Csn2 (casein beta) - Rat Genome Database

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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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81420,601,824 - 20,609,061 (+)NCBIGRCr8
mRatBN7.21420,322,581 - 20,329,818 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1420,322,581 - 20,329,817 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1420,252,631 - 20,259,869 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01421,571,515 - 21,578,753 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01420,308,760 - 20,316,001 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01421,972,274 - 21,979,511 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1421,972,274 - 21,979,510 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01421,887,084 - 21,894,550 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41421,847,981 - 21,855,216 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11421,847,980 - 21,855,213 (+)NCBI
Celera1419,725,645 - 19,732,882 (+)NCBICelera
Cytogenetic Map14p21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
lactation  (ISO)

Cellular Component
extracellular region  (IEA,ISO)
extracellular space  (IBA,IEA,ISO)

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 (+)NCBIGRCr8
mRatBN7.21420,322,581 - 20,329,818 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1420,322,581 - 20,329,817 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1420,252,631 - 20,259,869 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01421,571,515 - 21,578,753 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01420,308,760 - 20,316,001 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01421,972,274 - 21,979,511 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1421,972,274 - 21,979,510 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01421,887,084 - 21,894,550 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41421,847,981 - 21,855,216 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11421,847,980 - 21,855,213 (+)NCBI
Celera1419,725,645 - 19,732,882 (+)NCBICelera
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 (-)EnsemblGRCh38hg38GRCh38
GRCh37470,820,974 - 70,831,446 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36470,855,564 - 70,861,315 (-)NCBINCBI36Build 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 Ensembl
GRCm38587,692,619 - 87,699,429 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl587,692,624 - 87,699,630 (-)EnsemblGRCm38mm10GRCm38
MGSCv37588,121,649 - 88,128,446 (-)NCBIGRCm37MGSCv37mm9NCBIm37
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 (+)Ensemblpanpan1.1panPan2
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 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1359,165,262 - 59,172,933 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01360,232,447 - 60,300,688 (-)NCBIROS_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_1.0
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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Csn2
20 total Variants
miRNA Target Status

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 (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
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
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 nervous system reproductive system appendage
High
Medium
Low 1 1 1
Below cutoff 8 2 7 2 1 5 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000060265   ⟹   ENSRNOP00000057016
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1420,322,581 - 20,329,817 (+)Ensembl
Rnor_6.0 Ensembl1421,972,274 - 21,979,510 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000098581   ⟹   ENSRNOP00000089457
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1420,324,300 - 20,329,817 (+)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
  ENSRNOP00000057016.2
  ENSRNOP00000089457.1
GenBank Protein P02665 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_058816   ⟸   NM_017120
- Peptide Label: precursor
- UniProtKB: P02665 (UniProtKB/Swiss-Prot),   A6KU20 (UniProtKB/TrEMBL),   G3V9R5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000057016   ⟸   ENSRNOT00000060265
RefSeq Acc Id: ENSRNOP00000089457   ⟸   ENSRNOT00000098581

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, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000060265 ENTREZGENE
  ENSRNOT00000060265.4 UniProtKB/TrEMBL
  ENSRNOT00000098581.1 UniProtKB/TrEMBL
InterPro Casein UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Casein_beta UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Casein_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29173 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene Csn2 ENTREZGENE
PANTHER BETA-CASEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR11500 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Casein UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Csn2 PhenoGen
PIRSF Beta-casein UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CASEIN_ALPHA_BETA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000039326 RatGTEx
UniProt A0A8I6ABZ4_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