Susd4 (sushi domain containing 4) - Rat Genome Database
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Gene: Susd4 (sushi domain containing 4) Rattus norvegicus
Analyze
Symbol: Susd4
Name: sushi domain containing 4
RGD ID: 1564043
Description: Predicted to be involved in negative regulation of complement activation, alternative pathway and negative regulation of complement activation, classical pathway. Predicted to localize to integral component of membrane. Orthologous to human SUSD4 (sushi domain containing 4); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 3,3',4,4',5-pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC289335; RGD1564043; similar to RIKEN cDNA E430021N18; sushi domain-containing protein 4
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
mRatBN7.21394,455,180 - 94,577,773 (+)NCBI
Rnor_6.0 Ensembl13101,181,994 - 101,307,908 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.013101,181,932 - 101,307,912 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.013106,115,242 - 106,237,600 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41398,831,087 - 98,950,911 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1393,985,798 - 94,106,161 (+)NCBICelera
Cytogenetic Map13q26NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:23482636  


Genomics

Comparative Map Data
Susd4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21394,455,180 - 94,577,773 (+)NCBI
Rnor_6.0 Ensembl13101,181,994 - 101,307,908 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.013101,181,932 - 101,307,912 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.013106,115,242 - 106,237,600 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41398,831,087 - 98,950,911 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1393,985,798 - 94,106,161 (+)NCBICelera
Cytogenetic Map13q26NCBI
SUSD4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1223,220,819 - 223,364,178 (-)EnsemblGRCh38hg38GRCh38
GRCh381223,220,826 - 223,365,271 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371223,394,161 - 223,537,564 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh371223,394,173 - 223,537,518 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361221,460,784 - 221,604,167 (-)NCBINCBI36hg18NCBI36
Celera1196,613,537 - 196,756,905 (-)NCBI
Cytogenetic Map1q41NCBI
HuRef1194,069,335 - 194,212,677 (-)NCBIHuRef
CHM1_11224,667,308 - 224,810,684 (-)NCBICHM1_1
Susd4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391182,591,609 - 182,724,161 (+)NCBIGRCm39mm39
GRCm381182,764,044 - 182,896,596 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1182,763,860 - 182,896,591 (+)EnsemblGRCm38mm10GRCm38
MGSCv371184,695,037 - 184,825,785 (+)NCBIGRCm37mm9NCBIm37
MGSCv361184,601,581 - 184,732,329 (+)NCBImm8
Celera1189,807,460 - 189,939,824 (+)NCBICelera
Cytogenetic Map1H5NCBI
Susd4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555201,444,618 - 1,523,260 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555201,444,618 - 1,523,214 (+)NCBIChiLan1.0ChiLan1.0
SUSD4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11203,911,484 - 204,055,677 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1203,911,484 - 204,054,448 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01198,899,771 - 199,043,215 (-)NCBIMhudiblu_PPA_v0panPan3
SUSD4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl3823,639,616 - 23,685,304 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.13823,640,882 - 23,685,288 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Susd4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936526488,604 - 615,265 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SUSD4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1019,421,565 - 19,551,840 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11019,420,680 - 19,551,941 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21021,915,159 - 22,050,057 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SUSD4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1256,184,878 - 6,327,156 (+)NCBI
ChlSab1.1 Ensembl256,258,265 - 6,325,793 (+)Ensembl
Susd4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248355,531,507 - 5,600,181 (-)NCBI

Position Markers
D13Got88  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.013101,283,190 - 101,283,387NCBIRnor6.0
Rnor_5.013106,212,878 - 106,213,075UniSTSRnor5.0
RGSC_v3.41398,927,014 - 98,927,209RGDRGSC3.4
RGSC_v3.41398,927,015 - 98,927,212UniSTSRGSC3.4
RGSC_v3.11399,115,950 - 99,116,145RGD
Celera1394,082,265 - 94,082,462UniSTS
RH 3.4 Map13641.0RGD
RH 3.4 Map13641.0UniSTS
RH 2.0 Map13699.1RGD
Cytogenetic Map13q26UniSTS
N28096  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.013101,300,070 - 101,300,237NCBIRnor6.0
Rnor_5.013106,229,758 - 106,229,925UniSTSRnor5.0
RGSC_v3.41398,943,895 - 98,944,062UniSTSRGSC3.4
Celera1394,099,145 - 94,099,312UniSTS
Cytogenetic Map13q26UniSTS
RH131207  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.013101,307,690 - 101,307,887NCBIRnor6.0
Rnor_5.013106,237,378 - 106,237,575UniSTSRnor5.0
RGSC_v3.41398,951,515 - 98,951,712UniSTSRGSC3.4
Celera1394,106,765 - 94,106,962UniSTS
RH 3.4 Map13649.5UniSTS
Cytogenetic Map13q26UniSTS


