Cabs1 (calcium binding protein, spermatid associated 1) - Rat Genome Database

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Gene: Cabs1 (calcium binding protein, spermatid associated 1) Rattus norvegicus
Analyze
Symbol: Cabs1
Name: calcium binding protein, spermatid associated 1
RGD ID: 620592
Description: Predicted to enable calcium ion binding activity. Involved in spermatogenesis. Located in mitochondrial inner membrane. Orthologous to human CABS1 (calcium binding protein, spermatid associated 1); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; ammonium chloride; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: calcium-binding and spermatid-specific protein 1; calcium-binding protein, spermatid-specific 1; casein-like phosphoprotein; Clph; MGC94008; RSD-6; Rsd6
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
GRCr81420,376,214 - 20,378,276 (-)NCBIGRCr8
mRatBN7.21420,096,962 - 20,099,024 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1420,096,899 - 20,099,181 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1420,027,466 - 20,029,528 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01421,346,347 - 21,348,409 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01420,077,091 - 20,079,153 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01421,746,294 - 21,748,356 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1421,746,295 - 21,748,356 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01421,656,184 - 21,658,246 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41421,616,284 - 21,618,346 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11421,616,284 - 21,618,034 (-)NCBI
Celera1419,500,272 - 19,502,334 (-)NCBICelera
Cytogenetic Map14p22NCBI
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

Molecular Function
calcium ion binding  (IBA,ISO,ISS)

References

References - curated
# Reference Title Reference Citation
1. CLPH, a Novel Casein Kinase 2-Phosphorylated Disordered Protein, Is Specifically Associated with Post-Meiotic Germ Cells in Rat Spermatogenesis. Calvel P, etal., J Proteome Res. 2009 Mar 9.
2. 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.
3. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Information Derived from GenBank Report RGD, Sept. 2003
6. Calcium-binding protein, spermatid-specific 1 is expressed in human salivary glands and contains an anti-inflammatory motif. St Laurent CD, etal., Am J Physiol Regul Integr Comp Physiol. 2015 Apr 1;308(7):R569-75. doi: 10.1152/ajpregu.00153.2014. Epub 2015 Jan 28.
Additional References at PubMed
PMID:12477932   PMID:19208547  


Genomics

Comparative Map Data
Cabs1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81420,376,214 - 20,378,276 (-)NCBIGRCr8
mRatBN7.21420,096,962 - 20,099,024 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1420,096,899 - 20,099,181 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1420,027,466 - 20,029,528 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01421,346,347 - 21,348,409 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01420,077,091 - 20,079,153 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01421,746,294 - 21,748,356 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1421,746,295 - 21,748,356 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01421,656,184 - 21,658,246 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41421,616,284 - 21,618,346 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11421,616,284 - 21,618,034 (-)NCBI
Celera1419,500,272 - 19,502,334 (-)NCBICelera
Cytogenetic Map14p22NCBI
CABS1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38470,334,981 - 70,337,116 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl470,334,981 - 70,337,116 (+)EnsemblGRCh38hg38GRCh38
GRCh37471,200,698 - 71,202,833 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36471,235,260 - 71,237,422 (+)NCBINCBI36Build 36hg18NCBI36
Celera468,558,418 - 68,560,580 (+)NCBICelera
Cytogenetic Map4q13.3NCBI
HuRef467,002,910 - 67,005,072 (+)NCBIHuRef
CHM1_1471,236,753 - 71,238,916 (+)NCBICHM1_1
T2T-CHM13v2.0473,674,478 - 73,676,614 (+)NCBIT2T-CHM13v2.0
Cabs1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39588,127,310 - 88,129,400 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl588,127,298 - 88,129,403 (+)EnsemblGRCm39 Ensembl
GRCm38587,979,451 - 87,981,541 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl587,979,439 - 87,981,544 (+)EnsemblGRCm38mm10GRCm38
MGSCv37588,408,476 - 88,410,566 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36589,054,012 - 89,056,102 (+)NCBIMGSCv36mm8
MGSCv36587,583,853 - 87,585,943 (+)NCBIMGSCv36mm8
Cytogenetic Map5E1NCBI
cM Map543.56NCBI
Cabs1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554472,581,173 - 2,582,481 (-)NCBIChiLan1.0ChiLan1.0
CABS1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2359,753,727 - 59,758,566 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1459,950,375 - 59,955,213 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0453,894,739 - 53,896,868 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1460,238,252 - 60,240,418 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl460,239,140 - 60,240,327 (-)Ensemblpanpan1.1panPan2
CABS1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11359,691,575 - 59,712,204 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1359,418,497 - 59,439,174 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01360,486,542 - 60,507,218 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1360,486,605 - 60,487,795 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11360,099,952 - 60,120,613 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01359,604,290 - 59,624,969 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01360,751,762 - 60,772,442 (+)NCBIUU_Cfam_GSD_1.0
Cabs1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528515,881,047 - 15,882,389 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049365984,333,108 - 4,334,567 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CABS1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl867,161,879 - 67,163,057 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1867,161,203 - 67,163,535 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
CABS1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1718,820,405 - 18,828,746 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl718,821,696 - 18,822,886 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660844,096,279 - 4,098,418 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cabs1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248901,687,736 - 1,692,993 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cabs1
5 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:26
Count of miRNA genes:24
Interacting mature miRNAs:26
Transcripts:ENSRNOT00000002670
Prediction methods:Miranda, Rnahybrid, 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
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
619619Rf4Renal disease susceptibility QTL 44.10.002urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14381307421217635Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14381307424531477Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14381307430767156Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062228035204Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141103081230320092Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141487516830883947Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141762256142337007Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat


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 3
Medium 4
Low 1 1 4 2 3 2 1 2
Below cutoff 3 18 8 7 8 2 3 9 3 6 6 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000002670   ⟹   ENSRNOP00000002670
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1420,096,899 - 20,099,181 (-)Ensembl
Rnor_6.0 Ensembl1421,746,295 - 21,748,356 (-)Ensembl
RefSeq Acc Id: NM_022263   ⟹   NP_071599
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81420,376,214 - 20,378,276 (-)NCBI
mRatBN7.21420,096,962 - 20,099,024 (-)NCBI
Rnor_6.01421,746,294 - 21,748,356 (-)NCBI
Rnor_5.01421,656,184 - 21,658,246 (-)NCBI
RGSC_v3.41421,616,284 - 21,618,346 (-)RGD
Celera1419,500,272 - 19,502,334 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_071599 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAF76188 (Get FASTA)   NCBI Sequence Viewer  
  AAH79062 (Get FASTA)   NCBI Sequence Viewer  
  EDL83139 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000002670
  ENSRNOP00000002670.4
  ENSRNOP00055022580
  ENSRNOP00060031842
  ENSRNOP00065022685
GenBank Protein Q68FX6 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_071599   ⟸   NM_022263
- UniProtKB: Q9JI16 (UniProtKB/Swiss-Prot),   Q68FX6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002670   ⟸   ENSRNOT00000002670

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q68FX6-F1-model_v2 AlphaFold Q68FX6 1-390 view protein structure

Transcriptome

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

Promoters
RGD ID:13699245
Promoter ID:EPDNEW_R9769
Type:initiation region
Name:Cabs1_1
Description:calcium binding protein, spermatid associated 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_6.01421,748,380 - 21,748,440EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620592 AgrOrtholog
BioCyc Gene G2FUF-16146 BioCyc
Ensembl Genes ENSRNOG00000001950 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055016545 UniProtKB/Swiss-Prot
  ENSRNOG00060022291 UniProtKB/Swiss-Prot
  ENSRNOG00065017168 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000002670 ENTREZGENE
  ENSRNOT00000002670.5 UniProtKB/Swiss-Prot
  ENSRNOT00055028065 UniProtKB/Swiss-Prot
  ENSRNOT00060038583 UniProtKB/Swiss-Prot
  ENSRNOT00065028636 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7115934 IMAGE-MGC_LOAD
InterPro Ca-bd_spermatid UniProtKB/Swiss-Prot
KEGG Report rno:64029 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94008 IMAGE-MGC_LOAD
NCBI Gene 64029 ENTREZGENE
PANTHER CALCIUM-BINDING AND SPERMATID-SPECIFIC PROTEIN 1 UniProtKB/Swiss-Prot
  PTHR22810 UniProtKB/Swiss-Prot
Pfam CABS1 UniProtKB/Swiss-Prot
PhenoGen Cabs1 PhenoGen
RatGTEx ENSRNOG00000001950 RatGTEx
  ENSRNOG00055016545 RatGTEx
  ENSRNOG00060022291 RatGTEx
  ENSRNOG00065017168 RatGTEx
UniProt CABS1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q9JI16 ENTREZGENE
UniProt Secondary Q9JI16 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-08 Cabs1  calcium binding protein, spermatid associated 1  Cabs1  calcium-binding protein, spermatid-specific 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-08-01 Cabs1  calcium-binding protein, spermatid-specific 1  Clph  casein-like phosphoprotein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-02-13 Clph  casein-like phosphoprotein  Rsd6  RSD-6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-08-07 Rsd6  RSD-6      Symbol and Name status set to provisional 70820 PROVISIONAL