Snapc4 (small nuclear RNA activating complex, polypeptide 4) - Rat Genome Database

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Gene: Snapc4 (small nuclear RNA activating complex, polypeptide 4) Rattus norvegicus
Analyze
Symbol: Snapc4
Name: small nuclear RNA activating complex, polypeptide 4
RGD ID: 1309048
Description: Predicted to enable RNA polymerase II general transcription initiation factor activity; RNA polymerase III general transcription initiation factor activity; and RNA polymerase III type 3 promoter sequence-specific DNA binding activity. Predicted to contribute to RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in snRNA transcription by RNA polymerase II and snRNA transcription by RNA polymerase III. Predicted to be located in nucleus. Predicted to be part of snRNA-activating protein complex. Orthologous to human SNAPC4 (small nuclear RNA activating complex polypeptide 4); PARTICIPATES IN RNA polymerase III transcription pathway; INTERACTS WITH (+)-schisandrin B; 17beta-estradiol; 4,4'-sulfonyldiphenol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC362088; snRNA-activating protein complex subunit 4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Candidate Gene For: Arunc3
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8329,580,157 - 29,598,440 (-)NCBIGRCr8
mRatBN7.239,182,061 - 9,200,819 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl39,182,067 - 9,199,518 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx312,235,453 - 12,253,026 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0320,818,683 - 20,836,256 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0319,074,021 - 19,091,593 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.033,808,596 - 3,827,425 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl33,809,407 - 3,824,284 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.039,169,824 - 9,188,180 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.434,535,296 - 4,552,793 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.134,536,105 - 4,552,777 (-)NCBI
Celera34,001,978 - 4,020,230 (-)NCBICelera
Cytogenetic Map3p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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 MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Comprehensive gene review and curation RGD comprehensive gene curation
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:8889548   PMID:9418884   PMID:11056176  


Genomics

Comparative Map Data
Snapc4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8329,580,157 - 29,598,440 (-)NCBIGRCr8
mRatBN7.239,182,061 - 9,200,819 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl39,182,067 - 9,199,518 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx312,235,453 - 12,253,026 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0320,818,683 - 20,836,256 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0319,074,021 - 19,091,593 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.033,808,596 - 3,827,425 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl33,809,407 - 3,824,284 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.039,169,824 - 9,188,180 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.434,535,296 - 4,552,793 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.134,536,105 - 4,552,777 (-)NCBI
Celera34,001,978 - 4,020,230 (-)NCBICelera
Cytogenetic Map3p13NCBI
SNAPC4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389136,375,571 - 136,400,170 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9136,375,567 - 136,400,176 (-)EnsemblGRCh38hg38GRCh38
GRCh379139,270,023 - 139,294,622 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369138,389,850 - 138,412,710 (-)NCBINCBI36Build 36hg18NCBI36
Build 349136,545,865 - 136,569,086NCBI
Celera9109,784,965 - 109,807,827 (-)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9108,729,385 - 108,752,220 (-)NCBIHuRef
CHM1_19139,418,225 - 139,441,093 (-)NCBICHM1_1
T2T-CHM13v2.09148,604,905 - 148,629,504 (-)NCBIT2T-CHM13v2.0
Snapc4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39226,252,777 - 26,270,666 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl226,252,777 - 26,270,665 (-)EnsemblGRCm39 Ensembl
GRCm38226,362,765 - 26,380,661 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl226,362,765 - 26,380,653 (-)EnsemblGRCm38mm10GRCm38
MGSCv37226,218,285 - 26,236,173 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36226,184,783 - 26,202,628 (-)NCBIMGSCv36mm8
Celera226,080,406 - 26,098,304 (-)NCBICelera
Cytogenetic Map2A3NCBI
cM Map218.87NCBI
Snapc4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555134,330,293 - 4,350,012 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555134,330,579 - 4,349,136 (+)NCBIChiLan1.0ChiLan1.0
SNAPC4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2112,986,048 - 3,010,973 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan192,988,380 - 3,013,308 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09107,448,180 - 107,473,022 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19136,427,943 - 136,452,868 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9136,428,732 - 136,450,653 (-)Ensemblpanpan1.1panPan2
SNAPC4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1949,090,615 - 49,110,763 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl949,091,636 - 49,110,767 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha948,341,199 - 48,361,450 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0949,967,283 - 49,987,524 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl949,967,675 - 49,987,508 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1948,747,835 - 48,768,076 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0949,041,984 - 49,062,245 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0949,089,882 - 49,109,773 (+)NCBIUU_Cfam_GSD_1.0
Snapc4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947201,948,898 - 201,969,769 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366691,405,275 - 1,425,248 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366691,405,306 - 1,428,222 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SNAPC4
(Sus scrofa - pig)		 No map positions available.
SNAPC4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1121,801,975 - 1,829,823 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl121,802,937 - 1,829,968 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660583,386,543 - 3,414,358 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Snapc4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247601,543,498 - 1,561,178 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247601,542,979 - 1,561,164 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Snapc4
38 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:174
Count of miRNA genes:70
Interacting mature miRNAs:74
Transcripts:ENSRNOT00000061682, ENSRNOT00000068110
Prediction methods:Microtar, 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
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3865816227494778Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3865816227494778Rat

Markers in Region
BF386669  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.239,186,169 - 9,186,329 (+)MAPPERmRatBN7.2
Rnor_6.033,812,701 - 3,812,860NCBIRnor6.0
Rnor_5.039,173,929 - 9,174,088UniSTSRnor5.0
RGSC_v3.434,539,400 - 4,539,559UniSTSRGSC3.4
Celera34,006,083 - 4,006,242UniSTS
Cytogenetic Map3p13UniSTS
RH135436  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.239,182,071 - 9,182,279 (+)MAPPERmRatBN7.2
mRatBN7.2239,697,008 - 39,697,216 (+)MAPPERmRatBN7.2
Rnor_6.0239,484,171 - 39,484,378NCBIRnor6.0
Rnor_6.033,808,603 - 3,808,810NCBIRnor6.0
Rnor_5.039,169,831 - 9,170,038UniSTSRnor5.0
Rnor_5.0258,568,505 - 58,568,712UniSTSRnor5.0
RGSC_v3.4239,432,954 - 39,433,161UniSTSRGSC3.4
RGSC_v3.434,535,302 - 4,535,509UniSTSRGSC3.4
Celera34,001,985 - 4,002,192UniSTS
Celera235,538,129 - 35,538,336UniSTS
Cytogenetic Map3p13UniSTS


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 2 2 2 2 62 12 32 1
Low 3 41 55 39 19 39 8 11 12 23 9 10 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000061682   ⟹   ENSRNOP00000058393
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl39,182,876 - 9,199,518 (-)Ensembl
Rnor_6.0 Ensembl33,809,407 - 3,824,284 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000068110   ⟹   ENSRNOP00000061702
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl39,182,067 - 9,199,518 (-)Ensembl
Rnor_6.0 Ensembl33,809,407 - 3,824,284 (-)Ensembl
RefSeq Acc Id: NM_001108574   ⟹   NP_001102044
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8329,580,157 - 29,597,610 (-)NCBI
mRatBN7.239,182,065 - 9,199,518 (-)NCBI
RefSeq Acc Id: XM_006233716   ⟹   XP_006233778
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8329,580,157 - 29,598,440 (-)NCBI
mRatBN7.239,182,061 - 9,200,819 (-)NCBI
Rnor_6.033,808,596 - 3,827,425 (-)NCBI
Rnor_5.039,169,824 - 9,188,180 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001102044 (Get FASTA)   NCBI Sequence Viewer  
  XP_006233778 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL93506 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000058393.5
  ENSRNOP00000061702
  ENSRNOP00000061702.3
Reference Protein Sequences
RefSeq Acc Id: XP_006233778   ⟸   XM_006233716
- Peptide Label: isoform X1
- UniProtKB: D4A3C9 (UniProtKB/TrEMBL),   F1LYZ6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000058393   ⟸   ENSRNOT00000061682
RefSeq Acc Id: ENSRNOP00000061702   ⟸   ENSRNOT00000068110
RefSeq Acc Id: NP_001102044   ⟸   NM_001108574
- UniProtKB: D4A3C9 (UniProtKB/TrEMBL),   F1LYZ6 (UniProtKB/TrEMBL)
Protein Domains
HTH myb-type   Myb-like   SANT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A3C9-F1-model_v2 AlphaFold D4A3C9 1-1337 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:1309048 AgrOrtholog
BioCyc Gene G2FUF-50383 BioCyc
Ensembl Genes ENSRNOG00000018845 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000061682.5 UniProtKB/TrEMBL
  ENSRNOT00000068110 ENTREZGENE
  ENSRNOT00000068110.5 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro Homeodomain-like UniProtKB/TrEMBL
  Myb_dom UniProtKB/TrEMBL
  SANT/Myb UniProtKB/TrEMBL
  SANT_dom UniProtKB/TrEMBL
NCBI Gene 362088 ENTREZGENE
PANTHER SNRNA-ACTIVATING PROTEIN COMPLEX SUBUNIT 4 UniProtKB/TrEMBL
  SNRNA-ACTIVATING PROTEIN COMPLEX SUBUNIT 4 UniProtKB/TrEMBL
Pfam Myb_DNA-bind_6 UniProtKB/TrEMBL
  Myb_DNA-binding UniProtKB/TrEMBL
PhenoGen Snapc4 PhenoGen
PROSITE HTH_MYB UniProtKB/TrEMBL
  MYB_LIKE UniProtKB/TrEMBL
  SANT UniProtKB/TrEMBL
RatGTEx ENSRNOG00000018845 RatGTEx
SMART SANT UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt D4A3C9 ENTREZGENE, UniProtKB/TrEMBL
  F1LYZ6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Snapc4  small nuclear RNA activating complex, polypeptide 4   Snapc4_predicted  small nuclear RNA activating complex, polypeptide 4 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Snapc4_predicted  small nuclear RNA activating complex, polypeptide 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED