Capns2 (calpain, small subunit 2) - Rat Genome Database

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Gene: Capns2 (calpain, small subunit 2) Rattus norvegicus
Analyze
Symbol: Capns2
Name: calpain, small subunit 2
RGD ID: 1583620
Description: Orthologous to human CAPNS2 (calpain small subunit 2); INTERACTS WITH 17beta-estradiol 3-benzoate; 6-propyl-2-thiouracil; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: calpain small subunit 2; LOC679870; similar to Calpain small subunit 2 (CSS2) (Calcium-dependent protease small subunit 2)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
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
GRCr81930,277,324 - 30,278,266 (-)NCBIGRCr8GRCr8GRCr8
mRatBN7.21914,104,334 - 14,105,276 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx1915,800,101 - 15,801,043 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01920,994,873 - 20,995,815 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01923,940,465 - 23,941,407 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01915,485,258 - 15,486,200 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01926,581,115 - 26,603,016 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41915,193,882 - 15,194,824 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1914,027,865 - 14,028,807 (-)NCBICelera
Cytogenetic Map19p11NCBI
JBrowse:




References

References - curated
# Reference Title Reference Citation
1. GOA pipeline RGD automated data pipeline
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:17646163  


Genomics

Comparative Map Data
Capns2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81930,277,324 - 30,278,266 (-)NCBIGRCr8GRCr8GRCr8
mRatBN7.21914,104,334 - 14,105,276 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx1915,800,101 - 15,801,043 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01920,994,873 - 20,995,815 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01923,940,465 - 23,941,407 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01915,485,258 - 15,486,200 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01926,581,115 - 26,603,016 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41915,193,882 - 15,194,824 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1914,027,865 - 14,028,807 (-)NCBICelera
Cytogenetic Map19p11NCBI
CAPNS2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381655,566,684 - 55,567,687 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1655,566,684 - 55,567,687 (+)Ensemblhg38GRCh38
GRCh371655,600,596 - 55,601,599 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361654,158,085 - 54,159,093 (+)NCBIBuild 36Build 36hg18NCBI36
Build 341654,158,084 - 54,159,093NCBI
Celera1640,114,807 - 40,115,815 (+)NCBICelera
Cytogenetic Map16q12.2NCBI
HuRef1641,487,974 - 41,488,982 (+)NCBIHuRef
CHM1_11657,007,840 - 57,008,848 (+)NCBICHM1_1
T2T-CHM13v2.01661,364,815 - 61,365,818 (+)NCBIT2T-CHM13v2.0
Capns2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39893,628,023 - 93,629,037 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl893,628,035 - 93,629,039 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38892,901,395 - 92,902,409 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl892,901,407 - 92,902,411 (+)Ensemblmm10GRCm38
MGSCv37895,425,294 - 95,426,308 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36895,790,532 - 95,791,537 (+)NCBIMGSCv36mm8
Celera897,231,130 - 97,232,142 (+)NCBICelera
Cytogenetic Map8C5NCBI
cM Map844.99NCBI
Capns2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495543313,106,820 - 13,107,865 (+)NCBIChiLan1.0ChiLan1.0
CAPNS2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21864,984,325 - 64,998,220 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11670,913,091 - 70,915,074 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01635,799,223 - 35,800,347 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11654,904,681 - 54,905,690 (+)NCBIPanPan1.1PanPan1.1panPan2
CAPNS2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1260,417,970 - 60,426,891 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha257,051,507 - 57,059,958 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0260,963,456 - 60,971,913 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.1257,790,368 - 57,798,813 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0258,814,598 - 58,823,049 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0259,692,865 - 59,701,316 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Capns2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934951,715,231 - 51,726,394 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049364757,872,423 - 7,874,086 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CAPNS2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1541,351,760 - 41,353,261 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604734,993,859 - 34,995,692 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Capns2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247571,395,102 - 1,396,406 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Capns2
(Rattus rattus - black rat)		 No map positions available.

Variants

.
Variants in Capns2
4 total Variants

QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19131969901Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19799775052997750Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)191922068964220689Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19799775052997750Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191032907674246245Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)19574806450748064Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)193628974246245Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)192409397369093973Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191083361874246245Rat
2303628Vencon9Ventilatory control QTL 90.005respiration trait (VT:0001943)minute ventilation (CMO:0000132)192318858668188586Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19799775052997750Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19799775052997750Rat
1554318Bmd5Bone mineral density QTL 512.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)192318858668188586Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)192010930665109306Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19219431774246245Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19219431774246245Rat
61407Scl12Serum cholesterol level QTL 120.001blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)193009938347207961Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
hemolymphoid system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
sensory system
visual system
7 1 10 46 41 88 60 10 46 21 20 17 17

Sequence


RefSeq Acc Id: NM_001109380   ⟹   NP_001102850
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81930,277,324 - 30,278,266 (-)NCBI
mRatBN7.21914,104,334 - 14,105,276 (-)NCBI
Rnor_6.01915,485,258 - 15,486,200 (-)NCBI
Rnor_5.01926,581,115 - 26,603,016 (-)NCBI
RGSC_v3.41915,193,882 - 15,194,824 (-)RGD
Celera1914,027,865 - 14,028,807 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102850 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL87570 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001102850   ⟸   NM_001109380
- UniProtKB: A6KD57 (UniProtKB/TrEMBL)
- Sequence:
Protein Domains
EF-hand


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1583620 AgrOrtholog
BioCyc Gene G2FUF-6401 BioCyc
Gene3D-CATH EF-hand UniProtKB/TrEMBL
InterPro EF-hand-dom_pair UniProtKB/TrEMBL
  EF_hand_dom UniProtKB/TrEMBL
KEGG Report rno:679870 UniProtKB/TrEMBL
NCBI Gene 679870 ENTREZGENE
PANTHER CALPAIN SMALL SUBUNIT 2 UniProtKB/TrEMBL
  CALPAIN, SMALL SUBUNIT 1 A-RELATED UniProtKB/TrEMBL
Pfam EF-hand_8 UniProtKB/TrEMBL
PhenoGen Capns2 PhenoGen
PROSITE EF_HAND_2 UniProtKB/TrEMBL
Superfamily-SCOP EF-hand UniProtKB/TrEMBL
UniProt A6KD57 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-05 Capns2  calpain, small subunit 2  LOC679870  similar to Calpain small subunit 2 (CSS2) (Calcium-dependent protease small subunit 2)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC679870  similar to Calpain small subunit 2 (CSS2) (Calcium-dependent protease small subunit 2)  LOC682500  similar to Calpain small subunit 2 (CSS2) (Calcium-dependent protease small subunit 2)  Data merged from RGD:1597974 1643240 APPROVED
2006-11-20 LOC682500  similar to Calpain small subunit 2 (CSS2) (Calcium-dependent protease small subunit 2)      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC679870  similar to Calpain small subunit 2 (CSS2) (Calcium-dependent protease small subunit 2)      Symbol and Name status set to provisional 70820 PROVISIONAL