Sned1 (sushi, nidogen and EGF-like domains 1) - Rat Genome Database

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Gene: Sned1 (sushi, nidogen and EGF-like domains 1) Rattus norvegicus
Analyze
Symbol: Sned1
Name: sushi, nidogen and EGF-like domains 1
RGD ID: 1566079
Description: Predicted to have Notch binding activity. Predicted to be involved in cell-matrix adhesion. Predicted to localize to extracellular region. Orthologous to human SNED1 (sushi, nidogen and EGF like domains 1); INTERACTS WITH (+)-schisandrin B; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: insulin responsive sequence DNA binding protein 1; insulin responsive sequence DNA binding protein-1; insulin-responsive sequence DNA-binding protein 1; IRE-BP1; sushi, nidogen and EGF-like domain-containing protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2993,774,087 - 93,834,003 (+)NCBI
Rnor_6.0 Ensembl9100,380,515 - 100,437,056 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.09100,380,487 - 100,439,125 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.09100,037,552 - 100,095,480 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4992,509,499 - 92,568,597 (+)NCBIRGSC3.4rn4RGSC3.4
Celera991,309,255 - 91,365,649 (+)NCBICelera
Cytogenetic Map9q36NCBI
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

Molecular Function

References

Additional References at PubMed
PMID:15194686   PMID:15753094   PMID:18566119   PMID:19213832   PMID:23376485  


Genomics

Comparative Map Data
Sned1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2993,774,087 - 93,834,003 (+)NCBI
Rnor_6.0 Ensembl9100,380,515 - 100,437,056 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.09100,380,487 - 100,439,125 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.09100,037,552 - 100,095,480 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4992,509,499 - 92,568,597 (+)NCBIRGSC3.4rn4RGSC3.4
Celera991,309,255 - 91,365,649 (+)NCBICelera
Cytogenetic Map9q36NCBI
SNED1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2240,998,618 - 241,095,568 (+)EnsemblGRCh38hg38GRCh38
GRCh382240,997,410 - 241,095,568 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372241,938,035 - 242,034,983 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362241,586,928 - 241,682,316 (+)NCBINCBI36hg18NCBI36
Celera2235,639,389 - 235,703,345 (+)NCBI
Cytogenetic Map2q37.3NCBI
HuRef2233,693,935 - 233,789,651 (+)NCBIHuRef
CHM1_12241,941,955 - 242,039,698 (+)NCBICHM1_1
Sned1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39193,163,518 - 93,228,787 (+)NCBIGRCm39mm39
GRCm39 Ensembl193,163,563 - 93,228,787 (+)Ensembl
GRCm38193,235,796 - 93,301,065 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl193,235,841 - 93,301,065 (+)EnsemblGRCm38mm10GRCm38
MGSCv37195,132,474 - 95,193,025 (+)NCBIGRCm37mm9NCBIm37
MGSCv36195,066,247 - 95,131,471 (+)NCBImm8
Celera196,180,585 - 96,241,119 (+)NCBICelera
Cytogenetic Map1DNCBI
Sned1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955542589,746 - 627,519 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955542587,159 - 628,159 (-)NCBIChiLan1.0ChiLan1.0
SNED1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B247,067,282 - 247,149,093 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B247,085,509 - 247,144,421 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B128,253,888 - 128,351,819 (+)NCBIMhudiblu_PPA_v0panPan3
SNED1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12551,057,358 - 51,139,808 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2551,057,376 - 51,135,412 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2551,270,707 - 51,351,866 (+)NCBI
ROS_Cfam_1.02551,252,472 - 51,333,679 (+)NCBI
UMICH_Zoey_3.12551,100,189 - 51,181,355 (+)NCBI
UNSW_CanFamBas_1.02550,839,827 - 50,920,931 (+)NCBI
UU_Cfam_GSD_1.02551,115,989 - 51,197,175 (+)NCBI
Sned1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303192,442,944 - 192,509,852 (+)NCBI
SpeTri2.0NW_004936745709,446 - 761,932 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SNED1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15139,821,046 - 139,881,098 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115139,821,021 - 139,881,099 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215154,937,025 - 154,997,243 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SNED1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110127,058,188 - 127,142,945 (+)NCBI
ChlSab1.1 Ensembl10127,058,358 - 127,138,704 (+)Ensembl
Sned1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248475,146,973 - 5,207,481 (+)NCBI

Position Markers
RH134511  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.09100,436,371 - 100,436,564NCBIRnor6.0
Rnor_5.09100,092,726 - 100,092,919UniSTSRnor5.0
RGSC_v3.4992,567,912 - 92,568,105UniSTSRGSC3.4
Celera991,364,964 - 91,365,157UniSTS
RH 3.4 Map9798.4UniSTS
Cytogenetic Map9q36UniSTS
BI290549  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.09100,436,651 - 100,436,837NCBIRnor6.0
Rnor_5.09100,093,006 - 100,093,192UniSTSRnor5.0
RGSC_v3.4992,568,192 - 92,568,378UniSTSRGSC3.4
Celera991,365,244 - 91,365,430UniSTS
RH 3.4 Map9796.3UniSTS
Cytogenetic Map9q36UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)929075079122095297Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)929466970107878528Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)941261034102531865Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)961186278106186278Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)963270073107878387Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)966757444112943287Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)970241351115241351Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)970942881115942881Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)981411073119983851Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)983686153111609081Rat
4889852Pur26Proteinuria QTL 26150.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)990024661107199079Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)990024661119983851Rat
1582203Gluco19Glucose level QTL 193.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)999041068107878528Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:508
Count of miRNA genes:251
Interacting mature miRNAs:292
Transcripts:ENSRNOT00000022290
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 5 10 23 27 34 11
Low 3 42 50 39 9 39 8 11 51 8 7 8
Below cutoff 1 2 2 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001167842 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006245526 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767373 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767374 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596495 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083765 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083766 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083767 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083768 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083769 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005488918 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005488919 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005488920 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005488921 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005488922 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_594500 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF439714 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF439716 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473997 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212488 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220158 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220366 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224877 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000215 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000022290   ⟹   ENSRNOP00000022290
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl9100,380,515 - 100,437,056 (+)Ensembl
RefSeq Acc Id: NM_001167842   ⟹   NP_001161314
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2993,774,119 - 93,830,694 (+)NCBI
Rnor_6.09100,380,515 - 100,437,056 (+)NCBI
Rnor_5.09100,037,552 - 100,095,480 (+)NCBI
RGSC_v3.4992,509,499 - 92,568,597 (+)RGD
Celera991,309,255 - 91,365,649 (+)RGD
Sequence:
RefSeq Acc Id: XM_006245526   ⟹   XP_006245588
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.09100,380,489 - 100,439,125 (+)NCBI
Rnor_5.09100,037,552 - 100,095,480 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008767373   ⟹   XP_008765595
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.09100,380,487 - 100,439,125 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008767374   ⟹   XP_008765596
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.09100,380,487 - 100,429,935 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596495   ⟹   XP_017451984
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.09100,380,489 - 100,439,125 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039083765   ⟹   XP_038939693
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2993,774,088 - 93,834,003 (+)NCBI
RefSeq Acc Id: XM_039083766   ⟹   XP_038939694
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2993,774,088 - 93,823,473 (+)NCBI
RefSeq Acc Id: XM_039083767   ⟹   XP_038939695
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2993,774,089 - 93,834,003 (+)NCBI
RefSeq Acc Id: XM_039083768   ⟹   XP_038939696
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2993,774,089 - 93,834,003 (+)NCBI
RefSeq Acc Id: XM_039083769   ⟹   XP_038939697
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2993,774,088 - 93,815,907 (+)NCBI
RefSeq Acc Id: XR_005488918
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2993,774,088 - 93,824,214 (+)NCBI
RefSeq Acc Id: XR_005488919
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2993,774,088 - 93,824,212 (+)NCBI
RefSeq Acc Id: XR_005488920
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2993,774,087 - 93,834,003 (+)NCBI
RefSeq Acc Id: XR_005488921
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2993,774,088 - 93,816,227 (+)NCBI
RefSeq Acc Id: XR_005488922
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2993,774,088 - 93,816,227 (+)NCBI
RefSeq Acc Id: XR_594500
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.09100,380,487 - 100,429,934 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001161314   ⟸   NM_001167842
- Peptide Label: precursor
- UniProtKB: D3ZNR4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006245588   ⟸   XM_006245526
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008765595   ⟸   XM_008767373
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008765596   ⟸   XM_008767374
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017451984   ⟸   XM_017596495
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000022290   ⟸   ENSRNOT00000022290
RefSeq Acc Id: XP_038939693   ⟸   XM_039083765
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038939694   ⟸   XM_039083766
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038939697   ⟸   XM_039083769
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038939695   ⟸   XM_039083767
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038939696   ⟸   XM_039083768
- Peptide Label: isoform X4
Protein Domains
EGF-like   Fibronectin type-III   NIDO   Sushi

Transcriptome

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

Promoters
RGD ID:13696871
Promoter ID:EPDNEW_R7396
Type:single initiation site
Name:Sned1_1
Description:sushi, nidogen and EGF-like domains 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_6.09100,380,518 - 100,380,578EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 100080826 100080827 C T snv BBDP/WorN (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 100414815 100414816 C T snv FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (RGD), FHL/EurMcwi (RGD)
9 100421464 100421465 C T snv WKY/NHsd (RGD), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), WKY/N (MCW)
9 100424471 100424472 C T snv BBDP/Wor (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1566079 AgrOrtholog
Ensembl Genes ENSRNOG00000023548 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000022290 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022290 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro EGF-like_Ca-bd_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF-like_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF-type_Asp/Asn_hydroxyl_site UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_Ca-bd_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Growth_fac_rcpt_cys_sf UniProtKB/Swiss-Prot
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NIDO_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sushi/SCR/CCP_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sushi_SCR_CCP_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:316638 UniProtKB/TrEMBL
NCBI Gene 316638 ENTREZGENE
Pfam EGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  fn3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  hEGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NIDO UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Sned1 PhenoGen
PROSITE ASX_HYDROXYL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_CA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NIDO UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SUSHI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART CCP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_CA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NIDO UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49265 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF57184 UniProtKB/Swiss-Prot
  SSF57535 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt D3ZNR4 ENTREZGENE, UniProtKB/TrEMBL
  Q5ZQU0 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q336F3 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Sned1  sushi, nidogen and EGF-like domains 1  Sned1  insulin responsive sequence DNA binding protein-1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 Sned1  insulin responsive sequence DNA binding protein-1      Symbol and Name status set to provisional 70820 PROVISIONAL