Cylc1 (cylicin, basic protein of sperm head cytoskeleton 1) - Rat Genome Database

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Gene: Cylc1 (cylicin, basic protein of sperm head cytoskeleton 1) Mus musculus
Analyze
Symbol: Cylc1
Name: cylicin, basic protein of sperm head cytoskeleton 1
RGD ID: 1615114
MGI Page MGI
Description: Enables protein homodimerization activity. Acts upstream of or within several processes, including acrosome assembly; maintenance of cell number; and single fertilization. Is active in acrosomal membrane and perinuclear theca. Used to study male infertility. Human ortholog(s) of this gene implicated in X-linked spermatogenic failure 8. Orthologous to human CYLC1 (cylicin 1).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 4930401M13Rik; cylicin I; cylicin-1
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Biological Process

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:16141072   PMID:16141073   PMID:21873635   PMID:38013430   PMID:38573307  


Genomics

Comparative Map Data
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
(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
(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
(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
374 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:59
Count of miRNA genes:56
Interacting mature miRNAs:56
Transcripts:ENSMUST00000101282
Prediction methods:Miranda, Pita, 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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4141630Gct6_mgranulosa cell tumorigenesis 6 (mouse)Not determined47179121129764756Mouse
13208552Wght12_mweight 12 (mouse)X94043606149782996Mouse
4141803Lmr30_mleishmaniasis resistance 30 (mouse)Not determined85062606119062720Mouse
13208556Lgth14_mbody length 14 (mouse)X94043606149782996Mouse
13824980Ferq1_mgenetic fertility QTL 1 (mouse)X54045360148782996Mouse
11075102Modc2_mmodifier of Odc2 (mouse)X80189914114190059Mouse
1357823Spha3_msperm head anomaly 3 (mouse)Not determinedX102055848162758941Mouse
1357433Dbts2_mdiabetes 2 (mouse)Not determinedX7226295150107038Mouse
4141665Mhysq2_mmale hybrid sterility QTL 2 (mouse)Not determined71453852139203212Mouse


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000101282   ⟹   ENSMUSP00000098840
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 EnsemblX111,110,458 - 111,123,874 (+)Ensembl
Ensembl Acc Id: ENSMUST00000210720   ⟹   ENSMUSP00000147334
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 EnsemblX110,154,024 - 110,169,731 (+)Ensembl
GRCm38.p6 EnsemblX111,110,418 - 111,125,854 (+)Ensembl
RefSeq Acc Id: NM_026134   ⟹   NP_080410
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39X110,154,024 - 110,169,624 (+)NCBI
GRCm38X111,110,418 - 111,125,854 (+)NCBI
MGSCv37X108,305,757 - 108,319,213 (+)RGD
CeleraX97,930,115 - 97,943,867 (+)RGD
cM MapX ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_080410 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein A0A1B0GR13 (Get FASTA)   NCBI Sequence Viewer  
  BAB29786 (Get FASTA)   NCBI Sequence Viewer  
  EDL14020 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000147334
  ENSMUSP00000147334.2
RefSeq Acc Id: NP_080410   ⟸   NM_026134
- UniProtKB: A0A1B0GR13 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSMUSP00000147334   ⟸   ENSMUST00000210720
Ensembl Acc Id: ENSMUSP00000098840   ⟸   ENSMUST00000101282
Protein Domains
Cylicin N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A1B0GR13-F1-model_v2 AlphaFold A0A1B0GR13 1-642 view protein structure

Promoters
RGD ID:13681254
Promoter ID:EPDNEW_M24776
Type:initiation region
Name:Cylc1_1
Description:Mus musculus cylicin, basic protein of sperm head cytoskeleton1 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38X111,110,418 - 111,110,478EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1914657 AgrOrtholog
Ensembl Genes ENSMUSG00000073001 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000210720 ENTREZGENE
  ENSMUST00000210720.3 UniProtKB/Swiss-Prot
InterPro CYLC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cylicin_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:67407 UniProtKB/TrEMBL
MGD MGI:1914657 ENTREZGENE
NCBI Gene 67407 ENTREZGENE
PANTHER CYCLICIN UniProtKB/Swiss-Prot
  CYLICIN-1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR16742 UniProtKB/TrEMBL
Pfam Cylicin_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cylc1 PhenoGen
UniProt A0A1B0GR13 ENTREZGENE, UniProtKB/Swiss-Prot
  Q9CUM9_MOUSE UniProtKB/TrEMBL