Shroom3 (shroom family member 3) - Rat Genome Database
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Gene: Shroom3 (shroom family member 3) Rattus norvegicus
Analyze
Symbol: Shroom3
Name: shroom family member 3
RGD ID: 1310470
Description: Predicted to have actin binding activity. Predicted to be involved in several processes, including columnar/cuboidal epithelial cell development; neural tube closure; and regulation of cell shape. Predicted to localize to several cellular components, including adherens junction; apical junction complex; and apical plasma membrane. Orthologous to human SHROOM3 (shroom family member 3); INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; C60 fullerene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC305230; RGD1310470; Shrm; similar to PDZ domain actin binding protein Shroom
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
mRatBN7.21415,099,415 - 15,396,832 (-)NCBI
Rnor_6.0 Ensembl1416,622,760 - 16,903,242 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01416,622,767 - 16,903,265 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01416,547,964 - 16,817,192 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41416,658,357 - 16,954,651 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11416,659,176 - 16,710,986 (-)NCBI
Celera1414,501,250 - 14,791,213 (-)NCBICelera
Cytogenetic Map14p22NCBI
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:10589677   PMID:12477932   PMID:15037549   PMID:16249236   PMID:25273069  


Genomics

Comparative Map Data
Shroom3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21415,099,415 - 15,396,832 (-)NCBI
Rnor_6.0 Ensembl1416,622,760 - 16,903,242 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01416,622,767 - 16,903,265 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01416,547,964 - 16,817,192 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41416,658,357 - 16,954,651 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11416,659,176 - 16,710,986 (-)NCBI
Celera1414,501,250 - 14,791,213 (-)NCBICelera
Cytogenetic Map14p22NCBI
SHROOM3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl476,435,229 - 76,783,253 (+)EnsemblGRCh38hg38GRCh38
GRCh38476,435,229 - 76,783,253 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37477,356,382 - 77,704,406 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36477,575,277 - 77,923,430 (+)NCBINCBI36hg18NCBI36
Celera474,657,026 - 75,005,707 (+)NCBI
Cytogenetic Map4q21.1NCBI
HuRef473,108,515 - 73,456,416 (+)NCBIHuRef
CHM1_1477,332,743 - 77,680,889 (+)NCBICHM1_1
Shroom3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39592,831,294 - 93,113,618 (+)NCBIGRCm39mm39
GRCm39 Ensembl592,831,294 - 93,113,177 (+)Ensembl
GRCm38592,683,435 - 92,965,759 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl592,683,435 - 92,965,318 (+)EnsemblGRCm38mm10GRCm38
MGSCv37593,112,461 - 93,394,785 (+)NCBIGRCm37mm9NCBIm37
MGSCv36593,758,639 - 94,040,158 (+)NCBImm8
Celera590,826,109 - 91,115,823 (+)NCBICelera
Cytogenetic Map5E2NCBI
cM Map547.29NCBI
Shroom3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554331,358,444 - 1,422,498 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554331,135,589 - 1,423,449 (+)NCBIChiLan1.0ChiLan1.0
SHROOM3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1453,256,674 - 53,607,120 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl453,260,739 - 53,606,976 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0447,420,351 - 47,767,325 (-)NCBIMhudiblu_PPA_v0panPan3
