Snapc2 (small nuclear RNA activating complex, polypeptide 2) - Rat Genome Database

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Gene: Snapc2 (small nuclear RNA activating complex, polypeptide 2) Rattus norvegicus
Analyze
Symbol: Snapc2
Name: small nuclear RNA activating complex, polypeptide 2
RGD ID: 1304589
Description: Predicted to enable RNA polymerase II general transcription initiation factor activity. Predicted to be involved in snRNA transcription and transcription by RNA polymerase II. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in nuclear body. Orthologous to human SNAPC2 (small nuclear RNA activating complex polypeptide 2); PARTICIPATES IN RNA polymerase III transcription pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; cadmium dichloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC304204; small nuclear RNA-activating complex polypeptide 2; SNAPc 45 kDa subunit; SNAPc subunit 2; snRNA-activating protein complex 45 kDa subunit; snRNA-activating protein complex subunit 2
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
GRCr8127,403,650 - 7,406,840 (+)NCBIGRCr8
mRatBN7.2122,605,794 - 2,608,997 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl122,605,810 - 2,608,999 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx123,253,889 - 3,257,071 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0123,877,480 - 3,880,662 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0122,640,493 - 2,643,675 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0122,537,291 - 2,540,774 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl122,537,275 - 2,540,668 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0124,690,238 - 4,693,261 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4121,534,904 - 1,538,056 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1121,534,905 - 1,538,056 (-)NCBI
Celera124,421,340 - 4,424,527 (+)NCBICelera
Cytogenetic Map12p12NCBI
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

Cellular Component
cytosol  (IEA,ISO)
nuclear body  (IBA,ISO)
nucleoplasm  (ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
6. A structural perspective on RNA polymerase I and RNA polymerase III transcription machineries. Vannini A Biochim Biophys Acta. 2013 Mar-Apr;1829(3-4):258-64. doi: 10.1016/j.bbagrm.2012.09.009. Epub 2012 Sep 29.
Additional References at PubMed
PMID:15489334  


Genomics

Comparative Map Data
Snapc2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8127,403,650 - 7,406,840 (+)NCBIGRCr8
mRatBN7.2122,605,794 - 2,608,997 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl122,605,810 - 2,608,999 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx123,253,889 - 3,257,071 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0123,877,480 - 3,880,662 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0122,640,493 - 2,643,675 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0122,537,291 - 2,540,774 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl122,537,275 - 2,540,668 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0124,690,238 - 4,693,261 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4121,534,904 - 1,538,056 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1121,534,905 - 1,538,056 (-)NCBI
Celera124,421,340 - 4,424,527 (+)NCBICelera
Cytogenetic Map12p12NCBI
SNAPC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38197,920,338 - 7,923,250 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl197,920,338 - 7,923,250 (+)EnsemblGRCh38hg38GRCh38
GRCh37197,985,223 - 7,988,135 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36197,891,229 - 7,894,134 (+)NCBINCBI36Build 36hg18NCBI36
Build 34197,891,228 - 7,894,134NCBI
Celera197,856,396 - 7,859,338 (+)NCBICelera
Cytogenetic Map19p13.2NCBI
HuRef197,655,493 - 7,658,435 (+)NCBIHuRef
CHM1_1197,984,663 - 7,987,605 (+)NCBICHM1_1
T2T-CHM13v2.0197,921,293 - 7,924,205 (+)NCBIT2T-CHM13v2.0
Snapc2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3984,303,102 - 4,306,220 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl84,303,080 - 4,306,220 (+)EnsemblGRCm39 Ensembl
GRCm3884,253,102 - 4,256,220 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl84,253,080 - 4,256,220 (+)EnsemblGRCm38mm10GRCm38
MGSCv3784,253,102 - 4,256,220 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3684,253,102 - 4,256,220 (+)NCBIMGSCv36mm8
Celera84,453,691 - 4,456,809 (+)NCBICelera
Cytogenetic Map8A1.1NCBI
cM Map81.99NCBI
Snapc2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555631,343,085 - 1,347,496 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555631,345,100 - 1,347,593 (-)NCBIChiLan1.0ChiLan1.0
SNAPC2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22012,603,182 - 12,606,032 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11911,720,379 - 11,723,230 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0197,221,613 - 7,224,501 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1198,073,530 - 8,077,142 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl198,074,290 - 8,076,662 (+)Ensemblpanpan1.1panPan2
SNAPC2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12052,608,384 - 52,611,252 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2052,608,447 - 52,611,221 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2052,410,972 - 52,413,740 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02053,136,645 - 53,139,526 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2053,136,686 - 53,142,982 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12052,339,912 - 52,342,829 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02052,784,519 - 52,787,288 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02053,016,006 - 53,018,827 (+)NCBIUU_Cfam_GSD_1.0
Snapc2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118212,935,786 - 212,938,482 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365884,896,329 - 4,901,417 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365884,896,248 - 4,898,996 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SNAPC2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl271,291,257 - 71,294,006 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1271,291,256 - 71,294,508 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2271,691,644 - 71,694,334 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SNAPC2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.167,371,623 - 7,374,617 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl67,370,959 - 7,376,998 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666081439,688 - 442,719 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Snapc2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624828883,194 - 885,408 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624828882,370 - 885,866 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Snapc2
27 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:64
Count of miRNA genes:50
Interacting mature miRNAs:57
Transcripts:ENSRNOT00000001398
Prediction methods: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
1300174Bw15Body weight QTL 152.93body mass (VT:0001259)body weight loss (CMO:0001399)1219318387Rat
2312418Kidm41Kidney mass QTL 413.70.0001kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)12119611090Rat
10755457Coatc14Coat color QTL 140.01759coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)12122591684Rat
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12123297788Rat
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12129333307Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12134851688Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)12142110980Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)12142110980Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12142450532Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12144465750Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12144503507Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12144503507Rat
7243862Mcs30Mammary carcinoma susceptibility QTL 308.62mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)127977298525593Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12117200546172005Rat

Markers in Region
RH130973  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2122,608,723 - 2,608,937 (-)MAPPERmRatBN7.2
Rnor_6.0122,537,351 - 2,537,564NCBIRnor6.0
Rnor_5.0124,690,298 - 4,690,511UniSTSRnor5.0
RGSC_v3.4121,534,961 - 1,535,174UniSTSRGSC3.4
Celera124,424,257 - 4,424,470UniSTS
Cytogenetic Map12p12UniSTS


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 27 15 12 6 12 74 27 41 3
Low 16 42 29 13 29 8 11 8 8 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000001398   ⟹   ENSRNOP00000001398
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl122,605,810 - 2,608,999 (+)Ensembl
Rnor_6.0 Ensembl122,537,275 - 2,540,668 (-)Ensembl
RefSeq Acc Id: NM_001013121   ⟹   NP_001013139
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8127,403,650 - 7,406,837 (+)NCBI
mRatBN7.2122,605,807 - 2,608,994 (+)NCBI
Rnor_6.0122,537,294 - 2,540,489 (-)NCBI
Rnor_5.0124,690,238 - 4,693,261 (-)NCBI
RGSC_v3.4121,534,904 - 1,538,056 (-)RGD
Celera124,421,340 - 4,424,527 (+)RGD
Sequence:
RefSeq Acc Id: NM_001415804   ⟹   NP_001402733
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8127,403,920 - 7,406,840 (+)NCBI
mRatBN7.2122,606,077 - 2,608,997 (+)NCBI
RefSeq Acc Id: XM_008768956   ⟹   XP_008767178
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8127,403,668 - 7,406,840 (+)NCBI
mRatBN7.2122,605,794 - 2,608,997 (+)NCBI
Rnor_6.0122,537,291 - 2,540,774 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039089313   ⟹   XP_038945241
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8127,404,090 - 7,406,840 (+)NCBI
mRatBN7.2122,606,265 - 2,608,997 (+)NCBI
RefSeq Acc Id: NP_001013139   ⟸   NM_001013121
- Peptide Label: isoform 1
- UniProtKB: Q68FX5 (UniProtKB/Swiss-Prot),   A6KQ68 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008767178   ⟸   XM_008768956
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000001398   ⟸   ENSRNOT00000001398
RefSeq Acc Id: XP_038945241   ⟸   XM_039089313
- Peptide Label: isoform X2
RefSeq Acc Id: NP_001402733   ⟸   NM_001415804
- Peptide Label: isoform 2
- UniProtKB: A6KQ70 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q68FX5-F1-model_v2 AlphaFold Q68FX5 1-359 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:1304589 AgrOrtholog
BioCyc Gene G2FUF-20349 BioCyc
Ensembl Genes ENSRNOG00000001056 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055004127 UniProtKB/Swiss-Prot
  ENSRNOG00060002510 UniProtKB/Swiss-Prot
  ENSRNOG00065005804 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000001398 ENTREZGENE
  ENSRNOT00000001398.7 UniProtKB/Swiss-Prot
  ENSRNOT00055006595 UniProtKB/Swiss-Prot
  ENSRNOT00060004021 UniProtKB/Swiss-Prot
  ENSRNOT00065008682 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7122319 IMAGE-MGC_LOAD
InterPro SNAPC2 UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
KEGG Report rno:304204 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:94033 IMAGE-MGC_LOAD
NCBI Gene 304204 ENTREZGENE
PANTHER PTHR15132 UniProtKB/Swiss-Prot
  SNRNA-ACTIVATING PROTEIN COMPLEX SUBUNIT 2 UniProtKB/Swiss-Prot
  SNRNA-ACTIVATING PROTEIN COMPLEX SUBUNIT 2 UniProtKB/TrEMBL
  SNRNA-ACTIVATING PROTEIN COMPLEX SUBUNIT 2 UniProtKB/TrEMBL
Pfam SNAPC2 UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
PhenoGen Snapc2 PhenoGen
RatGTEx ENSRNOG00000001056 RatGTEx
  ENSRNOG00055004127 RatGTEx
  ENSRNOG00060002510 RatGTEx
  ENSRNOG00065005804 RatGTEx
UniProt A6KQ68 ENTREZGENE, UniProtKB/TrEMBL
  A6KQ69_RAT UniProtKB/TrEMBL
  A6KQ70 ENTREZGENE, UniProtKB/TrEMBL
  A6KQ71_RAT UniProtKB/TrEMBL
  Q68FX5 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Snapc2  small nuclear RNA activating complex, polypeptide 2  Snapc2_predicted  small nuclear RNA activating complex, polypeptide 2 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Snapc2_predicted  small nuclear RNA activating complex, polypeptide 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED