Csn2 (casein beta) - Rat Genome Database

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Advanced Search (OLGA)
Gene: Csn2 (casein beta) Rattus norvegicus
Analyze
Symbol: Csn2
Name: casein beta
RGD ID: 61981
Description: Predicted to enable cysteine-type endopeptidase inhibitor activity. Predicted to be involved in lactation. Predicted to be located in extracellular region. Predicted to be active in extracellular space. Orthologous to human CSN2 (casein beta); INTERACTS WITH (+)-pilocarpine; 17beta-estradiol; 3-methylcholanthrene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: beta-casein; Csn 2; Csnb; NOT NULL
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81420,601,824 - 20,609,061 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1420,601,824 - 20,609,060 (+)EnsemblGRCr8
mRatBN7.21420,322,581 - 20,329,818 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1420,322,581 - 20,329,817 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1420,252,631 - 20,259,869 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01421,571,515 - 21,578,753 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01420,308,760 - 20,316,001 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01421,972,274 - 21,979,511 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1421,972,274 - 21,979,510 (+)Ensemblrn6Rnor6.0
Rnor_5.01421,887,084 - 21,894,550 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41421,847,981 - 21,855,216 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1419,725,645 - 19,732,882 (+)NCBICelera
RGSC_v3.11421,847,980 - 21,855,213 (+)NCBI
Cytogenetic Map14p21NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
lactation  (ISO)

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Rat beta casein cDNA: sequence analysis and evolutionary comparisons. Blackburn DE, etal., Nucleic Acids Res 1982 Apr 10;10(7):2295-307.
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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Global gene expression profiling of chemically induced rat mammary gland carcinomas and adenomas. Shan L, etal., Toxicol Pathol. 2005;33(7):768-75.
Additional References at PubMed
PMID:3997858   PMID:7979373   PMID:8889548   PMID:12242456   PMID:12788072   PMID:16106354   PMID:16502470   PMID:16698927   PMID:18462607   PMID:21621605  


Genomics

Comparative Map Data
Csn2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81420,601,824 - 20,609,061 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1420,601,824 - 20,609,060 (+)EnsemblGRCr8
mRatBN7.21420,322,581 - 20,329,818 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1420,322,581 - 20,329,817 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1420,252,631 - 20,259,869 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01421,571,515 - 21,578,753 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01420,308,760 - 20,316,001 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01421,972,274 - 21,979,511 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1421,972,274 - 21,979,510 (+)Ensemblrn6Rnor6.0
Rnor_5.01421,887,084 - 21,894,550 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41421,847,981 - 21,855,216 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1419,725,645 - 19,732,882 (+)NCBICelera
RGSC_v3.11421,847,980 - 21,855,213 (+)NCBI
Cytogenetic Map14p21NCBI
CSN2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38469,955,256 - 69,965,728 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl469,955,256 - 69,965,728 (-)Ensemblhg38GRCh38
GRCh37470,820,974 - 70,831,446 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36470,855,564 - 70,861,315 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34471,001,734 - 71,007,486NCBI
Celera468,174,402 - 68,180,154 (-)NCBICelera
Cytogenetic Map4q13.3NCBI
HuRef466,618,709 - 66,624,461 (-)NCBIHuRef
CHM1_1470,857,351 - 70,863,103 (-)NCBICHM1_1
T2T-CHM13v2.0473,290,050 - 73,300,523 (-)NCBIT2T-CHM13v2.0
Csn2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39587,840,478 - 87,847,288 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl587,840,483 - 87,847,489 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38587,692,619 - 87,699,429 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl587,692,624 - 87,699,630 (-)Ensemblmm10GRCm38
MGSCv37588,121,649 - 88,128,446 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36588,767,185 - 88,773,982 (-)NCBIMGSCv36mm8
MGSCv36587,297,023 - 87,303,820 (-)NCBIMGSCv36mm8
Cytogenetic Map5E1NCBI
cM Map543.56NCBI
Csn2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554472,868,899 - 2,889,969 (+)NCBIChiLan1.0ChiLan1.0
CSN2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2360,124,394 - 60,134,813 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1460,327,438 - 60,337,859 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0454,276,495 - 54,282,221 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1460,613,091 - 60,618,815 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl460,613,091 - 60,618,815 (+)EnsemblpanPan2panpan1.1
CSN2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11359,436,726 - 59,444,398 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1359,438,601 - 59,444,398 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1359,165,262 - 59,172,933 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01360,232,447 - 60,300,688 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1360,232,445 - 60,240,119 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11359,846,853 - 59,854,524 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01359,307,115 - 59,314,836 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01360,452,610 - 60,460,347 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
LOC101959548
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528516,229,074 - 16,237,085 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049365984,683,300 - 4,687,605 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CSN2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl866,915,923 - 66,922,636 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1866,914,231 - 66,922,636 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28148,228,429 - 148,236,984 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CSN2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1718,439,757 - 18,448,210 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl718,441,387 - 18,445,142 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660844,486,917 - 4,494,573 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Csn2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248901,320,558 - 1,326,782 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Csn2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1111,209,952 - 1,217,161 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Csn2
114 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:129
Count of miRNA genes:92
Interacting mature miRNAs:104
Transcripts:ENSRNOT00000060265
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14395787821572472Rat
631528Scl11Serum cholesterol level QTL 114.9blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)141787564536079022Rat
7411573Bw139Body weight QTL 1394.70.001body mass (VT:0001259)body weight gain (CMO:0000420)14140068101Rat
9589814Gluco67Glucose level QTL 674.540.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14140068101Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14939329839411170Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141133490630674469Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141133471628389666Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14395787831121464Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14862139853621398Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141891545442433608Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14395787824886169Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1411334716100078267Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141889519263895192Rat
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)141790672654251504Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141415516Rat
70204Niddm20Non-insulin dependent diabetes mellitus QTL 205.10.000008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)14131893212Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14862139853621398Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141513759431238250Rat

Markers in Region
RH129562  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21420,328,604 - 20,329,657 (+)MAPPERmRatBN7.2
Rnor_6.01421,978,298 - 21,979,350NCBIRnor6.0
Rnor_5.01421,893,342 - 21,894,394UniSTSRnor5.0
RGSC_v3.41421,854,005 - 21,855,057UniSTSRGSC3.4
Celera1419,731,669 - 19,732,721UniSTS
RH 3.4 Map14282.3UniSTS
Cytogenetic Map14p21UniSTS


Expression

RNA-SEQ Expression

appendage
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
2 10 9 8 2 7 2 12 8 10 1 18 6

Sequence


Ensembl Acc Id: ENSRNOT00000060265   ⟹   ENSRNOP00000057016
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1420,603,543 - 20,609,060 (+)Ensembl
mRatBN7.2 Ensembl1420,322,581 - 20,329,817 (+)Ensembl
Rnor_6.0 Ensembl1421,972,274 - 21,979,510 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000098581   ⟹   ENSRNOP00000089457
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1420,603,543 - 20,609,060 (+)Ensembl
mRatBN7.2 Ensembl1420,324,300 - 20,329,817 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000150843   ⟹   ENSRNOP00000103172
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1420,601,824 - 20,607,291 (+)Ensembl
RefSeq Acc Id: NM_017120   ⟹   NP_058816
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81420,601,824 - 20,609,061 (+)NCBI
mRatBN7.21420,322,581 - 20,329,818 (+)NCBI
Rnor_6.01421,972,274 - 21,979,511 (+)NCBI
Rnor_5.01421,887,084 - 21,894,550 (+)NCBI
RGSC_v3.41421,847,981 - 21,855,216 (+)RGD
Celera1419,725,645 - 19,732,882 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_058816 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA40878 (Get FASTA)   NCBI Sequence Viewer  
  EDL83148 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000057016
GenBank Protein P02665 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_058816   ⟸   NM_017120
- Peptide Label: precursor
- UniProtKB: P02665 (UniProtKB/Swiss-Prot),   A6KU20 (UniProtKB/TrEMBL),   G3V9R5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000057016   ⟸   ENSRNOT00000060265
Ensembl Acc Id: ENSRNOP00000089457   ⟸   ENSRNOT00000098581
Ensembl Acc Id: ENSRNOP00000103172   ⟸   ENSRNOT00000150843

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P02665-F1-model_v2 AlphaFold P02665 1-231 view protein structure

Transcriptome

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

Promoters
RGD ID:13699247
Promoter ID:EPDNEW_R9772
Type:single initiation site
Name:Csn2_1
Description:casein beta
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_6.01421,972,256 - 21,972,316EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:61981 AgrOrtholog
BioCyc Gene G2FUF-16129 BioCyc
Ensembl Genes ENSRNOG00000039326 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000060265 ENTREZGENE
InterPro Casein UniProtKB/Swiss-Prot
  Casein_beta UniProtKB/Swiss-Prot
  Casein_CS UniProtKB/Swiss-Prot
KEGG Report rno:29173 UniProtKB/Swiss-Prot
NCBI Gene Csn2 ENTREZGENE
PANTHER BETA-CASEIN UniProtKB/Swiss-Prot
  PTHR11500 UniProtKB/Swiss-Prot
Pfam Casein UniProtKB/Swiss-Prot
PhenoGen Csn2 PhenoGen
PIRSF Beta-casein UniProtKB/Swiss-Prot
PROSITE CASEIN_ALPHA_BETA UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000039326 RatGTEx
UniProt A0A8I6ABZ4_RAT UniProtKB/TrEMBL
  A0ABK0LEL8_RAT UniProtKB/TrEMBL
  A6KU20 ENTREZGENE, UniProtKB/TrEMBL
  CASB_RAT UniProtKB/Swiss-Prot
  G3V9R5 ENTREZGENE, UniProtKB/TrEMBL
  P02665 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Csn2  casein beta      Name updated 70584 APPROVED
2001-12-06 Csn 2  casein beta      Symbol updated to reflect Human and Mouse nomenclature 69665 APPROVED

RGD Curation Notes
Note Type Note Reference