SHROOM3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl321,271,392 - 1,391,798 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1321,218,513 - 1,392,014 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Shroom3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936676533,654 - 703,549 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SHROOM3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1872,097,561 - 72,443,869 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2876,297,056 - 76,642,486 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SHROOM3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1725,185,130 - 25,279,765 (+)NCBI
ChlSab1.1 Ensembl725,215,232 - 25,283,214 (+)Ensembl
Shroom3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475714,187,911 - 14,524,999 (-)NCBI

Position Markers
D14Got132  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01416,674,087 - 16,674,352NCBIRnor6.0
Rnor_5.01416,599,284 - 16,599,549UniSTSRnor5.0
RGSC_v3.41416,711,387 - 16,711,652UniSTSRGSC3.4
Celera1414,553,193 - 14,553,457UniSTS
Cytogenetic Map14p22UniSTS
RH128692  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01416,622,851 - 16,623,070NCBIRnor6.0
Rnor_5.01416,548,048 - 16,548,267UniSTSRnor5.0
RGSC_v3.41416,658,441 - 16,658,660UniSTSRGSC3.4
Celera1414,501,334 - 14,501,553UniSTS
RH 3.4 Map14176.6UniSTS
Cytogenetic Map14p22UniSTS
AU046317  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01416,781,299 - 16,781,416NCBIRnor6.0
Rnor_5.01416,700,741 - 16,700,858UniSTSRnor5.0
RGSC_v3.41416,821,430 - 16,821,547UniSTSRGSC3.4
Celera1414,656,301 - 14,656,418UniSTS
Cytogenetic Map14p22UniSTS
AU049074  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01416,725,902 - 16,727,383NCBIRnor6.0
Rnor_5.01416,648,463 - 16,649,944UniSTSRnor5.0
RGSC_v3.41416,765,835 - 16,767,316UniSTSRGSC3.4
Celera1414,603,193 - 14,604,674UniSTS
Cytogenetic Map14p22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14127597761Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14127597761Rat
619619Rf4Renal disease susceptibility QTL 44.10.002total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14134403399Rat
9589814Gluco67Glucose level QTL 674.540.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14141333960Rat
7411573Bw139Body weight QTL 1394.70.001body mass (VT:0001259)body weight gain (CMO:0000420)14141333960Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14142766285Rat
70204Niddm20Non-insulin dependent diabetes mellitus QTL 205.10.000008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)14222782519230541Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)14483323319909932Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)14483323319909932Rat
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14483323323004027Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14483323326466248Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14483323333040042Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14975643572854397Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin141053997755539977Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)141053997755539977Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)141072926861873323Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141268042430155192Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1412680424106641756Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141268061332593926Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141633698833163485Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:124
Count of miRNA genes:90
Interacting mature miRNAs:113
Transcripts:ENSRNOT00000003001
Prediction methods: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 3 34 2 2 2 20 21 29 11
Low 9 47 39 13 39 1 2 52 14 12 1
Below cutoff 8 6 7 9 2 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003001   ⟹   ENSRNOP00000003001
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1416,622,760 - 16,903,242 (-)Ensembl
RefSeq Acc Id: NM_001100889   ⟹   NP_001094359
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21415,099,423 - 15,395,942 (-)NCBI
Rnor_6.01416,622,767 - 16,902,267 (-)NCBI
Rnor_5.01416,547,964 - 16,817,192 (-)NCBI
RGSC_v3.41416,658,357 - 16,954,651 (-)RGD
Celera1414,501,250 - 14,791,213 (-)RGD
Sequence:
RefSeq Acc Id: XM_006250723   ⟹   XP_006250785
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21415,099,415 - 15,396,832 (-)NCBI
Rnor_6.01416,622,767 - 16,903,265 (-)NCBI
Rnor_5.01416,547,964 - 16,817,192 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006250725   ⟹   XP_006250787
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01416,622,988 - 16,662,071 (-)NCBI
Rnor_5.01416,547,964 - 16,817,192 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599172   ⟹   XP_017454661
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01416,622,767 - 16,732,224 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599173   ⟹   XP_017454662
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21415,099,415 - 15,255,952 (-)NCBI
Rnor_6.01416,622,988 - 16,779,829 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039091851   ⟹   XP_038947779
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21415,099,415 - 15,165,575 (-)NCBI
RefSeq Acc Id: XM_039091852   ⟹   XP_038947780
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21415,099,415 - 15,130,743 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001094359   ⟸   NM_001100889
- Sequence:
RefSeq Acc Id: XP_006250785   ⟸   XM_006250723
- Peptide Label: isoform X1
- UniProtKB: F1LP26 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006250787   ⟸   XM_006250725
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017454661   ⟸   XM_017599172
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017454662   ⟸   XM_017599173
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000003001   ⟸   ENSRNOT00000003001
RefSeq Acc Id: XP_038947779   ⟸   XM_039091851
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038947780   ⟸   XM_039091852
- Peptide Label: isoform X2
Protein Domains
ASD1   ASD2   PDZ

Transcriptome

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


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)
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
MNS/Gib (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
MR/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
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
14 16559159 16559160 C T snv ACI/EurMcwi (MCW), ZFDM (KyushuU), ZF (KyushuU), HWY/Slc (KyushuU), HTX/Kyo (KyushuU), NIG-III/Hok (KyushuU), BUF/MNa (KyushuU), Crl:SD (UDEL), SDLEF7/Barth (UDEL), M520/N (KNAW), FHL/EurMcwi (KNAW), FHH/EurMcwi (KNAW), DA/BklArbNsi (KNAW), BUF/N (KNAW), ACI/EurMcwi (KNAW), ACI/N (KNAW), WAG/Rij (KNAW), MR/N (KNAW), MHS/Gib (KNAW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW)
14 16559357 16559358 C T snv KFRS3B/Kyo (KyushuU)
14 16561349 16561350 C T snv ACI/EurMcwi (MCW), WKY/Gcrc (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), BUF/MNa (KyushuU), DA/BklArbNsi (KNAW), DOB/Oda (KyushuU), FHH/EurMcwi (KNAW), NIG-III/Hok (KyushuU), FHL/EurMcwi (KNAW), HTX/Kyo (KyushuU), GK/Ox (KNAW), SHR/OlaIpcv (KNAW), SHR/NHsd (KNAW), SHR/NCrlPrin (KNAW), SBH/Ygl (KNAW), HWY/Slc (KyushuU), ACI/EurMcwi (KNAW), ACI/N (KNAW), IS/Kyo (KyushuU), Crl:SD (UDEL), WAG/Rij (KNAW), MR/N (KNAW), ZF (KyushuU), MHS/Gib (KNAW), SDLEF7/Barth (UDEL), FHL/EurMcwi (MCW), IS-Tlk/Kyo (KyushuU), FHH/EurMcwi (MCW), SBH/Ygl (MCW), ZFDM (KyushuU), SHR/OlaIpcvPrin (KNAW), SHRSP/Gcrc (KNAW)