QTLs in Region (Rnor_6.0)
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)systolic blood pressure (CMO:0000004)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131107975663Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1312193394108478121Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1324502279108770533Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1335301263107975663Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1357903612102903612Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1362975663107975663Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1366971778111971778Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1371230858114033958Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1371230858114033958Rat
7387280Uae43Urinary albumin excretion QTL 435.690.4174urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1372583716114033958Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)777694986114033958Rat
8655959Pur32Proteinuria QTL 328.4total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1379567081103613733Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1380403559108770687Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1386833393114033958Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:410
Count of miRNA genes:229
Interacting mature miRNAs:275
Transcripts:ENSRNOT00000052407
Prediction methods:Microtar, Miranda, 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 6 72 22
Low 3 30 24 18 8 18 8 11 2 22 16 11 8
Below cutoff 7 29 19 11 19 13 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000052407   ⟹   ENSRNOP00000045726
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl13101,181,994 - 101,307,908 (+)Ensembl
RefSeq Acc Id: NM_001105982   ⟹   NP_001099452
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21394,455,488 - 94,576,947 (+)NCBI
Rnor_6.013101,182,006 - 101,307,086 (+)NCBI
Rnor_5.013106,115,242 - 106,237,600 (+)NCBI
RGSC_v3.41398,831,087 - 98,950,911 (+)RGD
Celera1393,985,798 - 94,106,161 (+)RGD
Sequence:
RefSeq Acc Id: XM_008769820   ⟹   XP_008768042
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21394,455,345 - 94,577,773 (+)NCBI
Rnor_6.013101,181,932 - 101,306,586 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008769822   ⟹   XP_008768044
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21394,455,902 - 94,577,773 (+)NCBI
Rnor_6.013101,182,182 - 101,306,586 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598729   ⟹   XP_017454218
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013101,211,652 - 101,306,586 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598730   ⟹   XP_017454219
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013101,211,652 - 101,306,586 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598731   ⟹   XP_017454220
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013101,211,652 - 101,307,912 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039090563   ⟹   XP_038946491
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21394,455,180 - 94,577,773 (+)NCBI
RefSeq Acc Id: XM_039090564   ⟹   XP_038946492
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21394,455,346 - 94,577,773 (+)NCBI
RefSeq Acc Id: XM_039090565   ⟹   XP_038946493
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21394,455,347 - 94,577,773 (+)NCBI
RefSeq Acc Id: XM_039090566   ⟹   XP_038946494
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21394,455,186 - 94,577,773 (+)NCBI
RefSeq Acc Id: XM_039090567   ⟹   XP_038946495
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21394,455,343 - 94,577,773 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001099452   ⟸   NM_001105982
- UniProtKB: D4A231 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008768042   ⟸   XM_008769820
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008768044   ⟸   XM_008769822
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017454220   ⟸   XM_017598731
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017454218   ⟸   XM_017598729
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017454219   ⟸   XM_017598730
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000045726   ⟸   ENSRNOT00000052407
RefSeq Acc Id: XP_038946491   ⟸   XM_039090563
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038946494   ⟸   XM_039090566
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038946495   ⟸   XM_039090567
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038946492   ⟸   XM_039090564
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038946493   ⟸   XM_039090565
- Peptide Label: isoform X3
Protein Domains
Sushi

Transcriptome

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

Promoters
RGD ID:13699081
Promoter ID:EPDNEW_R9606
Type:single initiation site
Name:Susd4_1
Description:sushi domain containing 4
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_6.013101,182,042 - 101,182,102EPDNEW

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)
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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
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_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
13 101300214 101300215 A C snv SHR/NHsd (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564043 AgrOrtholog
Ensembl Genes ENSRNOG00000003562 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000045726 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000052407 ENTREZGENE, UniProtKB/TrEMBL
InterPro SUSD4 UniProtKB/TrEMBL
  Sushi/SCR/CCP_sf UniProtKB/TrEMBL
  Sushi_SCR_CCP UniProtKB/TrEMBL
KEGG Report rno:289335 UniProtKB/TrEMBL
NCBI Gene 289335 ENTREZGENE
PANTHER PTHR47007 UniProtKB/TrEMBL
Pfam Sushi UniProtKB/TrEMBL
PhenoGen Susd4 PhenoGen
PROSITE SUSHI UniProtKB/TrEMBL
SMART CCP UniProtKB/TrEMBL
Superfamily-SCOP Complement_control_module UniProtKB/TrEMBL
UniProt D4A231 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-06 Susd4  sushi domain containing 4  RGD1564043_predicted  similar to RIKEN cDNA E430021N18 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1564043_predicted  similar to RIKEN cDNA E430021N18 (predicted)  LOC289335  similar to RIKEN cDNA E430021N18  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC289335  similar to RIKEN cDNA E430021N18      Symbol and Name status set to provisional 70820 PROVISIONAL