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Gene: Cacfd1 (calcium channel flower domain containing 1) Ictidomys tridecemlineatus

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Symbol:

Cacfd1

Name:

calcium channel flower domain containing 1

RGD ID:

12532668

Description:

INVOLVED IN vesicle-mediated transport (inferred); ASSOCIATED WITH developmental and epileptic encephalopathy 14 (ortholog); Ehlers-Danlos syndrome classic type 1 (ortholog); Kleefstra syndrome 1 (ortholog); FOUND IN endomembrane system (inferred); membrane (inferred)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

calcium channel flower homolog

RGD Orthologs

Alliance Orthologs

More Info

more info ...

Latest Assembly:

SpeTri2.0 - Squirrel SpeTri2.0 Assembly

Position:

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404947	199,926,387 - 199,934,113 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936669	3,441,018 - 3,448,669 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936669	3,439,174 - 3,448,637 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
Cacfd1	Squirrel	developmental and epileptic encephalopathy 14		ISO	RGD:1322993	8554872	ClinVar Annotator: match by term: Developmental and epileptic encephalopathy, 14	ClinVar	PMID:28492532
Cacfd1	Squirrel	Ehlers-Danlos syndrome classic type 1		ISO	RGD:1322993	8554872	ClinVar Annotator: match by term: Ehlers-Danlos syndrome, classic type	ClinVar	PMID:28492532
Cacfd1	Squirrel	Kleefstra syndrome 1		ISO	RGD:1322993	8554872	ClinVar Annotator: match by term: Kleefstra syndrome 1	ClinVar	PMID:22318994\|PMID:22890305\|PMID:28492532\|PMID:31209758
Cacfd1	Squirrel	Leigh disease		ISO	RGD:1322993	8554872	ClinVar Annotator: match by term: Leigh syndrome	ClinVar	PMID:28492532
Cacfd1	Squirrel	primary coenzyme Q10 deficiency 7		ISO	RGD:1322993	8554872	ClinVar Annotator: match by term: Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome	ClinVar	PMID:28492532
Cacfd1	Squirrel	Rafiq syndrome		ISO	RGD:1322993	8554872	ClinVar Annotator: match by term: Rafiq syndrome	ClinVar	PMID:28492532
Cacfd1	Squirrel	tuberous sclerosis 1		ISO	RGD:1322993	8554872	ClinVar Annotator: match by term: Tuberous sclerosis 1	ClinVar	PMID:28492532

Biological Process

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
Cacfd1	Squirrel	vesicle-mediated transport	involved_in	IEA	PANTHER:PTN000330031	150520179		TreeGrafter	GO_REF:0000118

Cellular Component

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
Cacfd1	Squirrel	endomembrane system	located_in	IEA	UniProtKB-SubCell:SL-0147	150520179		UniProt	GO_REF:0000044
Cacfd1	Squirrel	membrane	located_in	IEA	InterPro:IPR019365	150520179		InterPro	GO_REF:0000002
Cacfd1	Squirrel	membrane	located_in	IEA	UniProtKB-KW:KW-0472	150520179		UniProt	GO_REF:0000043

Molecular Function

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
Cacfd1	Squirrel	protein binding	enables	ISO	UniProtKB:Q96B96	9068941	PMID:21516116, PMID:25416956	IntAct	PMID:21516116\|PMID:25416956
Cacfd1	Squirrel	protein binding	enables	ISO	UniProtKB:Q8N0V3\|UniProtKB:Q96E29\|UniProtKB:Q96T60\|UniProtKB:Q9UBD0\|UniProtKB:Q9UKF7-2\|UniProtKB:Q9ULP0-2\|UniProtKB:Q9Y371	9068941	PMID:32296183	IntAct	PMID:32296183

PMID:22301074	PMID:30032202

Cacfd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404947	199,926,387 - 199,934,113 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936669	3,441,018 - 3,448,669 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936669	3,439,174 - 3,448,637 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CACFD1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	9	133,459,978 - 133,470,848 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	9	133,459,965 - 133,470,848 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	9	136,325,100 - 136,335,970 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	9	135,314,952 - 135,325,706 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	9	133,354,684 - 133,365,439	NCBI
Celera	9	106,875,680 - 106,886,533 (+)	NCBI		Celera
Cytogenetic Map	9	q34.2	NCBI
HuRef	9	105,826,781 - 105,837,598 (+)	NCBI		HuRef
CHM1_1	9	136,475,590 - 136,486,412 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	9	145,674,420 - 145,685,255 (+)	NCBI		T2T-CHM13v2.0

Cacfd1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	26,899,867 - 26,911,102 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	2	26,899,938 - 26,911,101 (+)	Ensembl		GRCm39 Ensembl
GRCm38	2	27,009,855 - 27,021,090 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	27,009,926 - 27,021,089 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	26,865,486 - 26,876,609 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	2	26,831,959 - 26,843,098 (+)	NCBI		MGSCv36	mm8
Celera	2	26,722,797 - 26,723,730 (+)	NCBI		Celera
Cytogenetic Map	2	A3	NCBI
cM Map	2	19.17	NCBI

Cacfd1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	3	30,733,958 - 30,750,237 (+)	NCBI		GRCr8
mRatBN7.2	3	10,335,881 - 10,352,437 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	10,335,881 - 10,343,406 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	13,395,897 - 13,406,703 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	21,981,298 - 21,992,104 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	20,236,599 - 20,247,405 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	5,555,807 - 5,571,205 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	5,555,807 - 5,572,064 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	10,917,547 - 10,932,900 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	5,905,478 - 5,916,284 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	3	5,908,674 - 5,917,132 (+)	NCBI
Celera	3	5,133,913 - 5,144,719 (+)	NCBI		Celera
Cytogenetic Map	3	p12	NCBI

Cacfd1
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955513	2,787,099 - 2,796,132 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955513	2,787,098 - 2,796,132 (+)	NCBI	ChiLan1.0	ChiLan1.0

CACFD1
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	11	5,882,653 - 5,893,642 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	9	5,884,989 - 5,895,983 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	9	104,582,983 - 104,593,960 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	9	133,194,490 - 133,205,686 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	9	133,194,490 - 133,205,686 (+)	Ensembl	panpan1.1		panPan2

CACFD1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	9	49,868,218 - 49,878,254 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
Dog10K_Boxer_Tasha	9	49,148,870 - 49,159,388 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	9	50,741,637 - 50,752,154 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	9	50,741,595 - 50,752,149 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	9	49,503,703 - 49,514,206 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	9	49,845,445 - 49,855,955 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	9	49,923,585 - 49,934,115 (+)	NCBI		UU_Cfam_GSD_1.0

CACFD1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	273,056,532 - 273,066,914 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	273,045,620 - 273,066,916 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	307,030,340 - 307,040,730 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CACFD1
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	12	4,665,927 - 4,676,671 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	12	4,668,013 - 4,676,571 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666058	312,533 - 323,324 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Cacfd1
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624760	1,889,949 - 1,897,703 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624760	1,889,793 - 1,897,703 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.


RefSeq Transcripts	XM_005336961	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_040286576	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAESOR010000006	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSSTOT00000003798 ⟹ ENSSTOP00000003404

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
SpeTri2.0 Ensembl	NW_004936669	3,441,018 - 3,448,669 (-)	Ensembl

RefSeq Acc Id:

XM_005336961 ⟹ XP_005337018

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024404947	199,926,390 - 199,934,113 (+)	NCBI
SpeTri2.0	NW_004936669	3,439,174 - 3,448,637 (-)	NCBI

Sequence:

show sequence

GTCTTTGTGCCGGCCCGGGGCTTCACCAAGGCGCCGCGGCAGCATGAGCGGCTCAGGCGCTGCGGGGGCGTCGGCCAGCCCCGCGCCACCCGCGCAGGAGGAGGGCATGACGTGGTGGTACCGTTGGC
TGTGTCGCCTGTCAGGCGTGCTGGGGGCCATCTCTTGTGCCATCTCCGGACTCTTCAGCTGCATCACTATCTACCCTTTGAAAATTGCCGCTGGCGTGTGGATGATCATGAACGCCTTCGTGCTGTTG
CTGTGTGAGGCGCCCTTCTGCTGCCAGTTCGTGGAGTTTGCAAACACAGTGGCTGAGAGGGTGGACCGGCTGCGCTCCTGGCAGAAGGCTCTCTTCTACTGTGGGATGGCCATCGTCCCCATCATCAT
GAGCCTGAGCCTGACCACACTGCTGGGCAATGCCATCGCCTTTGCCACAGGGGTGCTGTATGGACTTGCTGCCTTGGGCAAAAAGGGTGATGCCATCTCCTATGCCCGGATCCAGCAGCAGAGGCAGC
AGGCAGACGAAGAGAAGCTGGCAGAGACCCTGGAGGGGGAGCTGTGACGAGTCCACAGTGGGGTCCATGGGCTTCTCTGGAGGAAGCAGAGCATCAGCCCTATGGGACAGCCTGGGAGAGGACCCCCC
ACTGCCTGACCCTCTTCTGCCAGCCTGTTCTCCAAGCCTGACTTGGCTGGTGCTCAGGGCCTGGGCTGTATGGCCCATCTCAGTGCAGTGGGGATGGCCACCTGGCCTGATCCTGCCAGCCTGGCTTA
GTGGACTGGGCTTCTGGTGGGTCTGCAGGCCCCACGTGATAGGGTCCACCCCAGGCCTAGGAGCAGCTTCCCCCAGACACACTGGCCCTGGCTGGGAGTTGAGGGGCATGTCACCTGGGCTCTGGACT
CCCCAACCAGGTCCCTGAGGCCCGAGCACTGAAGCTTAGGGAAAGTTTCCCAGCTCTCCTGGCAGGTGGAGTTCCAATCCTGCCCAATTTCCCTGTCCTCAAGGCAGAGGTTGGGGAGAACAATGTCT
CCAAGCTGACTGCTGCTGCCCAGGGACATGGCCAGTCCTCTGGGAGGGAGCCCATAGTGCTCCCAAGTTGCACCCCTGCCCCCACAGCAGGCCTGGCAGTGGCTGGCTGGTCAGGTGGACCCCCTCCC
AGTCCCTGGCATGTTGGACAGGCTCCTCCAGGCACCCTAGCTGCTCTGCCTTCTCAGCTGCCCCAGGCTGCTGGCTTCTGCCTCTCACTCCACCTCAGGCCCTGGTGCTAAGGGGGTGGGGAGTGGTG
CTCATAGGGTCCCACCCACTCCTCTGCTGTGGTCCTGTGGGTGGTAGCAGCTGCGGCATCCTATAGTAGGGACTGAGCTTGGTACACCTCAGGTATGCTTGCCAGCCTGCCCCTGGGGAGCTTCCTGC
CTTTGCAGAGCTGGGCAGAAGCCAGAGCCCATCTCCCCCACAGAGCTATATCCCCTGTCCCAGTGCCAGGCCACCAGGCACAAGCCTCTATGCAGGCACATGGGGAAGCAGGGACCCCTCCTGGATGT
ATCTGTTCATGCCTCCCATCCTCCTCCCACACTGCTGACTCTTCCTTCTGCCCTGTGGCCTTGACCCTGGTTTGATTAGCAGATTGGCTCTTGGCCACTAAGCATATGTCTGACAAGGTCTGGCCACG
CCTCGATGGACCTGGACAGAATAGGCTGCTGTGGAAAACTCTGCTTCTGGGCCCAGCTCCCTGTCTCCCTCCCTCCCAAACCCCCAGGTGGGCCTGCAGTGGGCCCCCAGAACTCAGGGACTGGCTCT
TGCTCCCAGGAAAGCAGCCCCAGGTCTGTTTCCCAGGGGGAACACGCAAGCCTGCAGAGTTTGGGGCTGGGAGCAGGGCCTCTGCCCAGCACTGCCCCAGGACACATCAGTGGGGTCTGGAGTGGGCC
TTGGCCCTCCAGGATCCTGGCCAGGCTCAGTCCTAGGTTGGTGGGACACGTGCCTTCAGGGTTCCTTAAGGGCTACCATCCTCAGGCCATGCTGGGCTCAAAGGGCTATGCGTGTGTGTGCAGTGGTA
AGACCCATCTACCTCCCGGGAGGAGCAGCCCTGCCTGCCCCCCGCTCACTTGTCTGGGTGTGGGGCTTGAGTCACTCCTGCCAGGCCCCAACCCATTCAGAGGGACCTTGCTGCAGGTGCAGGGAGAG
GAGGTGCTGGCTGTGTGTAGTATTAAGGAAGGTGACATCCACCTTGAGGGGAAACCCATTGCTGGGCTGGGCAGGCCATAGGTTGGGTCCGAGGCAGGAGGGCCTTGGTCACAGGCCAGAGTGGGGTG
TTGCTTGCCAGGAGATTCCCAGGTGGCCTGAAGTCAGCTCTGGAGGCCCGCATCGGGGGCGGGGGACATCACTGGGACTCCAGCCCCACACCTCCTCTGTGCCCGTTCCTGGTGTGCTCCTCCATGCA
GCTGCATTTTGAGCAGTAAAGCAGGGCTGCAGTTCCTCCGC

hide sequence

RefSeq Acc Id:

XM_040286576 ⟹ XP_040142510

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024404947	199,926,387 - 199,934,113 (+)	NCBI


Protein RefSeqs	XP_005337018	(Get FASTA)	NCBI Sequence Viewer
	XP_040142510	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSTOP00000003404.2
GenBank Protein	KAG3288280	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	XP_005337018 ⟸ XM_005336961
- Peptide Label:	isoform X1
- UniProtKB:	I3M304 (UniProtKB/TrEMBL)
- Sequence:	show sequence MSGSGAAGASASPAPPAQEEGMTWWYRWLCRLSGVLGAISCAISGLFSCITIYPLKIAAGVWMIMNAFVLLLCEAPFCCQFVEFANTVAERVDRLRSWQKALFYCGMAIVPIIMSLSLTTLLGNAIAF ATGVLYGLAALGKKGDAISYARIQQQRQQADEEKLAETLEGEL hide sequence

RefSeq Acc Id:	XP_040142510 ⟸ XM_040286576
- Peptide Label:	isoform X2

Ensembl Acc Id:

ENSSTOP00000003404 ⟸ ENSSTOT00000003798

Database	Acc Id	Source(s)
Ensembl Genes	ENSSTOG00000003808	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSSTOT00000003798.3	UniProtKB/TrEMBL
InterPro	TVP18/Ca-channel_flower	UniProtKB/TrEMBL
NCBI Gene	Cacfd1	ENTREZGENE
PANTHER	CALCIUM CHANNEL FLOWER HOMOLOG	UniProtKB/TrEMBL
	PTHR13314	UniProtKB/TrEMBL
Pfam	Cg6151-P	UniProtKB/TrEMBL
SMART	Cg6151-P	UniProtKB/TrEMBL
UniProt	I3M304	ENTREZGENE, UniProtKB/TrEMBL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailable


InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailable


Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
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MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable

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