14 16571302 16571303 C T snv ACI/EurMcwi (MCW), SBH/Ygl (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), MHS/Gib (KNAW), MR/N (KNAW), WAG/Rij (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), SBH/Ygl (KNAW), SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), SHRSP/Gcrc (KNAW), WKY/Gcrc (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), BUF/N (KNAW), DA/BklArbNsi (KNAW), FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), GK/Ox (KNAW), M520/N (KNAW), SDLEF7/Barth (UDEL), IS/Kyo (KyushuU), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), HTX/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU), HWY/Slc (KyushuU), DOB/Oda (KyushuU)
14 16571590 16571591 G A snv F344/NRrrc (Illumina) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), F344/Jcl (KyushuU), F344/NSlc (KyushuU), F344/Stm (KyushuU), F344/DuCrlCrlj (KyushuU)
14 16571965 16571966 C T snv F344/NRrrc (Illumina) (KNAW), F344/NRrrc (SOLiD) (KNAW), LE/OrlBarth (UDEL), F344/NHsd (KNAW), F344/NCrl (KNAW)
14 16572490 16572491 T C snv ACI/EurMcwi (MCW), ZFDM (KyushuU), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), MHS/Gib (KNAW), MR/N (KNAW), WAG/Rij (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), SBH/Ygl (KNAW), SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), SHRSP/Gcrc (KNAW), WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), BUF/N (KNAW), DA/BklArbNsi (KNAW), FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), GK/Ox (KNAW), M520/N (KNAW), SDLEF7/Barth (UDEL), IS/Kyo (KyushuU), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), HTX/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU), HWY/Slc (KyushuU), DOB/Oda (KyushuU), ZF (KyushuU), SBH/Ygl (MCW)
14 16572988 16572989 C T snv ACI/EurMcwi (MCW), ZFDM (KyushuU), GH/OmrMcwi (MCW), SBH/Ygl (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), LH/MavRrrc (KNAW), LL/MavRrrc (KNAW), LN/MavRrrc (KNAW), MHS/Gib (KNAW), MR/N (KNAW), SR/JrHsd (KNAW), SS/Jr (KNAW), SS/JrHsdMcwi (KNAW), WAG/Rij (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), SBH/Ygl (KNAW), SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), SHRSP/Gcrc (KNAW), F344/NRrrc (Illumina) (KNAW), WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), BUF/N (KNAW), DA/BklArbNsi (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), GK/Ox (KNAW), M520/N (KNAW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), IS/Kyo (KyushuU), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), F344/DuCrlCrlj (KyushuU), HTX/Kyo (KyushuU), F344/NSlc (KyushuU), IS-Tlk/Kyo (KyushuU), F344/Stm (KyushuU), HWY/Slc (KyushuU), F344/Jcl (KyushuU), DOB/Oda (KyushuU), ZF (KyushuU), COP/CrCrl (MCW & UW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 16633962 16633963 C T snv FHL/EurMcwi (MCW), FHL/EurMcwi (RGD), ACI/EurMcwi (RGD), FHH/EurMcwi (RGD), MR/N (MCW), FHH/EurMcwi (MCW), MHS/Gib (RGD), ACI/EurMcwi (MCW), CDS, ACI/N (MCW), WAG/Rij (RGD), Buf/N (MCW), M520/N (MCW)
14 16636152 16636153 C T snv FHL/EurMcwi (RGD), MR/N (MCW), CDS, FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), SBH/Ygl (MCW), ACI/EurMcwi (MCW), ACI/EurMcwi (RGD), WKY/Gcrc (RGD), WKY/NCrl (RGD), WAG/Rij (RGD), SHRSP/Gcrc (RGD), SHR/NHsd (RGD), SBH/Ygl (RGD), MHS/Gib (RGD), GK/Ox (RGD), FHH/EurMcwi (RGD), WKY/NHsd (RGD)
14 16636380 16636381 G A snv ACI/N (MCW), FHL/EurMcwi (RGD), WAG/Rij (RGD), SHR/NHsd (RGD), WKY/NHsd (RGD), MHS/Gib (RGD), M520/N (MCW), GK/Ox (RGD), WKY/Gcrc (RGD), WKY/NCrl (RGD), MR/N (MCW), FHH/EurMcwi (RGD), SHRSP/Gcrc (RGD), WKY/N (MCW), ACI/EurMcwi (RGD), SBH/Ygl (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 16670618 16670619 C T snv ACI/N (KNAW), DA/BklArbNsi (ICAHN), M520/N (KNAW), MR/N (KNAW), ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), ACI/EurMcwi (ICL), FHH/EurMcwi (ICL), FHL/EurMcwi (ICL), MHS/Gib (ICL), WAG/Rij (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), BUF/N (KNAW)
14 16682736 16682737 C T snv SHR/OlaIpcv (ICL), LCR/2Mco (UMich), HCR/2Mco (UMich), LCR/1Mco (UMich), HCR/1Mco (UMich), WKY/NCrl (ICL), WKY/NHsd (ICL), WKY/Gcrc (ICL), WAG/Rij (ICL), SHRSP/Gcrc (ICL), SHR/NHsd (ICL), SHR/OlaIpcv (ICL), SBH/Ygl (ICL), MHS/Gib (ICL), GK/Ox (ICL), FHL/EurMcwi (ICL), FHH/EurMcwi (ICL), ACI/EurMcwi (ICL), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), ACI/EurMcwi (MCW), SHR/OlaIpcv (KNAW), MR/N (KNAW), FHH/EurMcwi (MDC)
14 16683399 16683400 C T snv F344/NRrrc (KNAW), F344/NCrl (ICL), F344/NHsd (ICAHN)
14 16683924 16683925 T C snv GK/Ox (ICL), LCR/2Mco (UMich), WKY/NHsd (ICL), MHS/Gib (ICL), SBH/Ygl (ICL), LCR/1Mco (UMich), FHH/EurMcwi (ICL), HCR/1Mco (UMich), ACI/EurMcwi (ICL), SHRSP/Gcrc (ICL), FHL/EurMcwi (MCW), HCR/2Mco (UMich), FHH/EurMcwi (MCW), ACI/EurMcwi (MCW), SHR/NHsd (ICL), SHR/OlaIpcv (KNAW), WKY/N (KNAW), MR/N (KNAW), WKY/NCrl (ICL), M520/N (KNAW), BUF/N (KNAW), ACI/N (KNAW), SHRSP/Gcrc (MDC), SHR/OlaIpcv (ICL), FHH/EurMcwi (MDC), DA/BklArbNsi (ICAHN), WKY/Gcrc (ICL), SHR/OlaIpcv (ICL), WAG/Rij (ICL), FHL/EurMcwi (ICL)
14 16684422 16684423 C T snv SHR/OlaIpcv (ICL), FHH/EurMcwi (MDC), SHRSP/Gcrc (MDC), SS/JrHsdMcwi (MDC), ACI/N (KNAW), BUF/N (KNAW), F344/NRrrc (KNAW), M520/N (KNAW), MR/N (KNAW), WKY/N (KNAW), SHR/OlaIpcv (KNAW), ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), ACI/EurMcwi (ICL), F344/NCrl (ICL), FHH/EurMcwi (ICL), FHL/EurMcwi (ICL), GK/Ox (ICL), LH/MavRrrc (ICL), LL/MavRrrc (ICL), LN/MavRrrc (ICL), MHS/Gib (ICL), SBH/Ygl (ICL), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), SR/JrHsd (ICL), SS/Jr (ICL), SS/JrHsdMcwi (ICL), WAG/Rij (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL), WKY/NCrl (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), LCR/2Mco (UMich), F344/NHsd (ICAHN), DA/BklArbNsi (ICAHN)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310470 AgrOrtholog
Ensembl Genes ENSRNOG00000002208 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000003001 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003001 UniProtKB/TrEMBL
Gene3D-CATH 2.30.42.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7368269 IMAGE-MGC_LOAD
InterPro ASD1 UniProtKB/TrEMBL
  ASD2 UniProtKB/TrEMBL
  PDZ UniProtKB/TrEMBL
  PDZ_sf UniProtKB/TrEMBL
  Shrm3 UniProtKB/TrEMBL
  Shroom_fam UniProtKB/TrEMBL
MGC_CLONE MGC:109649 IMAGE-MGC_LOAD
NCBI Gene 305230 ENTREZGENE
PANTHER PTHR15012 UniProtKB/TrEMBL
  PTHR15012:SF33 UniProtKB/TrEMBL
Pfam ASD1 UniProtKB/TrEMBL
  ASD2 UniProtKB/TrEMBL
  PDZ UniProtKB/TrEMBL
PhenoGen Shroom3 PhenoGen
PROSITE ASD1 UniProtKB/TrEMBL
  ASD2 UniProtKB/TrEMBL
  PDZ UniProtKB/TrEMBL
SMART PDZ UniProtKB/TrEMBL
Superfamily-SCOP PDZ UniProtKB/TrEMBL
UniProt F1LP26 ENTREZGENE, UniProtKB/TrEMBL
  Q5BJL1_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-27 Shroom3  shroom family member 3  RGD1310470  similar to PDZ domain actin binding protein Shroom  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1310470  similar to PDZ domain actin binding protein Shroom  RGD1310470_predicted  similar to PDZ domain actin binding protein Shroom (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1310470_predicted  similar to PDZ domain actin binding protein Shroom (predicted)  LOC305230_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC305230_predicted  similar to PDZ domain actin binding protein Shroom (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL