Spidr (scaffold protein involved in DNA repair) - Rat Genome Database

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Gene: Spidr (scaffold protein involved in DNA repair) Rattus norvegicus
Analyze
Symbol: Spidr
Name: scaffold protein involved in DNA repair
RGD ID: 1566036
Description: Predicted to be involved in several processes, including cellular response to camptothecin; cellular response to hydroxyurea; and regulation of double-strand break repair. Predicted to be active in nuclear chromosome and nucleoplasm. Human ortholog(s) of this gene implicated in 46 XX gonadal dysgenesis. Orthologous to human SPIDR (scaffold protein involved in DNA repair); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: hypothetical protein LOC498119; LOC498119; MGC156776; RGD1566036; scaffolding protein involved in DNA repair; similar to RIKEN cDNA 2310008H04; uncharacterized protein LOC498119
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
mRatBN7.21184,766,593 - 85,007,597 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1184,766,593 - 85,007,600 (-)Ensembl
Rnor_6.01189,009,931 - 89,260,361 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1189,009,931 - 89,260,297 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01192,071,681 - 92,113,042 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01192,163,149 - 92,313,960 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41186,830,121 - 86,918,203 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1183,509,894 - 83,748,337 (-)NCBICelera
Cytogenetic Map11q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

Additional References at PubMed
PMID:12477932   PMID:23509288   PMID:23754376  


Genomics

Comparative Map Data
Spidr
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21184,766,593 - 85,007,597 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1184,766,593 - 85,007,600 (-)Ensembl
Rnor_6.01189,009,931 - 89,260,361 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1189,009,931 - 89,260,297 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01192,071,681 - 92,113,042 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01192,163,149 - 92,313,960 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41186,830,121 - 86,918,203 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1183,509,894 - 83,748,337 (-)NCBICelera
Cytogenetic Map11q23NCBI
SPIDR
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38847,260,878 - 47,736,306 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl847,260,878 - 47,736,306 (+)EnsemblGRCh38hg38GRCh38
GRCh37848,173,470 - 48,648,868 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36848,336,095 - 48,811,028 (+)NCBINCBI36hg18NCBI36
Celera844,177,794 - 44,633,625 (+)NCBI
Cytogenetic Map8q11.21NCBI
HuRef843,638,756 - 44,111,478 (+)NCBIHuRef
CHM1_1848,225,097 - 48,700,450 (+)NCBICHM1_1
T2T-CHM13v2.0847,636,640 - 48,112,023 (+)NCBI
Spidr
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391615,707,088 - 15,964,715 (-)NCBIGRCm39mm39
GRCm39 Ensembl1615,707,088 - 15,964,715 (-)Ensembl
GRCm381615,889,224 - 16,146,851 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1615,889,224 - 16,146,851 (-)EnsemblGRCm38mm10GRCm38
MGSCv371615,889,320 - 16,146,926 (-)NCBIGRCm37mm9NCBIm37
MGSCv361615,802,805 - 16,060,411 (-)NCBImm8
Celera1616,460,508 - 16,718,485 (-)NCBICelera
Cytogenetic Map16A2NCBI
Spidr
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554547,359,670 - 7,711,680 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554547,360,144 - 7,710,077 (+)NCBIChiLan1.0ChiLan1.0
SPIDR
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1841,083,934 - 41,559,683 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl841,083,964 - 41,558,170 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0843,691,454 - 44,166,259 (+)NCBIMhudiblu_PPA_v0panPan3
SPIDR
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13579,188 - 503,687 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3579,185 - 514,797 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3590,608 - 526,254 (-)NCBI
ROS_Cfam_1.03528,419 - 463,757 (-)NCBI
UMICH_Zoey_3.13513,433 - 448,429 (-)NCBI
UNSW_CanFamBas_1.03531,778 - 466,957 (-)NCBI
UU_Cfam_GSD_1.0351,366,967 - 1,802,342 (-)NCBI
Spidr
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530379,731,806 - 80,126,422 (-)NCBI
SpeTri2.0NW_0049365904,921,755 - 5,041,573 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SPIDR
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl479,874,828 - 80,190,655 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1479,874,937 - 80,190,744 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2487,754,732 - 87,756,996 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SPIDR
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1843,380,207 - 43,872,077 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl843,380,244 - 43,872,937 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603998,198,670 - 98,702,703 (-)NCBIVero_WHO_p1.0
Spidr
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247357,724,048 - 8,172,725 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D11Got76  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera1183,540,545 - 83,540,677UniSTS
RH 2.0 Map110.0RGD
Cytogenetic Map11q23UniSTS
RH132793  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21184,766,809 - 84,767,021 (+)MAPPERmRatBN7.2
Rnor_6.01189,010,148 - 89,010,359NCBIRnor6.0
Rnor_5.01192,071,898 - 92,072,109UniSTSRnor5.0
Celera1183,510,111 - 83,510,322UniSTS
RH 3.4 Map2859.79UniSTS
Cytogenetic Map11q23UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116034659086241447Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)116642214886241447Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116642214886241447Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:509
Count of miRNA genes:253
Interacting mature miRNAs:295
Transcripts:ENSRNOT00000057502
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.


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 22 12 15 12 16 17 37 11
Low 3 43 35 29 4 29 8 11 58 18 4 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001100988 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008768898 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598050 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598051 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598052 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088589 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088590 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088591 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088592 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088593 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088594 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088595 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088596 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088597 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088598 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC129120 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473999 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000222 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000057502   ⟹   ENSRNOP00000054310
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1184,766,593 - 85,007,563 (-)Ensembl
Rnor_6.0 Ensembl1189,010,377 - 89,260,297 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000089517   ⟹   ENSRNOP00000071950
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1184,766,593 - 85,002,150 (-)Ensembl
Rnor_6.0 Ensembl1189,009,931 - 89,239,798 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000111413   ⟹   ENSRNOP00000078167
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1184,766,597 - 85,007,600 (-)Ensembl
RefSeq Acc Id: NM_001100988   ⟹   NP_001094458
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21184,766,593 - 85,007,563 (-)NCBI
Rnor_6.01189,009,931 - 89,260,332 (-)NCBI
Rnor_5.01192,071,681 - 92,113,042 (-)NCBI
Rnor_5.01192,163,149 - 92,313,960 (-)NCBI
RGSC_v3.41186,830,121 - 86,918,203 (-)RGD
Celera1183,509,894 - 83,748,337 (-)RGD
Sequence:
RefSeq Acc Id: XM_008768898   ⟹   XP_008767120
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21184,766,596 - 85,007,597 (-)NCBI
Rnor_6.01189,009,934 - 89,260,361 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017598050   ⟹   XP_017453539
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21184,766,596 - 85,007,597 (-)NCBI
Rnor_6.01189,009,934 - 89,260,361 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039088589   ⟹   XP_038944517
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21184,766,596 - 85,007,597 (-)NCBI
RefSeq Acc Id: XM_039088590   ⟹   XP_038944518
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21184,766,596 - 85,007,597 (-)NCBI
RefSeq Acc Id: XM_039088591   ⟹   XP_038944519
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21184,766,596 - 85,007,597 (-)NCBI
RefSeq Acc Id: XM_039088592   ⟹   XP_038944520
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21184,771,453 - 85,007,597 (-)NCBI
RefSeq Acc Id: XM_039088593   ⟹   XP_038944521
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21184,766,596 - 85,007,597 (-)NCBI
RefSeq Acc Id: XM_039088594   ⟹   XP_038944522
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21184,766,596 - 85,007,597 (-)NCBI
RefSeq Acc Id: XM_039088595   ⟹   XP_038944523
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21184,766,596 - 85,007,597 (-)NCBI
RefSeq Acc Id: XM_039088596   ⟹   XP_038944524
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21184,766,596 - 84,974,832 (-)NCBI
RefSeq Acc Id: XM_039088597   ⟹   XP_038944525
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21184,808,399 - 85,007,597 (-)NCBI
RefSeq Acc Id: XM_039088598   ⟹   XP_038944526
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21184,766,596 - 84,850,670 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001094458   ⟸   NM_001100988
- UniProtKB: A2VD15 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008767120   ⟸   XM_008768898
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017453539   ⟸   XM_017598050
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000054310   ⟸   ENSRNOT00000057502
RefSeq Acc Id: ENSRNOP00000071950   ⟸   ENSRNOT00000089517
RefSeq Acc Id: XP_038944523   ⟸   XM_039088595
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038944522   ⟸   XM_039088594
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038944521   ⟸   XM_039088593
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038944518   ⟸   XM_039088590
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038944519   ⟸   XM_039088591
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038944517   ⟸   XM_039088589
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038944524   ⟸   XM_039088596
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038944526   ⟸   XM_039088598
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038944520   ⟸   XM_039088592
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038944525   ⟸   XM_039088597
- Peptide Label: isoform X11
RefSeq Acc Id: ENSRNOP00000078167   ⟸   ENSRNOT00000111413
Protein Domains
DUF4502   DUF4503

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A2VD15-F1-model_v2 AlphaFold A2VD15 1-878 view protein structure

Transcriptome

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

Promoters
RGD ID:13698347
Promoter ID:EPDNEW_R8872
Type:initiation region
Name:Spidr_1
Description:scaffolding protein involved in DNA repair
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_6.01189,260,324 - 89,260,384EPDNEW

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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
11 89017241 89017242 C G snv SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), SR/JrHsd (RGD), SS/Jr (RGD), SS/JrHsdMcwi (RGD), LL/MavRrrcAek (2020), SS/JrHsdMcwi (2019), LH/MavRrrcAek (2020), LL/MavRrrc (RGD), LH/MavRrrc (RGD), SR/JrHsd (2020)
11 89017246 89017247 C G snv FHL/EurMcwi (RGD), FHL/EurMcwi (MCW), CDR, MR/N (2020), FHH/EurMcwi (2019), MNS/Gib (RGD), FHH/EurMcwi (MCW), FHH/EurMcwi (RGD)
11 89034547 89034548 G A snv FHL/EurMcwi (MCW), CDR, MR/N (2020), FHH/EurMcwi (2019), MNS/Gib (RGD), FHH/EurMcwi (RGD), FHH/EurMcwi (MCW), FHL/EurMcwi (RGD)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
11 84773903 84773904 C G snv SR/JrHsd (2020), SS/JrHsdMcwi (2019), LH/MavRrrcAek (2020), LL/MavRrrcAek (2020)
11 84773908 84773909 C G snv MR/N (2020), FHH/EurMcwi (2019)
11 84789236 84789237 G A snv FHH/EurMcwi (2019), MR/N (2020)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1566036 AgrOrtholog
BioCyc Gene G2FUF-20544 BioCyc
Ensembl Genes ENSRNOG00000037851 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000054310 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000071950 UniProtKB/TrEMBL
  ENSRNOP00000078167 ENTREZGENE
Ensembl Transcript ENSRNOT00000057502 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000089517 UniProtKB/TrEMBL
  ENSRNOT00000111413 ENTREZGENE
IMAGE_CLONE IMAGE:7123928 IMAGE-MGC_LOAD
InterPro DUF4502 UniProtKB/TrEMBL
  DUF4503 UniProtKB/TrEMBL
KEGG Report rno:498119 UniProtKB/TrEMBL
MGC_CLONE MGC:156776 IMAGE-MGC_LOAD
NCBI Gene 498119 ENTREZGENE
Pfam DUF4502 UniProtKB/TrEMBL
  DUF4503 UniProtKB/TrEMBL
PhenoGen Spidr PhenoGen
UniProt A0A0G2K1R3_RAT UniProtKB/TrEMBL
  A2VD15 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary E9PSZ4 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-03-16 Spidr  scaffold protein involved in DNA repair  Spidr  scaffolding protein involved in DNA repair  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-07 Spidr  scaffolding protein involved in DNA repair  RGD1566036  similar to RIKEN cDNA 2310008H04  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1566036  similar to RIKEN cDNA 2310008H04   RGD1566036_predicted  similar to RIKEN cDNA 2310008H04 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1566036_predicted  similar to RIKEN cDNA 2310008H04 (predicted)  LOC498119  similar to RIKEN cDNA 2310008H04  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC498119  similar to RIKEN cDNA 2310008H04      Symbol and Name status set to provisional 70820 PROVISIONAL