Cacfd1 (calcium channel flower domain containing 1) - Rat Genome Database

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Gene: Cacfd1 (calcium channel flower domain containing 1) Rattus norvegicus
Analyze
Symbol: Cacfd1
Name: calcium channel flower domain containing 1
RGD ID: 1311501
Description: Predicted to be involved in vesicle-mediated transport. Predicted to be located in Golgi apparatus; plasma membrane; and synaptic vesicle. Orthologous to human CACFD1 (calcium channel flower domain containing 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: calcium channel flower domain-containing protein 1; calcium channel flower homolog; Fwe; Fwe2; hypothetical protein LOC296599; LOC296599; RGD1311501; similar to chromosome 9 open reading frame 7
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
GRCr8330,733,958 - 30,750,237 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl330,736,637 - 30,744,764 (+)EnsemblGRCr8
mRatBN7.2310,335,881 - 10,352,437 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl310,335,881 - 10,343,406 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx313,395,897 - 13,406,703 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0321,981,298 - 21,992,104 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0320,236,599 - 20,247,405 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.035,555,807 - 5,571,205 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl35,555,807 - 5,572,064 (+)Ensemblrn6Rnor6.0
Rnor_5.0310,917,547 - 10,932,900 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.435,905,478 - 5,916,284 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera35,133,913 - 5,144,719 (+)NCBICelera
RGSC_v3.135,908,674 - 5,917,132 (+)NCBI
Cytogenetic Map3p12NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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. 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:28414717  


Genomics

Comparative Map Data
Cacfd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8330,733,958 - 30,750,237 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl330,736,637 - 30,744,764 (+)EnsemblGRCr8
mRatBN7.2310,335,881 - 10,352,437 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl310,335,881 - 10,343,406 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx313,395,897 - 13,406,703 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0321,981,298 - 21,992,104 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0320,236,599 - 20,247,405 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.035,555,807 - 5,571,205 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl35,555,807 - 5,572,064 (+)Ensemblrn6Rnor6.0
Rnor_5.0310,917,547 - 10,932,900 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.435,905,478 - 5,916,284 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera35,133,913 - 5,144,719 (+)NCBICelera
RGSC_v3.135,908,674 - 5,917,132 (+)NCBI
Cytogenetic Map3p12NCBI
CACFD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389133,459,978 - 133,470,848 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9133,459,965 - 133,470,848 (+)Ensemblhg38GRCh38
GRCh379136,325,100 - 136,335,970 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369135,314,952 - 135,325,706 (+)NCBIBuild 36Build 36hg18NCBI36
Build 349133,354,684 - 133,365,439NCBI
Celera9106,875,680 - 106,886,533 (+)NCBICelera
Cytogenetic Map9q34.2NCBI
HuRef9105,826,781 - 105,837,598 (+)NCBIHuRef
CHM1_19136,475,590 - 136,486,412 (+)NCBICHM1_1
T2T-CHM13v2.09145,674,420 - 145,685,255 (+)NCBIT2T-CHM13v2.0
Cacfd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39226,899,867 - 26,911,102 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl226,899,938 - 26,911,101 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38227,009,855 - 27,021,090 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl227,009,926 - 27,021,089 (+)Ensemblmm10GRCm38
MGSCv37226,865,486 - 26,876,609 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36226,831,959 - 26,843,098 (+)NCBIMGSCv36mm8
Celera226,722,797 - 26,723,730 (+)NCBICelera
Cytogenetic Map2A3NCBI
cM Map219.17NCBI
Cacfd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555132,787,099 - 2,796,132 (+)Ensembl
ChiLan1.0NW_0049555132,787,098 - 2,796,132 (+)NCBIChiLan1.0ChiLan1.0
CACFD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2115,882,653 - 5,893,642 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan195,884,989 - 5,895,983 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09104,582,983 - 104,593,960 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19133,194,490 - 133,205,686 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9133,194,490 - 133,205,686 (+)EnsemblpanPan2panpan1.1
CACFD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1949,868,218 - 49,878,254 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha949,148,870 - 49,159,388 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0950,741,637 - 50,752,154 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl950,741,595 - 50,752,149 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1949,503,703 - 49,514,206 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0949,845,445 - 49,855,955 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0949,923,585 - 49,934,115 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Cacfd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947199,926,387 - 199,934,113 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366693,441,018 - 3,448,669 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366693,439,174 - 3,448,637 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CACFD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1273,056,532 - 273,066,914 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11273,045,620 - 273,066,916 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21307,030,340 - 307,040,730 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CACFD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1124,665,927 - 4,676,671 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl124,668,013 - 4,676,571 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666058312,533 - 323,324 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cacfd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247601,889,949 - 1,897,703 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247601,889,793 - 1,897,703 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Cacfd1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v159,633,336 - 9,646,721 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Cacfd1
133 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:87
Count of miRNA genes:74
Interacting mature miRNAs:77
Transcripts:ENSRNOT00000007677
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)32267715050766390Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)32905627547904329Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
10450811Scl73Serum cholesterol level QTL 734.70.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3655634751556347Rat
10450808Scl72Serum cholesterol level QTL 724.40.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
10450806Scl71Serum cholesterol level QTL 715.80.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)32862533967641995Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)3612543751125437Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3136721849Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31141509147Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3655634751556347Rat
1558657Cm43Cardiac mass QTL 436.63e-08heart mass (VT:0007028)heart wet weight (CMO:0000069)32267715050766390Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)31527234860272348Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)32905627547904329Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35675975141509147Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3655634751556347Rat

Markers in Region
BF414460  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2310,343,352 - 10,343,472 (+)MAPPERmRatBN7.2
Rnor_6.035,563,279 - 5,563,398NCBIRnor6.0
Rnor_5.0310,925,019 - 10,925,138UniSTSRnor5.0
RGSC_v3.435,912,950 - 5,913,069UniSTSRGSC3.4
Celera35,141,385 - 5,141,504UniSTS
RH 3.4 Map311.1UniSTS
Cytogenetic Map3p12UniSTS


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
16 12 67 163 91 90 59 92 59 6 356 192 11 142 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000007677   ⟹   ENSRNOP00000007677
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl330,736,637 - 30,741,483 (+)Ensembl
mRatBN7.2 Ensembl310,335,881 - 10,343,406 (+)Ensembl
Rnor_6.0 Ensembl35,555,807 - 5,566,613 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000083078   ⟹   ENSRNOP00000072807
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl35,558,680 - 5,572,064 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000155871   ⟹   ENSRNOP00000109944
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl330,736,637 - 30,744,764 (+)Ensembl
RefSeq Acc Id: NM_001106561   ⟹   NP_001100031
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8330,733,958 - 30,744,764 (+)NCBI
mRatBN7.2310,335,881 - 10,346,687 (+)NCBI
Rnor_6.035,555,807 - 5,566,613 (+)NCBI
Rnor_5.0310,917,547 - 10,932,900 (+)NCBI
RGSC_v3.435,905,478 - 5,916,284 (+)RGD
Celera35,133,913 - 5,144,719 (+)RGD
Sequence:
RefSeq Acc Id: XM_006233756   ⟹   XP_006233818
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8330,736,838 - 30,750,237 (+)NCBI
mRatBN7.2310,338,750 - 10,352,437 (+)NCBI
Rnor_6.035,558,637 - 5,571,205 (+)NCBI
Rnor_5.0310,917,547 - 10,932,900 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008761633   ⟹   XP_008759855
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8330,736,838 - 30,746,194 (+)NCBI
mRatBN7.2310,338,750 - 10,347,990 (+)NCBI
Rnor_6.035,558,635 - 5,568,037 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039104726   ⟹   XP_038960654
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8330,736,838 - 30,742,862 (+)NCBI
mRatBN7.2310,338,750 - 10,344,773 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001100031 (Get FASTA)   NCBI Sequence Viewer  
  XP_006233818 (Get FASTA)   NCBI Sequence Viewer  
  XP_008759855 (Get FASTA)   NCBI Sequence Viewer  
  XP_038960654 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein D4A9I3 (Get FASTA)   NCBI Sequence Viewer  
  EDL93448 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000109944
RefSeq Acc Id: NP_001100031   ⟸   NM_001106561
- UniProtKB: D4A9I3 (UniProtKB/Swiss-Prot),   A6JTJ9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233818   ⟸   XM_006233756
- Peptide Label: isoform X1
- UniProtKB: D4A9I3 (UniProtKB/Swiss-Prot),   A6JTJ9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008759855   ⟸   XM_008761633
- Peptide Label: isoform X3
- Sequence:
Ensembl Acc Id: ENSRNOP00000072807   ⟸   ENSRNOT00000083078
Ensembl Acc Id: ENSRNOP00000007677   ⟸   ENSRNOT00000007677
RefSeq Acc Id: XP_038960654   ⟸   XM_039104726
- Peptide Label: isoform X2
- UniProtKB: A0A8L2Q414 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000109944   ⟸   ENSRNOT00000155871

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A9I3-F1-model_v2 AlphaFold D4A9I3 1-171 view protein structure

Transcriptome

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

Promoters
RGD ID:13691923
Promoter ID:EPDNEW_R2446
Type:initiation region
Name:Cacfd1_1
Description:calcium channel flower domain containing 1
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_6.035,558,666 - 5,558,726EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311501 AgrOrtholog
BioCyc Gene G2FUF-50310 BioCyc
Ensembl Genes ENSRNOG00000005840 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000155871 ENTREZGENE
InterPro TVP18/Ca-channel_flower UniProtKB/Swiss-Prot
KEGG Report rno:296599 UniProtKB/Swiss-Prot
NCBI Gene 296599 ENTREZGENE
PANTHER CALCIUM CHANNEL FLOWER HOMOLOG UniProtKB/Swiss-Prot
  PTHR13314 UniProtKB/Swiss-Prot
Pfam Cg6151-P UniProtKB/Swiss-Prot
PhenoGen Cacfd1 PhenoGen
RatGTEx ENSRNOG00000005840 RatGTEx
SMART Cg6151-P UniProtKB/Swiss-Prot
UniProt A0A8L2Q414 ENTREZGENE, UniProtKB/TrEMBL
  A6JTJ9 ENTREZGENE, UniProtKB/TrEMBL
  D4A9I3 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-10-10 Cacfd1  calcium channel flower domain containing 1  RGD1311501  similar to chromosome 9 open reading frame 7  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1311501  similar to chromosome 9 open reading frame 7   RGD1311501_predicted  similar to chromosome 9 open reading frame 7 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1311501_predicted  similar to chromosome 9 open reading frame 7 (predicted)  LOC296599_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC296599_predicted  similar to chromosome 9 open reading frame 7 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL