Cfc1 (cripto, FRL-1, cryptic family 1) - Rat Genome Database

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Gene: Cfc1 (cripto, FRL-1, cryptic family 1) Rattus norvegicus
Analyze
Symbol: Cfc1
Name: cripto, FRL-1, cryptic family 1
RGD ID: 1562188
Description: Predicted to enable activin receptor binding activity and nodal binding activity. Involved in female pregnancy. Predicted to be active in cell surface and extracellular region. Human ortholog(s) of this gene implicated in tetralogy of Fallot and visceral heterotaxy. Orthologous to human CFC1 (cryptic, EGF-CFC family member 1) and CFC1B (cryptic, EGF-CFC family member 1B); INTERACTS WITH 17beta-estradiol 3-benzoate; 6-propyl-2-thiouracil; acrylamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: cryptic protein; LOC501121; RGD1562188; similar to CRYPTIC
RGD Orthologs
Human
Mouse
Bonobo
Dog
Pig
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8944,234,997 - 44,247,846 (+)NCBIGRCr8
mRatBN7.2936,742,106 - 36,751,931 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl936,739,071 - 36,751,930 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx945,241,509 - 45,248,846 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0950,372,685 - 50,380,022 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0948,654,596 - 48,661,933 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0941,045,352 - 41,051,979 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl941,045,363 - 41,052,024 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0940,715,518 - 40,722,102 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4933,280,037 - 33,287,118 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera934,533,261 - 34,540,347 (+)NCBICelera
Cytogenetic Map9q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Embryo presence regulates NODAL/LEFTY2 system in the rat oviduct in vivo. Argañaraz ME, etal., Mol Reprod Dev. 2019 Nov;86(11):1652-1662. doi: 10.1002/mrd.23254. Epub 2019 Aug 16.
2. Loss-of-function mutations in the EGF-CFC gene CFC1 are associated with human left-right laterality defects. Bamford RN, etal., Nat Genet. 2000 Nov;26(3):365-9. doi: 10.1038/81695.
3. Duplication and deletion of CFC1 associated with heterotaxy syndrome. Cao R, etal., DNA Cell Biol. 2015 Feb;34(2):101-6. doi: 10.1089/dna.2014.2616. Epub 2014 Nov 25.
4. A role of the cryptic gene in the correct establishment of the left-right axis. Gaio U, etal., Curr Biol. 1999 Nov 18;9(22):1339-42. doi: 10.1016/s0960-9822(00)80059-7.
5. 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.
6. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Association of promoter methylation statuses of congenital heart defect candidate genes with Tetralogy of Fallot. Sheng W, etal., J Transl Med. 2014 Jan 31;12:31. doi: 10.1186/1479-5876-12-31.
Additional References at PubMed
PMID:10521397   PMID:11412024   PMID:12052855   PMID:17360443   PMID:25807483  


Genomics

Comparative Map Data
Cfc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8944,234,997 - 44,247,846 (+)NCBIGRCr8
mRatBN7.2936,742,106 - 36,751,931 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl936,739,071 - 36,751,930 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx945,241,509 - 45,248,846 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0950,372,685 - 50,380,022 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0948,654,596 - 48,661,933 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0941,045,352 - 41,051,979 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl941,045,363 - 41,052,024 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0940,715,518 - 40,722,102 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4933,280,037 - 33,287,118 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera934,533,261 - 34,540,347 (+)NCBICelera
Cytogenetic Map9q21NCBI
CFC1B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382130,521,222 - 130,528,603 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2130,521,197 - 130,528,604 (+)EnsemblGRCh38hg38GRCh38
GRCh372131,278,795 - 131,286,176 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362130,995,137 - 131,002,035 (+)NCBINCBI36Build 36hg18NCBI36
Cytogenetic Map2q21.1NCBI
HuRef2123,494,573 - 123,501,471 (-)NCBIHuRef
T2T-CHM13v2.02130,955,059 - 130,962,469 (+)NCBIT2T-CHM13v2.0
Cfc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39134,574,729 - 34,583,392 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl134,574,729 - 34,583,394 (+)EnsemblGRCm39 Ensembl
GRCm38134,535,648 - 34,544,311 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl134,535,648 - 34,544,313 (+)EnsemblGRCm38mm10GRCm38
MGSCv37134,592,493 - 34,601,156 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36134,480,194 - 34,488,857 (+)NCBIMGSCv36mm8
Celera134,300,622 - 34,309,253 (+)NCBICelera
Cytogenetic Map1BNCBI
cM Map113.34NCBI
CFC1B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21344,953,766 - 44,962,222 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B44,968,741 - 44,977,173 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B29,354,004 - 29,362,161 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B131,440,871 - 131,448,310 (+)NCBIpanpan1.1PanPan1.1panPan2
LOC609557
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11920,318,937 - 20,384,369 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1920,622,155 - 20,687,786 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01921,635,233 - 21,700,948 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1921,690,527 - 21,700,978 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11920,274,928 - 20,339,946 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01920,565,378 - 20,602,313 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01921,578,101 - 21,643,757 (+)NCBIUU_Cfam_GSD_1.0
CFC1B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11556,943,183 - 56,951,929 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215156,796,746 - 156,838,845 (-)NCBISscrofa10.2Sscrofa10.2susScr3

Variants

.
Variants in Cfc1
74 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:35
Count of miRNA genes:33
Interacting mature miRNAs:35
Transcripts:ENSRNOT00000066284
Prediction methods: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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)93253550577535505Rat
1300180Bw14Body weight QTL 143.776body mass (VT:0001259)body weight (CMO:0000012)92375402461381613Rat
631680Cm11Cardiac mass QTL 113.10.00089heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)92043051965430519Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)92526804479271759Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
7207805Bmd88Bone mineral density QTL 884femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)92375402458157242Rat
631643Bp120Blood pressure QTL 12030.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)92207120067071200Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)9895256053952560Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9510982650109826Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9895256053952560Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92207116986369743Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)92375414483851531Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9510982642921101Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
724543Cm20Cardiac mass QTL 203.9heart mass (VT:0007028)calculated heart weight (CMO:0000073)91696139840594091Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)91353377042791750Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9728325252283252Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)93253550577535505Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1598823Memor16Memory QTL 161.9exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)92213332249968732Rat
1641894Alcrsp12Alcohol response QTL 12response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)92746863972468639Rat

Markers in Region
AW531099  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2936,751,748 - 36,751,930 (+)MAPPERmRatBN7.2
Rnor_6.0941,051,798 - 41,051,979NCBIRnor6.0
Rnor_5.0940,721,921 - 40,722,102UniSTSRnor5.0
RGSC_v3.4933,286,937 - 33,287,118UniSTSRGSC3.4
Celera934,540,166 - 34,540,347UniSTS
RH 3.4 Map9353.2UniSTS
Cytogenetic Map9q21UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 12 29 39 53 27 9 27 70 21 29 13 46 26

Sequence


Ensembl Acc Id: ENSRNOT00000066284   ⟹   ENSRNOP00000062738
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl936,744,591 - 36,751,930 (+)Ensembl
Rnor_6.0 Ensembl941,045,363 - 41,052,024 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000104316   ⟹   ENSRNOP00000084880
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl936,739,071 - 36,751,930 (+)Ensembl
RefSeq Acc Id: NM_001109304   ⟹   NP_001102774
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8944,240,508 - 44,247,845 (+)NCBI
mRatBN7.2936,744,591 - 36,751,930 (+)NCBI
Rnor_6.0941,045,352 - 41,051,979 (+)NCBI
Rnor_5.0940,715,518 - 40,722,102 (+)NCBI
RGSC_v3.4933,280,037 - 33,287,118 (+)RGD
Celera934,533,261 - 34,540,347 (+)RGD
Sequence:
RefSeq Acc Id: XM_039084069   ⟹   XP_038939997
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8944,235,014 - 44,247,846 (+)NCBI
mRatBN7.2936,742,106 - 36,751,931 (+)NCBI
RefSeq Acc Id: XM_063267583   ⟹   XP_063123653
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8944,235,056 - 44,247,846 (+)NCBI
RefSeq Acc Id: XM_063267584   ⟹   XP_063123654
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8944,234,997 - 44,247,846 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001102774 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939997 (Get FASTA)   NCBI Sequence Viewer  
  XP_063123653 (Get FASTA)   NCBI Sequence Viewer  
  XP_063123654 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL99305 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000062738.4
  ENSRNOP00000084880.1
RefSeq Acc Id: NP_001102774   ⟸   NM_001109304
- UniProtKB: A0A8I6GC89 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000062738   ⟸   ENSRNOT00000066284
RefSeq Acc Id: XP_038939997   ⟸   XM_039084069
- Peptide Label: isoform X1
- UniProtKB: A0A8I6GC89 (UniProtKB/TrEMBL),   A6INA5 (UniProtKB/TrEMBL),   F1LV65 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000084880   ⟸   ENSRNOT00000104316
RefSeq Acc Id: XP_063123654   ⟸   XM_063267584
- Peptide Label: isoform X1
- UniProtKB: A0A8I6GC89 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063123653   ⟸   XM_063267583
- Peptide Label: isoform X1
- UniProtKB: A0A8I6GC89 (UniProtKB/TrEMBL)
Protein Domains
EGF-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LV65-F1-model_v2 AlphaFold F1LV65 1-164 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562188 AgrOrtholog
BioCyc Gene G2FUF-27858 BioCyc
Ensembl Genes ENSRNOG00000042646 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066284.4 UniProtKB/TrEMBL
  ENSRNOT00000104316.1 UniProtKB/TrEMBL
Gene3D-CATH Laminin UniProtKB/TrEMBL
InterPro Cryptic/Cripto_CFC-dom UniProtKB/TrEMBL
  Dev_Signal_Modulators UniProtKB/TrEMBL
  EGF_3 UniProtKB/TrEMBL
KEGG Report rno:501121 UniProtKB/TrEMBL
NCBI Gene 501121 ENTREZGENE
PANTHER CRYPTIC FAMILY PROTEIN 1B-RELATED UniProtKB/TrEMBL
  EGF-LIKE-DOMAIN, MULTIPLE 7, 8 UniProtKB/TrEMBL
Pfam CFC UniProtKB/TrEMBL
PhenoGen Cfc1 PhenoGen
PROSITE EGF_1 UniProtKB/TrEMBL
  EGF_3 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000042646 RatGTEx
Superfamily-SCOP EGF/Laminin UniProtKB/TrEMBL
UniProt A0A8I6GC89 ENTREZGENE, UniProtKB/TrEMBL
  A6INA5 ENTREZGENE, UniProtKB/TrEMBL
  F1LV65 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-29 Cfc1  cripto, FRL-1, cryptic family 1  RGD1562188_predicted  similar to CRYPTIC (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1562188_predicted  similar to CRYPTIC (predicted)  LOC501121  similar to CRYPTIC  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC501121  similar to CRYPTIC      Symbol and Name status set to provisional 70820 PROVISIONAL