Fyco1 (FYVE and coiled-coil domain autophagy adaptor 1) - Rat Genome Database

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Gene: Fyco1 (FYVE and coiled-coil domain autophagy adaptor 1) Rattus norvegicus
Analyze
Symbol: Fyco1
Name: FYVE and coiled-coil domain autophagy adaptor 1
RGD ID: 1309069
Description: Predicted to enable metal ion binding activity. Predicted to be involved in plus-end-directed vesicle transport along microtubule and positive regulation of autophagosome maturation. Predicted to be located in Golgi apparatus. Predicted to be active in autophagosome; late endosome; and lysosome. Human ortholog(s) of this gene implicated in cataract 18. Orthologous to human FYCO1 (FYVE and coiled-coil domain autophagy adaptor 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; aflatoxin B1.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: FYVE and coiled-coil domain containing 1; FYVE and coiled-coil domain-containing protein 1; LOC301085
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
GRCr88132,289,538 - 132,356,810 (-)NCBIGRCr8
mRatBN7.28123,412,105 - 123,479,315 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8123,412,112 - 123,479,021 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8129,003,808 - 129,071,231 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08127,202,785 - 127,270,208 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08125,032,024 - 125,099,409 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08132,844,042 - 132,910,905 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8132,844,043 - 132,911,193 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08131,995,143 - 132,061,908 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48128,543,895 - 128,612,184 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18128,566,529 - 128,632,267 (-)NCBI
Celera8122,520,323 - 122,587,206 (-)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:19946888   PMID:20100911   PMID:26468287  


Genomics

Comparative Map Data
Fyco1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88132,289,538 - 132,356,810 (-)NCBIGRCr8
mRatBN7.28123,412,105 - 123,479,315 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8123,412,112 - 123,479,021 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8129,003,808 - 129,071,231 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08127,202,785 - 127,270,208 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08125,032,024 - 125,099,409 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08132,844,042 - 132,910,905 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8132,844,043 - 132,911,193 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08131,995,143 - 132,061,908 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48128,543,895 - 128,612,184 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18128,566,529 - 128,632,267 (-)NCBI
Celera8122,520,323 - 122,587,206 (-)NCBICelera
Cytogenetic Map8q32NCBI
FYCO1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38345,917,903 - 45,995,824 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl345,917,903 - 45,995,824 (-)EnsemblGRCh38hg38GRCh38
GRCh37345,959,395 - 46,037,316 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36345,934,399 - 46,012,311 (-)NCBINCBI36Build 36hg18NCBI36
Build 34345,934,399 - 46,012,304NCBI
Celera345,897,023 - 45,974,921 (-)NCBICelera
Cytogenetic Map3p21.31NCBI
HuRef346,003,424 - 46,081,373 (-)NCBIHuRef
CHM1_1345,909,364 - 45,987,237 (-)NCBICHM1_1
T2T-CHM13v2.0345,933,786 - 46,011,702 (-)NCBIT2T-CHM13v2.0
Fyco1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399123,618,565 - 123,681,110 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9123,618,565 - 123,680,964 (-)EnsemblGRCm39 Ensembl
GRCm389123,789,500 - 123,851,899 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9123,789,500 - 123,851,899 (-)EnsemblGRCm38mm10GRCm38
MGSCv379123,698,628 - 123,761,020 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv369123,638,208 - 123,700,267 (-)NCBIMGSCv36mm8
Celera9124,237,925 - 124,300,275 (-)NCBICelera
Cytogenetic Map9F4NCBI
cM Map974.52NCBI
Fyco1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542026,019,514 - 26,074,492 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542026,019,621 - 26,076,846 (+)NCBIChiLan1.0ChiLan1.0
FYCO1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2245,882,811 - 45,960,720 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1345,887,576 - 45,965,488 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0345,825,670 - 45,903,595 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1346,932,148 - 47,009,676 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl346,932,148 - 47,009,676 (-)Ensemblpanpan1.1panPan2
FYCO1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12042,520,241 - 42,593,886 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2042,525,435 - 42,590,243 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2042,436,100 - 42,509,739 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02043,002,992 - 43,076,845 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2043,003,044 - 43,074,828 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12042,244,102 - 42,317,757 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02042,651,320 - 42,724,955 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02042,926,619 - 43,000,264 (+)NCBIUU_Cfam_GSD_1.0
Fyco1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118200,454,799 - 200,532,091 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365963,720 - 81,257 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365963,938 - 81,226 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FYCO1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1329,066,986 - 29,146,755 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11329,068,107 - 29,146,792 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21332,200,269 - 32,239,205 (-)NCBISscrofa10.2Sscrofa10.2susScr3
FYCO1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1227,388,796 - 7,466,463 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl227,388,704 - 7,466,430 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041159,699,253 - 159,777,243 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Fyco1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473074,923,027 - 74,982,990 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473074,923,072 - 74,982,882 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Fyco1
304 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:830
Count of miRNA genes:293
Interacting mature miRNAs:399
Transcripts:ENSRNOT00000008630
Prediction methods:Microtar, Miranda, 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
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat

Markers in Region
BQ205885  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28123,439,115 - 123,439,281 (+)MAPPERmRatBN7.2
Rnor_6.08132,871,049 - 132,871,214NCBIRnor6.0
Rnor_5.08132,022,149 - 132,022,314UniSTSRnor5.0
RGSC_v3.48128,570,901 - 128,571,066UniSTSRGSC3.4
Celera8122,547,331 - 122,547,496UniSTS
RH 3.4 Map81333.2UniSTS
Cytogenetic Map8q32UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 43 41 25 19 25 8 11 4 35 41 11 8
Low 1 16 16 16 70
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008630   ⟹   ENSRNOP00000008630
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8123,412,112 - 123,479,021 (-)Ensembl
Rnor_6.0 Ensembl8132,844,043 - 132,910,905 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000087799   ⟹   ENSRNOP00000073803
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8123,412,112 - 123,467,743 (-)Ensembl
Rnor_6.0 Ensembl8132,846,626 - 132,911,193 (-)Ensembl
RefSeq Acc Id: NM_001106870   ⟹   NP_001100340
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88132,289,539 - 132,356,451 (-)NCBI
mRatBN7.28123,412,112 - 123,479,021 (-)NCBI
Rnor_6.08132,844,043 - 132,910,905 (-)NCBI
Rnor_5.08131,995,143 - 132,061,908 (-)NCBI
RGSC_v3.48128,543,895 - 128,612,184 (-)RGD
Celera8122,520,323 - 122,587,206 (-)RGD
Sequence:
RefSeq Acc Id: XM_017595602   ⟹   XP_017451091
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88132,289,538 - 132,347,904 (-)NCBI
mRatBN7.28123,412,105 - 123,470,540 (-)NCBI
Rnor_6.08132,844,042 - 132,903,293 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039081318   ⟹   XP_038937246
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88132,289,538 - 132,356,810 (-)NCBI
mRatBN7.28123,412,105 - 123,479,315 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001100340 (Get FASTA)   NCBI Sequence Viewer  
  XP_017451091 (Get FASTA)   NCBI Sequence Viewer  
  XP_038937246 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL76750 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000008630
  ENSRNOP00000008630.5
  ENSRNOP00000073803
  ENSRNOP00000073803.2
Reference Protein Sequences
RefSeq Acc Id: NP_001100340   ⟸   NM_001106870
- UniProtKB: D3Z9D2 (UniProtKB/TrEMBL),   A6I4C6 (UniProtKB/TrEMBL),   A0A0G2K6G5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017451091   ⟸   XM_017595602
- Peptide Label: isoform X1
- UniProtKB: D3Z9D2 (UniProtKB/TrEMBL),   A6I4C6 (UniProtKB/TrEMBL),   A0A0G2K6G5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000008630   ⟸   ENSRNOT00000008630
RefSeq Acc Id: ENSRNOP00000073803   ⟸   ENSRNOT00000087799
RefSeq Acc Id: XP_038937246   ⟸   XM_039081318
- Peptide Label: isoform X1
- UniProtKB: D3Z9D2 (UniProtKB/TrEMBL),   A6I4C6 (UniProtKB/TrEMBL),   A0A0G2K6G5 (UniProtKB/TrEMBL)
Protein Domains
FYVE-type   GOLD   RUN

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3Z9D2-F1-model_v2 AlphaFold D3Z9D2 1-1451 view protein structure

Transcriptome

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

Promoters
RGD ID:13696420
Promoter ID:EPDNEW_R6938
Type:multiple initiation site
Name:Fyco1_1
Description:FYVE and coiled-coil 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_6.08132,911,147 - 132,911,207EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309069 AgrOrtholog
BioCyc Gene G2FUF-28606 BioCyc
Ensembl Genes ENSRNOG00000006336 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008630 ENTREZGENE
  ENSRNOT00000008630.7 UniProtKB/TrEMBL
  ENSRNOT00000087799.2 UniProtKB/TrEMBL
Gene3D-CATH 1.20.58.900 UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/TrEMBL
  GOLD domain UniProtKB/TrEMBL
InterPro FYVE_FYCO1 UniProtKB/TrEMBL
  GOLD UniProtKB/TrEMBL
  GOLD_dom_sf UniProtKB/TrEMBL
  Run UniProtKB/TrEMBL
  Run_dom_sf UniProtKB/TrEMBL
  RUN_FYCO1 UniProtKB/TrEMBL
  Znf_FYVE UniProtKB/TrEMBL
  Znf_FYVE-rel UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
KEGG Report rno:301085 UniProtKB/TrEMBL
NCBI Gene 301085 ENTREZGENE
PANTHER FYVE AND COILED-COIL DOMAIN-CONTAINING PROTEIN 1 UniProtKB/TrEMBL
  FYVE AND COILED-COIL DOMAIN-CONTAINING PROTEIN 1 UniProtKB/TrEMBL
Pfam FYVE UniProtKB/TrEMBL
  RUN UniProtKB/TrEMBL
PhenoGen Fyco1 PhenoGen
PROSITE GOLD UniProtKB/TrEMBL
  RUN UniProtKB/TrEMBL
  ZF_FYVE UniProtKB/TrEMBL
RatGTEx ENSRNOG00000006336 RatGTEx
SMART FYVE UniProtKB/TrEMBL
Superfamily-SCOP FYVE_PHD_ZnF UniProtKB/TrEMBL
  GOLD UniProtKB/TrEMBL
  SSF140741 UniProtKB/TrEMBL
UniProt A0A0G2K6G5 ENTREZGENE, UniProtKB/TrEMBL
  A6I4C6 ENTREZGENE, UniProtKB/TrEMBL
  D3Z9D2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-10-04 Fyco1  FYVE and coiled-coil domain autophagy adaptor 1  Fyco1  FYVE and coiled-coil domain containing 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Fyco1  FYVE and coiled-coil domain containing 1   Fyco1_predicted  FYVE and coiled-coil domain containing 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Fyco1_predicted  FYVE and coiled-coil domain containing 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED