Csn1s1 (casein alpha s1) - Rat Genome Database

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Gene: Csn1s1 (casein alpha s1) Rattus norvegicus
Analyze
Symbol: Csn1s1
Name: casein alpha s1
RGD ID: 2430
Description: Predicted to be involved in response to dehydroepiandrosterone; response to estradiol; and response to steroid hormone. Predicted to be located in extracellular region. Predicted to be active in extracellular space. Orthologous to human CSN1S1 (casein alpha s1); INTERACTS WITH 6-propyl-2-thiouracil; 7,12-dimethyltetraphene; amitrole.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: alpha-casein; alpha-S1-casein; Casa; Casein, alpha; Csn1; Csna
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81420,622,858 - 20,638,849 (-)NCBIGRCr8
mRatBN7.21420,343,620 - 20,359,614 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1420,343,619 - 20,359,614 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1420,273,646 - 20,289,594 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01421,592,528 - 21,608,476 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01420,329,827 - 20,345,807 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01421,993,450 - 22,009,308 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1421,993,427 - 22,009,308 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01421,908,365 - 21,924,353 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41421,869,011 - 21,885,203 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11421,869,010 - 21,885,203 (-)NCBI
Celera1419,746,841 - 19,762,629 (-)NCBICelera
Cytogenetic Map14p21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. Sequence of rat alpha- and gamma-casein mRNAs: evolutionary comparison of the calcium-dependent rat casein multigene family. Hobbs AA and Rosen JM, Nucleic Acids Res 1982 Dec 20;10(24):8079-98.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Evolution of the casein multigene family: conserved sequences in the 5' flanking and exon regions. Yu-Lee LY, etal., Nucleic Acids Res 1986 Feb 25;14(4):1883-902.
Additional References at PubMed
PMID:16106354   PMID:16502470   PMID:20704729  


Genomics

Comparative Map Data
Csn1s1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81420,622,858 - 20,638,849 (-)NCBIGRCr8
mRatBN7.21420,343,620 - 20,359,614 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1420,343,619 - 20,359,614 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1420,273,646 - 20,289,594 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01421,592,528 - 21,608,476 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01420,329,827 - 20,345,807 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01421,993,450 - 22,009,308 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1421,993,427 - 22,009,308 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01421,908,365 - 21,924,353 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41421,869,011 - 21,885,203 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11421,869,010 - 21,885,203 (-)NCBI
Celera1419,746,841 - 19,762,629 (-)NCBICelera
Cytogenetic Map14p21NCBI
CSN1S1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38469,931,068 - 69,946,574 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl469,931,068 - 69,946,574 (+)EnsemblGRCh38hg38GRCh38
GRCh37470,796,786 - 70,812,292 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36470,831,388 - 70,846,877 (+)NCBINCBI36Build 36hg18NCBI36
Celera468,150,256 - 68,165,733 (+)NCBICelera
Cytogenetic Map4q13.3NCBI
HuRef466,594,565 - 66,610,040 (+)NCBIHuRef
CHM1_1470,833,196 - 70,848,682 (+)NCBICHM1_1
T2T-CHM13v2.0473,265,893 - 73,281,385 (+)NCBIT2T-CHM13v2.0
Csn1s1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39587,814,067 - 87,830,437 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl587,814,067 - 87,830,437 (+)EnsemblGRCm39 Ensembl
GRCm38587,666,208 - 87,682,578 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl587,666,208 - 87,682,578 (+)EnsemblGRCm38mm10GRCm38
MGSCv37588,095,249 - 88,111,599 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36588,740,785 - 88,757,135 (+)NCBIMGSCv36mm8
Celera585,369,865 - 85,382,927 (+)NCBICelera
Cytogenetic Map5E1NCBI
cM Map543.56NCBI
Csn1s1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554472,908,095 - 2,928,444 (-)NCBIChiLan1.0ChiLan1.0
CSN1S1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2360,143,772 - 60,159,323 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1460,346,797 - 60,362,343 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0454,291,159 - 54,306,712 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1460,627,758 - 60,643,358 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl460,627,758 - 60,643,358 (-)Ensemblpanpan1.1panPan2
CSN1S1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11359,420,761 - 59,432,463 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1359,417,974 - 59,432,106 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1359,149,515 - 59,160,993 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01360,216,703 - 60,221,887 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.11359,831,104 - 59,842,590 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01359,291,362 - 59,296,547 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01360,436,627 - 60,448,340 (+)NCBIUU_Cfam_GSD_1.0
Csn1s1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528516,269,217 - 16,279,920 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049365984,710,875 - 4,735,033 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CSN1S1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl866,888,231 - 66,907,913 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1866,888,231 - 66,908,306 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28148,201,997 - 148,222,498 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Csn1s1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248901,283,303 - 1,297,021 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Csn1s1
88 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:131
Count of miRNA genes:105
Interacting mature miRNAs:116
Transcripts:ENSRNOT00000060209
Prediction methods:Microtar, 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

Markers in Region
D14Wox14  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01422,009,849 - 22,009,966NCBIRnor6.0
Rnor_5.01421,924,894 - 21,925,011UniSTSRnor5.0
RGSC_v3.41421,885,743 - 21,885,861RGDRGSC3.4
RGSC_v3.41421,885,744 - 21,885,861UniSTSRGSC3.4
RGSC_v3.11421,885,743 - 21,885,861RGD
Celera1419,763,170 - 19,763,287UniSTS
RH 3.4 Map14283.6UniSTS
RH 3.4 Map14283.6RGD
RH 2.0 Map14276.7RGD
Cytogenetic Map14p21UniSTS
D14Got29  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21420,344,304 - 20,344,439 (+)MAPPERmRatBN7.2
Rnor_6.01421,994,005 - 21,994,137NCBIRnor6.0
Rnor_5.01421,909,050 - 21,909,182UniSTSRnor5.0
RGSC_v3.41421,869,695 - 21,869,828RGDRGSC3.4
RGSC_v3.41421,869,696 - 21,869,828UniSTSRGSC3.4
RGSC_v3.11421,869,696 - 21,869,828RGD
Celera1419,747,526 - 19,747,636UniSTS
RH 3.4 Map14278.3UniSTS
RH 3.4 Map14278.3RGD
RH 2.0 Map14273.6RGD
Cytogenetic Map14p21UniSTS
D14Arb18  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21420,360,158 - 20,360,286 (+)MAPPERmRatBN7.2
Rnor_6.01422,009,853 - 22,009,980NCBIRnor6.0
Rnor_5.01421,924,898 - 21,925,025UniSTSRnor5.0
RGSC_v3.41421,885,748 - 21,885,875UniSTSRGSC3.4
RGSC_v3.11421,885,747 - 21,885,875RGD
Celera1419,763,174 - 19,763,301UniSTS
Cytogenetic Map14p21UniSTS
RH133429  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map14282.79UniSTS
Cytogenetic Map14p21UniSTS


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

endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system reproductive system respiratory system appendage
High
Medium
Low 1 2 2 1
Below cutoff 6 2 5 2 1 2 8 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000087923   ⟹   ENSRNOP00000072759
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1421,993,450 - 22,009,308 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000088491   ⟹   ENSRNOP00000073955
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1420,343,619 - 20,359,614 (-)Ensembl
Rnor_6.0 Ensembl1421,993,427 - 22,009,300 (-)Ensembl
RefSeq Acc Id: NM_138874   ⟹   NP_620229
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81420,622,861 - 20,638,849 (-)NCBI
mRatBN7.21420,343,620 - 20,359,614 (-)NCBI
Rnor_6.01421,993,450 - 22,009,308 (-)NCBI
Rnor_5.01421,908,365 - 21,924,353 (-)NCBI
RGSC_v3.41421,869,011 - 21,885,203 (-)RGD
Celera1419,746,841 - 19,762,629 (-)RGD
Sequence:
RefSeq Acc Id: XM_063272857   ⟹   XP_063128927
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81420,622,858 - 20,638,849 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_620229   ⟸   NM_138874
- Peptide Label: precursor
- UniProtKB: P02661 (UniProtKB/Swiss-Prot),   A6KU22 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072759   ⟸   ENSRNOT00000087923
RefSeq Acc Id: ENSRNOP00000073955   ⟸   ENSRNOT00000088491
RefSeq Acc Id: XP_063128927   ⟸   XM_063272857
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P02661-F1-model_v2 AlphaFold P02661 1-284 view protein structure

Transcriptome

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

Promoters
RGD ID:13699252
Promoter ID:EPDNEW_R9773
Type:single initiation site
Name:Csn1s1_1
Description:casein alpha s1
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_6.01422,009,308 - 22,009,368EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2430 AgrOrtholog
BioCyc Gene G2FUF-16128 BioCyc
Ensembl Genes ENSRNOG00000055596 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000088491.2 UniProtKB/TrEMBL
InterPro Alpha-s1_casein UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Casein UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Casein_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24284 UniProtKB/Swiss-Prot
NCBI Gene 24284 ENTREZGENE
PANTHER ALPHA-S1-CASEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10240 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Casein UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Csn1s1 PhenoGen
PROSITE CASEIN_ALPHA_BETA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000055596 RatGTEx
UniProt A0A0G2K6V4_RAT UniProtKB/TrEMBL
  A6KU21_RAT UniProtKB/TrEMBL
  A6KU22 ENTREZGENE, UniProtKB/TrEMBL
  CASA1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2007-01-29 Csn1s1    CSN1S1  casein alpha s1  Symbol updated 1299863 APPROVED
2004-09-10 CSN1S1  casein alpha s1  Csn1  Casein, alpha  Symbol and Name updated 1299863 APPROVED
2002-06-10 Csn1  Casein, alpha      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression phosphoprotein expressed in mammary gland and in milk 1298824
gene_other form calcium-dependent micelles in milk 1298824
gene_regulation expression in mammary gland is regulated by steroid and peptide hormones 1298824