Rcsd1 (RCSD domain containing 1) - 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 QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) RatMine GViewer (Genome Viewer) Overgo Probe Designer VCMap
Aging & Age-Related Disease Cancer Cardiovascular Disease COVID-19 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 PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) 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 Poster Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Rcsd1 (RCSD domain containing 1) Rattus norvegicus
Analyze
Symbol: Rcsd1
Name: RCSD domain containing 1
RGD ID: 1304715
Description: Predicted to enable actin filament binding activity. Involved in skeletal muscle contraction. Orthologous to human RCSD1 (RCSD domain containing 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acetamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: capZ-interacting protein; LOC360872; RGD1304715; similar to Hypothetical protein MGC32399
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
mRatBN7.21377,901,898 - 77,964,336 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1377,901,898 - 77,966,228 (-)Ensembl
Rnor_6.01383,854,650 - 83,917,040 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1383,854,664 - 83,917,021 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01388,734,809 - 88,797,190 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41381,370,795 - 81,387,656 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11381,384,961 - 81,401,846 (-)NCBI
Celera1377,614,795 - 77,676,707 (-)NCBICelera
Cytogenetic Map13q23NCBI
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

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. The phosphorylation of CapZ-interacting protein (CapZIP) by stress-activated protein kinases triggers its dissociation from CapZ. Eyers CE, etal., Biochem J. 2005 Jul 1;389(Pt 1):127-35.
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. 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

