Csn1s2a (casein alpha s2-like A) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Csn1s2a (casein alpha s2-like A) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Csn1s2a
Name: casein alpha s2-like A
RGD ID: 621152
Description: Predicted to enable protein homodimerization activity and zymogen binding activity. Predicted to be located in extracellular region. Predicted to be active in extracellular space.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: alpha-S2-casein-like A; casein gamma; Csng; gamma-casein
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81420,560,408 - 20,574,471 (-)NCBIGRCr8
mRatBN7.21420,281,167 - 20,295,232 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1420,281,167 - 20,295,232 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1420,211,233 - 20,225,285 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01421,530,119 - 21,544,171 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01420,267,323 - 20,281,367 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01421,930,858 - 21,944,921 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1421,930,858 - 21,944,921 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01421,845,520 - 21,859,731 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41421,805,291 - 21,819,354 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11421,805,290 - 21,819,354 (-)NCBI
Celera1419,683,768 - 19,698,313 (-)NCBICelera
Cytogenetic Map14p21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in Csn1s2a
40 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:27
Count of miRNA genes:27
Interacting mature miRNAs:27
Transcripts:ENSRNOT00000060273
Prediction methods:Miranda, 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 (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

endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system appendage
High
Medium
Low 1 1 1
Below cutoff 6 1 6 1 2 3 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000060273   ⟹   ENSRNOP00000057022
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1420,281,167 - 20,295,232 (-)Ensembl
Rnor_6.0 Ensembl1421,930,858 - 21,944,921 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000105182   ⟹   ENSRNOP00000084302
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1420,281,167 - 20,295,224 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000108881   ⟹   ENSRNOP00000087233
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1420,281,167 - 20,295,224 (-)Ensembl
RefSeq Acc Id: NM_001105741   ⟹   NP_001099211
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81420,560,408 - 20,574,471 (-)NCBI
mRatBN7.21420,281,167 - 20,295,232 (-)NCBI
Rnor_6.01421,930,858 - 21,944,921 (-)NCBI
Rnor_5.01421,845,520 - 21,859,731 (-)NCBI
RGSC_v3.41421,805,291 - 21,819,354 (-)RGD
Celera1419,683,768 - 19,698,313 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001099211 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL83147 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000057022
  ENSRNOP00000057022.3
  ENSRNOP00000084302.1
  ENSRNOP00000087233.1
GenBank Protein P02667 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001099211   ⟸   NM_001105741
- Peptide Label: precursor
- UniProtKB: P02667 (UniProtKB/Swiss-Prot),   G3V9R6 (UniProtKB/TrEMBL),   A6KU19 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000057022   ⟸   ENSRNOT00000060273
RefSeq Acc Id: ENSRNOP00000087233   ⟸   ENSRNOT00000108881
RefSeq Acc Id: ENSRNOP00000084302   ⟸   ENSRNOT00000105182

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P02667-F1-model_v2 AlphaFold P02667 1-179 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621152 AgrOrtholog
BioCyc Gene G2FUF-16131 BioCyc
Ensembl Genes ENSRNOG00000039331 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000060273 ENTREZGENE
  ENSRNOT00000060273.4 UniProtKB/TrEMBL
  ENSRNOT00000105182.1 UniProtKB/TrEMBL
  ENSRNOT00000108881.1 UniProtKB/TrEMBL
InterPro Alpha-s2_casein UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Casein_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:114595 UniProtKB/TrEMBL
NCBI Gene 114595 ENTREZGENE
PANTHER ALPHA-S2-CASEIN-LIKE A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR16656 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Csn1s2a PhenoGen
PROSITE CASEIN_ALPHA_BETA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000039331 RatGTEx
UniProt A0A8I5ZXS5_RAT UniProtKB/TrEMBL
  A0A8I6GEX6_RAT UniProtKB/TrEMBL
  A6KU19 ENTREZGENE, UniProtKB/TrEMBL
  CS2LA_RAT UniProtKB/Swiss-Prot
  G3V9R6 ENTREZGENE, UniProtKB/TrEMBL
  P02667 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-19 Csn1s2a  casein alpha s2-like A  Csng  casein gamma  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Csng  casein gamma      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Csng  casein gamma      Symbol and Name status set to provisional 70820 PROVISIONAL