Cylc1 (cylicin 1) - Rat Genome Database

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Gene: Cylc1 (cylicin 1) Rattus norvegicus
Analyze
Symbol: Cylc1
Name: cylicin 1
RGD ID: 2323810
Description: Predicted to be a structural constituent of cytoskeleton. Predicted to be involved in cytoskeleton organization. Predicted to be active in acrosomal matrix. Orthologous to human CYLC1 (cylicin 1); INTERACTS WITH aflatoxin B1 (ortholog); cadmium dichloride (ortholog); CGP 52608 (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: cylicin, basic protein of sperm head cytoskeleton 1; cylicin-1; LOC100359483; rCG38076-like
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X80,224,288 - 80,313,698 (+)NCBIGRCr8
mRatBN7.2X76,108,111 - 76,197,431 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX76,108,136 - 76,197,422 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0X82,217,133 - 82,302,106 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX82,217,143 - 82,302,094 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01116,176,979 - 116,259,876 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X99,549,629 - 99,556,431 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX77,356,790 - 77,443,608 (+)NCBICelera
Cytogenetic MapXq31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
acrosomal matrix  (IBA,ISO)
nucleus  (IEA)

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:8354692   PMID:21630459  


Genomics

Comparative Map Data
Cylc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X80,224,288 - 80,313,698 (+)NCBIGRCr8
mRatBN7.2X76,108,111 - 76,197,431 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX76,108,136 - 76,197,422 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0X82,217,133 - 82,302,106 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX82,217,143 - 82,302,094 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01116,176,979 - 116,259,876 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X99,549,629 - 99,556,431 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX77,356,790 - 77,443,608 (+)NCBICelera
Cytogenetic MapXq31NCBI
CYLC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X83,861,146 - 83,886,698 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX83,861,126 - 83,886,699 (+)EnsemblGRCh38hg38GRCh38
GRCh37X83,116,154 - 83,141,706 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X83,002,826 - 83,028,282 (+)NCBINCBI36Build 36hg18NCBI36
Build 34X82,932,707 - 82,947,850NCBI
CeleraX83,353,564 - 83,379,026 (+)NCBICelera
Cytogenetic MapXq21.1NCBI
HuRefX76,689,811 - 76,705,058 (+)NCBIHuRef
HuRefX76,709,174 - 76,715,338 (+)NCBIHuRef
CHM1_1X83,009,847 - 83,035,639 (+)NCBICHM1_1
T2T-CHM13v2.0X82,294,715 - 82,321,619 (+)NCBIT2T-CHM13v2.0
Cylc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X110,154,024 - 110,169,624 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX110,154,024 - 110,169,731 (+)EnsemblGRCm39 Ensembl
GRCm38X111,110,418 - 111,125,854 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX111,110,418 - 111,125,854 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X108,305,757 - 108,319,213 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X107,313,137 - 107,326,593 (+)NCBIMGSCv36mm8
CeleraX97,930,115 - 97,943,867 (+)NCBICelera
Cytogenetic MapXE1NCBI
cM MapX48.2NCBI
Cylc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555292,996,909 - 3,052,074 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555292,996,909 - 3,052,053 (+)NCBIChiLan1.0ChiLan1.0
CYLC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X83,341,896 - 83,367,037 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X83,345,506 - 83,370,643 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X72,934,398 - 72,959,533 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X83,046,221 - 83,071,349 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX83,046,221 - 83,071,349 (+)Ensemblpanpan1.1panPan2
CYLC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X64,649,681 - 64,784,157 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX64,649,657 - 64,784,156 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX55,406,880 - 55,541,317 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X65,966,840 - 66,108,621 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX65,966,830 - 66,108,620 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X63,627,607 - 63,762,522 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X65,255,905 - 65,393,841 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X64,834,191 - 64,968,640 (+)NCBIUU_Cfam_GSD_1.0
Cylc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X58,364,147 - 58,393,158 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049365474,678,172 - 4,706,407 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CYLC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX67,026,711 - 67,090,330 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X66,975,125 - 67,090,165 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X76,761,524 - 76,825,134 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CYLC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X72,684,771 - 72,772,378 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX72,756,071 - 72,761,603 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660678,112,991 - 8,154,803 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cylc1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248524,561,267 - 4,652,329 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cylc1
301 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:66
Count of miRNA genes:63
Interacting mature miRNAs:64
Transcripts:ENSRNOT00000034564
Prediction methods:Microtar, 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
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
1598837Memor13Memory QTL 133.2exploratory 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)X41052407146860749Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X75294106120294106Rat


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

integumental system musculoskeletal system nervous system reproductive system appendage
High
Medium 7
Low
Below cutoff 2 2 3 3 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000086866   ⟹   ENSRNOP00000072824
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX76,108,136 - 76,197,422 (+)Ensembl
Rnor_6.0 EnsemblX82,217,143 - 82,302,094 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000106046   ⟹   ENSRNOP00000077737
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX76,125,664 - 76,197,422 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000107593   ⟹   ENSRNOP00000079753
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX76,108,136 - 76,197,422 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000112969   ⟹   ENSRNOP00000093191
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX76,189,946 - 76,197,422 (+)Ensembl
RefSeq Acc Id: NM_001427602   ⟹   NP_001414531
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X80,224,316 - 80,313,698 (+)NCBI
RefSeq Acc Id: XM_039100632   ⟹   XP_038956560
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X80,224,288 - 80,313,698 (+)NCBI
mRatBN7.2X76,108,138 - 76,197,431 (+)NCBI
RefSeq Acc Id: XM_063279690   ⟹   XP_063135760
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X80,224,288 - 80,312,848 (+)NCBI
RefSeq Acc Id: XM_063279691   ⟹   XP_063135761
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X80,224,288 - 80,312,848 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000072824   ⟸   ENSRNOT00000086866
RefSeq Acc Id: XP_038956560   ⟸   XM_039100632
- Peptide Label: isoform X3
- UniProtKB: A0A0G2K3Y3 (UniProtKB/TrEMBL),   A0A8I6GK60 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000093191   ⟸   ENSRNOT00000112969
RefSeq Acc Id: ENSRNOP00000077737   ⟸   ENSRNOT00000106046
RefSeq Acc Id: ENSRNOP00000079753   ⟸   ENSRNOT00000107593
RefSeq Acc Id: XP_063135760   ⟸   XM_063279690
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063135761   ⟸   XM_063279691
- Peptide Label: isoform X2
RefSeq Acc Id: NP_001414531   ⟸   NM_001427602
- UniProtKB: A0A8I6G5P6 (UniProtKB/TrEMBL)
Protein Domains
Cylicin N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K3Y3-F1-model_v2 AlphaFold A0A0G2K3Y3 1-622 view protein structure

Transcriptome

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

Promoters
RGD ID:13701919
Promoter ID:EPDNEW_R12436
Type:single initiation site
Name:Cylc1_1
Description:cylicin 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_6.0X82,217,142 - 82,217,202EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2323810 AgrOrtholog
BioCyc Gene G2FUF-1846 BioCyc
Ensembl Genes ENSRNOG00000056740 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000086866.2 UniProtKB/TrEMBL
  ENSRNOT00000106046.1 UniProtKB/TrEMBL
  ENSRNOT00000107593.1 UniProtKB/TrEMBL
  ENSRNOT00000112969.1 UniProtKB/TrEMBL
InterPro CYLC UniProtKB/TrEMBL
  Cylicin_N UniProtKB/TrEMBL
KEGG Report rno:100359483 UniProtKB/TrEMBL
NCBI Gene 100359483 ENTREZGENE
PANTHER CYLICIN-1 UniProtKB/TrEMBL
  PTHR16742 UniProtKB/TrEMBL
Pfam Cylicin_N UniProtKB/TrEMBL
PhenoGen Cylc1 PhenoGen
RatGTEx ENSRNOG00000056740 RatGTEx
UniProt A0A0G2K3Y3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5Y7V0_RAT UniProtKB/TrEMBL
  A0A8I6G5P6 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GK60 ENTREZGENE, UniProtKB/TrEMBL
  A6IV86_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-09 Cylc1  cylicin 1  Cylc1  cylicin, basic protein of sperm head cytoskeleton 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-07-23 Cylc1  cylicin, basic protein of sperm head cytoskeleton 1  LOC100359483  rCG38076-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-06 LOC100359483  rCG38076-like      Symbol and Name status set to provisional 70820 PROVISIONAL