Genomics

Comparative Map Data
Rcsd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21377,901,898 - 77,964,336 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1377,901,898 - 77,966,228 (-)Ensembl
Rnor_6.01383,854,650 - 83,917,040 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1383,854,664 - 83,917,021 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01388,734,809 - 88,797,190 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41381,370,795 - 81,387,656 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11381,384,961 - 81,401,846 (-)NCBI
Celera1377,614,795 - 77,676,707 (-)NCBICelera
Cytogenetic Map13q23NCBI
RCSD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381167,630,232 - 167,708,696 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1167,630,093 - 167,708,696 (+)EnsemblGRCh38hg38GRCh38
GRCh371167,599,469 - 167,677,933 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361165,865,954 - 165,942,110 (+)NCBINCBI36hg18NCBI36
Celera1140,708,754 - 140,784,746 (+)NCBI
Cytogenetic Map1q24.2NCBI
HuRef1138,845,527 - 138,921,574 (+)NCBIHuRef
CHM1_11169,021,745 - 169,097,714 (+)NCBICHM1_1
T2T-CHM13v2.01166,981,734 - 167,060,191 (+)NCBI
Rcsd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391165,476,503 - 165,537,632 (-)NCBIGRCm39mm39
GRCm39 Ensembl1165,474,085 - 165,537,326 (-)Ensembl
GRCm381165,648,945 - 165,710,063 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1165,646,516 - 165,709,757 (-)EnsemblGRCm38mm10GRCm38
MGSCv371167,579,076 - 167,638,225 (-)NCBIGRCm37mm9NCBIm37
MGSCv361167,485,620 - 167,544,769 (-)NCBImm8
Celera1168,093,649 - 168,153,153 (-)NCBICelera
Cytogenetic Map1H2.3NCBI
Rcsd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554629,318,218 - 9,384,637 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554629,321,624 - 9,383,962 (-)NCBIChiLan1.0ChiLan1.0
RCSD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11146,895,246 - 146,921,977 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1146,899,485 - 146,921,977 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01143,062,602 - 143,138,987 (+)NCBIMhudiblu_PPA_v0panPan3
RCSD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1730,756,524 - 30,852,309 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl730,756,645 - 30,852,818 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha730,291,890 - 30,363,980 (-)NCBI
ROS_Cfam_1.0730,573,456 - 30,645,719 (-)NCBI
ROS_Cfam_1.0 Ensembl730,574,560 - 30,670,802 (-)Ensembl
UMICH_Zoey_3.1730,413,478 - 30,485,522 (-)NCBI
UNSW_CanFamBas_1.0730,444,773 - 30,541,796 (-)NCBI
UU_Cfam_GSD_1.0730,683,174 - 30,780,128 (-)NCBI
Rcsd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344100,548,850 - 100,600,630 (-)NCBI
SpeTri2.0NW_00493648118,395,577 - 18,447,323 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RCSD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl483,324,187 - 83,404,102 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1483,322,175 - 83,404,102 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2490,999,951 - 91,088,740 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RCSD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12561,325,591 - 61,401,287 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2561,327,144 - 61,400,754 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605563,049,339 - 63,125,421 (-)NCBIVero_WHO_p1.0
Rcsd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248265,729,704 - 5,744,327 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_0046248265,673,114 - 5,745,948 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D13Got63  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21377,960,345 - 77,960,556 (+)MAPPERmRatBN7.2
Rnor_6.01383,913,038 - 83,913,248NCBIRnor6.0
Rnor_5.01388,793,204 - 88,793,414UniSTSRnor5.0
Celera1377,672,744 - 77,672,954UniSTS
RH 3.4 Map13480.1RGD
RH 3.4 Map13480.1UniSTS
RH 2.0 Map13580.0RGD
Cytogenetic Map13q23UniSTS
RH128967  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21377,901,923 - 77,902,117 (+)MAPPERmRatBN7.2
Rnor_6.01383,854,690 - 83,854,883NCBIRnor6.0
Rnor_5.01388,734,856 - 88,735,049UniSTSRnor5.0
RGSC_v3.41381,370,821 - 81,371,014UniSTSRGSC3.4
Celera1377,614,821 - 77,615,014UniSTS
Cytogenetic Map13q23UniSTS
RH142931  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21377,902,961 - 77,903,109 (+)MAPPERmRatBN7.2
Rnor_6.01383,855,728 - 83,855,875NCBIRnor6.0
Rnor_5.01388,735,894 - 88,736,041UniSTSRnor5.0
RGSC_v3.41381,371,859 - 81,372,006UniSTSRGSC3.4
Celera1377,615,859 - 77,616,006UniSTS
Cytogenetic Map13q23UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131101056920Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)138897350101631289Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1320605871101339738Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1330395351101056920Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133124133193395974Rat
61340Bp25Blood pressure QTL 254.20.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133453521879535218Rat
12879477Bp401Blood pressure QTL 401arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133726209282262092Rat
61349Bp31Blood pressure QTL 315.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133737450982374509Rat
70220Bp55Blood pressure QTL 555.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133737450982374509Rat
4889861Pur29Proteinuria QTL 2913.80.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)133741558480753406Rat
1331750Bp220Blood pressure QTL 2202.98arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133741558482415584Rat
1549897Stresp12Stress response QTL 123.35stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)133843340883433408Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133975454484754544Rat
12879444Bp397Blood pressure QTL 397arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134504940490049404Rat
12879471Bp398Blood pressure QTL 398arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134551471990514719Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134569998390699983Rat
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134608804691088046Rat
71119Thym2Thymus enlargement QTL 23.8thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)134619797684753113Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)135236217197362171Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1356056920101056920Rat
738026Lnnr5Liver neoplastic nodule remodeling QTL 53.29liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)135987440885581182Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1361825626106807694Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1365103704106807694Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1365103704106807694Rat
8655945Rf61Renal function QTL 613.6blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)136906051986800898Rat
1331783Bp221Blood pressure QTL 2213.72886arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)136906051986800898Rat
1300166Kidm6Kidney mass QTL 63.93kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)136906051986800898Rat
11530006Niddm72Non-insulin dependent diabetes mellitus QTL 720.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)137402391880753406Rat
8655959Pur32Proteinuria QTL 328.4total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)137402391897213863Rat
738027Lnnr6Liver neoplastic nodule remodeling QTL 63.3liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)137486211785581182Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1374862117101339893Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:300
Count of miRNA genes:185
Interacting mature miRNAs:219
Transcripts:ENSRNOT00000004387
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.


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 43 17 6 19 6 8 11 1 32 31 11 8
Low 1 40 35 35 73 3 10
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000004387   ⟹   ENSRNOP00000004387
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1377,901,898 - 77,966,228 (-)Ensembl
Rnor_6.0 Ensembl1383,854,664 - 83,917,001 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000082422   ⟹   ENSRNOP00000074219
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1377,908,750 - 77,918,891 (-)Ensembl
Rnor_6.0 Ensembl1383,855,444 - 83,917,021 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000112592   ⟹   ENSRNOP00000084185
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1377,901,898 - 77,965,294 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000113367   ⟹   ENSRNOP00000077388
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1377,901,898 - 77,966,228 (-)Ensembl
RefSeq Acc Id: NM_001108349   ⟹   NP_001101819
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21377,901,898 - 77,964,309 (-)NCBI
Rnor_6.01383,854,664 - 83,917,001 (-)NCBI
Rnor_5.01388,734,809 - 88,797,190 (-)NCBI
RGSC_v3.41381,370,795 - 81,387,656 (-)RGD
Celera1377,614,795 - 77,676,707 (-)RGD
Sequence:
RefSeq Acc Id: XM_006250181   ⟹   XP_006250243
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21377,901,898 - 77,964,336 (-)NCBI
Rnor_6.01383,854,650 - 83,917,040 (-)NCBI
Rnor_5.01388,734,809 - 88,797,190 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008769663   ⟹   XP_008767885
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21377,901,898 - 77,960,052 (-)NCBI
Rnor_6.01383,854,650 - 83,870,263 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001101819 (Get FASTA)   NCBI Sequence Viewer  
  XP_006250243 (Get FASTA)   NCBI Sequence Viewer  
  XP_008767885 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM09318 (Get FASTA)   NCBI Sequence Viewer  
  EDM09319 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001101819   ⟸   NM_001108349
- UniProtKB: F1M4V3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006250243   ⟸   XM_006250181
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K7I4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008767885   ⟸   XM_008769663
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000074219   ⟸   ENSRNOT00000082422
RefSeq Acc Id: ENSRNOP00000004387   ⟸   ENSRNOT00000004387
RefSeq Acc Id: ENSRNOP00000077388   ⟸   ENSRNOT00000113367
RefSeq Acc Id: ENSRNOP00000084185   ⟸   ENSRNOT00000112592

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K7I4-F1-model_v2 AlphaFold A0A0G2K7I4 1-412 view protein structure

Transcriptome

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

Promoters
RGD ID:13698962
Promoter ID:EPDNEW_R9487
Type:initiation region
Name:Rcsd1_1
Description:RCSD domain containing 1
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_6.01383,916,994 - 83,917,054EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304715 AgrOrtholog
BioCyc Gene G2FUF-17563 BioCyc
Ensembl Genes ENSRNOG00000003283 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000004387 ENTREZGENE
  ENSRNOP00000004387.6 UniProtKB/TrEMBL
  ENSRNOP00000074219.2 UniProtKB/TrEMBL
  ENSRNOP00000077388 ENTREZGENE
  ENSRNOP00000077388.1 UniProtKB/TrEMBL
  ENSRNOP00000084185 ENTREZGENE
  ENSRNOP00000084185.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000004387 ENTREZGENE
  ENSRNOT00000004387.7 UniProtKB/TrEMBL
  ENSRNOT00000082422.2 UniProtKB/TrEMBL
  ENSRNOT00000112592 ENTREZGENE
  ENSRNOT00000112592.1 UniProtKB/TrEMBL
  ENSRNOT00000113367 ENTREZGENE
  ENSRNOT00000113367.1 UniProtKB/TrEMBL
InterPro FAM21/CAPZIP UniProtKB/TrEMBL
KEGG Report rno:360872 UniProtKB/TrEMBL
NCBI Gene 360872 ENTREZGENE
Pfam CAP-ZIP_m UniProtKB/TrEMBL
PhenoGen Rcsd1 PhenoGen
UniProt A0A0G2K7I4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5YCC4_RAT UniProtKB/TrEMBL
  A0A8I5ZYN8_RAT UniProtKB/TrEMBL
  F1M4V3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Rcsd1  RCSD domain containing 1   Rcsd1_predicted  RCSD domain containing 1 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Rcsd1_predicted  RCSD domain containing 1 (predicted)  RGD1304715_predicted  similar to Hypothetical protein MGC32399 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1304715_predicted  similar to Hypothetical protein MGC32399 (predicted)  LOC360872_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC360872_predicted  similar to Hypothetical protein MGC32399 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL