 - 186,347,263 (+)NCBICHM1_1
T2T-CHM13v2.04188,748,560 - 188,793,104 (+)NCBIT2T-CHM13v2.0
Cfap96
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39846,387,980 - 46,428,290 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl846,406,643 - 46,428,477 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38845,939,196 - 45,975,488 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl845,953,606 - 45,975,440 (-)Ensemblmm10GRCm38
GRCm38.p6 Ensembl845,953,606 - 45,975,252 (-)Ensemblmm10GRCm38
MGSCv37847,038,960 - 47,060,606 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36847,452,423 - 47,474,069 (-)NCBIMGSCv36mm8
Celera848,636,534 - 48,658,134 (-)NCBICelera
Cytogenetic Map8B1.1NCBI
cM Map825.94NCBI
Cfap96
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540323,619,399 - 23,634,731 (-)Ensembl
ChiLan1.0NW_00495540323,617,764 - 23,634,689 (-)NCBIChiLan1.0ChiLan1.0
CFAP96
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v23183,161,235 - 183,184,786 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan14183,509,622 - 183,533,153 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v04177,589,308 - 177,612,834 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.14189,805,849 - 189,828,919 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4189,805,849 - 189,828,919 (+)EnsemblpanPan2panpan1.1
CFAP96
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11645,175,351 - 45,208,647 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1645,192,032 - 45,207,964 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1645,659,950 - 45,696,251 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01647,388,187 - 47,424,657 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1647,407,942 - 47,421,691 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11645,356,199 - 45,392,486 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01645,968,604 - 46,005,328 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01646,100,390 - 46,136,694 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Cfap96
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494334,184,084 - 34,200,991 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365543,908,413 - 3,925,942 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365543,908,570 - 3,925,957 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CFAP96
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1546,470,765 - 46,490,006 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11546,470,680 - 46,612,173 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21553,252,277 - 53,271,631 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CFAP96
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.17131,375,653 - 131,399,429 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl7131,375,619 - 131,399,235 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666037111,637,331 - 111,661,131 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cfap96
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476916,283,614 - 16,307,579 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462476916,281,200 - 16,314,879 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Cfap96
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11341,916,101 - 41,940,866 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Cfap96
132 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:17
Count of miRNA genes:16
Interacting mature miRNAs:17
Transcripts:ENSRNOT00000059317
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)164445512389455123Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)163692878281928782Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)164199206486992064Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16423421266955197Rat
2302057Pia29Pristane induced arthritis QTL 293.60.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)162846870173468701Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164909919691442908Rat
1357403Slep4Serum leptin concentration QTL 43.91blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)163236104377361043Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16423421253708481Rat
631833Sach2Saccharin preference QTL 240.01consumption behavior trait (VT:0002069)calculated saccharin drink intake rate (CMO:0001613)164975766656898388Rat
8694453Bw172Body weight QTL 1728.330.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)163105803976058039Rat
1298529Arunc1Aerobic running capacity QTL 14exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)163439829479398294Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683908666195506Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683908666195506Rat
6903294Stl30Serum triglyceride level QTL 302.60.0013blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)163188527176885271Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)164445512389455123Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683908666195506Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161773081872536785Rat
2301406Kidm39Kidney mass QTL 390.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)161590580260905802Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683908666195506Rat


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
13 10 56 146 80 79 48 34 48 6 267 121 10 125 77 89 31 12 12

Sequence


Ensembl Acc Id: ENSRNOT00000059317   ⟹   ENSRNOP00000056079
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1653,023,878 - 53,048,965 (+)Ensembl
mRatBN7.2 Ensembl1646,291,311 - 46,315,625 (+)Ensembl
Rnor_6.0 Ensembl1649,485,256 - 49,509,767 (+)Ensembl
RefSeq Acc Id: XM_006253169   ⟹   XP_006253231
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81653,023,863 - 53,048,176 (+)NCBI
mRatBN7.21646,291,310 - 46,315,616 (+)NCBI
Rnor_6.01649,485,119 - 49,509,756 (+)NCBI
Rnor_5.01649,211,727 - 49,236,305 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006253170   ⟹   XP_006253232
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81653,023,623 - 53,048,176 (+)NCBI
mRatBN7.21646,291,075 - 46,315,616 (+)NCBI
Rnor_6.01649,485,022 - 49,509,756 (+)NCBI
Rnor_5.01649,211,727 - 49,236,305 (+)NCBI
Sequence:
RefSeq Acc Id: XM_577523   ⟹   XP_577523
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81653,023,871 - 53,048,176 (+)NCBI
mRatBN7.21646,291,306 - 46,315,616 (+)NCBI
Rnor_6.01649,485,119 - 49,509,756 (+)NCBI
Rnor_5.01649,211,727 - 49,236,305 (+)NCBI
RGSC_v3.41649,573,429 - 49,596,596 (+)RGD
Sequence:
RefSeq Acc Id: XP_577523   ⟸   XM_577523
- Sequence:
RefSeq Acc Id: XP_006253232   ⟸   XM_006253170
- Sequence:
RefSeq Acc Id: XP_006253231   ⟸   XM_006253169
- Sequence:
Ensembl Acc Id: ENSRNOP00000056079   ⟸   ENSRNOT00000059317

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZVL4-F1-model_v2 AlphaFold D3ZVL4 1-316 view protein structure

Transcriptome

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

Promoters
RGD ID:13700112
Promoter ID:EPDNEW_R10628
Type:initiation region
Name:RGD1564308_1
Description:similar to LOC495042 protein
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_6.01649,485,225 - 49,485,285EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564308 AgrOrtholog
BioCyc Gene G2FUF-11330 BioCyc
Ensembl Genes ENSRNOG00000038819 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000059317 ENTREZGENE
  ENSRNOT00000059317.5 UniProtKB/TrEMBL
InterPro DUF4586 UniProtKB/TrEMBL
KEGG Report rno:502086 UniProtKB/TrEMBL
NCBI Gene 502086 ENTREZGENE
PANTHER PTHR31144 UniProtKB/TrEMBL
  UPF0602 PROTEIN C4ORF47 UniProtKB/TrEMBL
Pfam DUF4586 UniProtKB/TrEMBL
PhenoGen Cfap96 PhenoGen
RatGTEx ENSRNOG00000038819 RatGTEx
UniProt A6JPQ5 ENTREZGENE, UniProtKB/TrEMBL
  D3ZVL4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-05-12 Cfap96  cilia and flagella associated protein 96  C16h4orf47  similar to human chromosome 4 open reading frame 47  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2022-07-13 C16h4orf47  similar to human chromosome 4 open reading frame 47  RGD1564308  similar to LOC495042 protein  Name and Symbol changed 629549 APPROVED
2021-03-09 RGD1564308  similar to LOC495042 protein  LOC100911106  UPF0602 protein C4orf47 homolog  Data merged from RGD:6495075 737654 PROVISIONAL
2012-07-05 LOC100911106  UPF0602 protein C4orf47 homolog      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 RGD1564308  similar to LOC495042 protein   RGD1564308_predicted  similar to LOC495042 protein (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1564308_predicted  similar to LOC495042 protein (predicted)  LOC502086  similar to LOC495042 protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC502086  similar to LOC495042 protein      Symbol and Name status set to provisional 70820 PROVISIONAL