Shroom2 (shroom family member 2) - Rat Genome Database

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Gene: Shroom2 (shroom family member 2) Rattus norvegicus
Analyze
Symbol: Shroom2
Name: shroom family member 2
RGD ID: 1565163
Description: Predicted to have actin filament binding activity; beta-catenin binding activity; and protein domain specific binding activity. Predicted to be involved in several processes, including cell-cell junction maintenance; melanosome organization; and negative regulation of actin filament depolymerization. Predicted to localize to several cellular components, including adherens junction; apical plasma membrane; and bicellular tight junction. Orthologous to human SHROOM2 (shroom family member 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 3,3',4,4',5-pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Ab2-404; apical protein-like; apical protein-like (Xenopus laevis); Apxl; liver regeneration-related protein LRRG167; LOC317435; similar to apical protein, Xenopus laevis-like
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
mRatBN7.2X21,812,469 - 21,983,724 (-)NCBI
Rnor_6.0 EnsemblX23,478,871 - 23,649,466 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X23,478,869 - 23,649,424 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X23,895,809 - 24,066,198 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X42,290,709 - 42,462,067 (-)NCBIRGSC3.4rn4RGSC3.4
CeleraX22,219,215 - 22,383,703 (-)NCBICelera
Cytogenetic MapXq13NCBI
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

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:12477932   PMID:16684770   PMID:16987870   PMID:17666436   PMID:19056867  


Genomics

Comparative Map Data
Shroom2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X21,812,469 - 21,983,724 (-)NCBI
Rnor_6.0 EnsemblX23,478,871 - 23,649,466 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X23,478,869 - 23,649,424 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X23,895,809 - 24,066,198 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X42,290,709 - 42,462,067 (-)NCBIRGSC3.4rn4RGSC3.4
CeleraX22,219,215 - 22,383,703 (-)NCBICelera
Cytogenetic MapXq13NCBI
SHROOM2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX9,786,429 - 9,949,443 (+)EnsemblGRCh38hg38GRCh38
GRCh38X9,786,406 - 9,949,443 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X9,754,469 - 9,917,483 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X9,714,496 - 9,877,481 (+)NCBINCBI36hg18NCBI36
Build 34X9,564,231 - 9,727,217NCBI
CeleraX13,926,415 - 14,088,764 (+)NCBI
Cytogenetic MapXp22.2NCBI
HuRefX7,649,792 - 7,749,592 (+)NCBIHuRef
CHM1_1X9,784,898 - 9,947,903 (+)NCBICHM1_1
Shroom2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X151,392,505 - 151,553,784 (-)NCBIGRCm39mm39
GRCm39 EnsemblX151,392,505 - 151,552,461 (-)Ensembl
GRCm38X152,609,509 - 152,770,788 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX152,609,509 - 152,769,465 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X149,044,052 - 149,204,004 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X147,950,225 - 148,110,177 (-)NCBImm8
CeleraX136,481,951 - 136,643,123 (+)NCBICelera
Cytogenetic MapXF3NCBI
cM MapX68.46NCBI
Shroom2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554998,031,615 - 8,100,952 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554998,031,961 - 8,103,307 (+)NCBIChiLan1.0ChiLan1.0
SHROOM2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X9,673,879 - 9,832,733 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX9,755,524 - 9,832,733 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X2,418,883 - 2,580,853 (+)NCBIMhudiblu_PPA_v0panPan3
SHROOM2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X6,499,570 - 6,642,738 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX6,499,354 - 6,641,946 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX6,454,916 - 6,598,952 (+)NCBI
ROS_Cfam_1.0X6,445,261 - 6,589,721 (+)NCBI
UMICH_Zoey_3.1X6,436,580 - 6,580,045 (+)NCBI
UNSW_CanFamBas_1.0X6,472,007 - 6,615,248 (+)NCBI
UU_Cfam_GSD_1.0X6,462,126 - 6,605,626 (+)NCBI
Shroom2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049534,249,252 - 4,334,127 (+)NCBI
SpeTri2.0NW_00493664442,620 - 127,481 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SHROOM2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX6,296,133 - 6,448,126 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X6,296,212 - 6,450,401 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1Y4,753,733 - 4,785,766 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X6,699,136 - 6,801,756 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SHROOM2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X8,242,714 - 8,405,051 (+)NCBI
ChlSab1.1 EnsemblX8,345,056 - 8,405,552 (+)Ensembl
Shroom2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248347,329,651 - 7,504,960 (+)NCBI

Position Markers
DXRat84  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X21,940,546 - 21,940,694 (+)MAPPER
Rnor_6.0X23,606,760 - 23,606,907NCBIRnor6.0
Rnor_5.0X24,023,403 - 24,023,550UniSTSRnor5.0
RGSC_v3.4X42,418,861 - 42,419,244RGDRGSC3.4
RGSC_v3.4X42,418,908 - 42,419,055UniSTSRGSC3.4
RGSC_v3.1X42,472,330 - 42,472,713RGD
CeleraX22,340,970 - 22,341,117UniSTS
RH 2.0 Map21250.5RGD
SHRSP x BN MapX6.8999RGD
Cytogenetic MapXq21UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X144092703Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X166260933443848Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X183816624331837Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X428214049282140Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X595407850954078Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat
71116Niddm16Non-insulin dependent diabetes mellitus QTL 167.81blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X1815335263153352Rat
1598873Memor2Memory QTL 22.5exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)X2159262344320739Rat
2290375Gluco34Glucose level QTL 342.75blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X2159262344468300Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:698
Count of miRNA genes:314
Interacting mature miRNAs:416
Transcripts:ENSRNOT00000050819, ENSRNOT00000059431
Prediction methods:Miranda, Pita, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 5 2 2 68 34 26 11
Low 3 39 52 39 19 39 5 5 6 1 15 5
Below cutoff 2 3 6 3

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001047893 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256816 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256817 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008773126 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008773127 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008773128 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008773129 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008773130 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008773131 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008773132 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF348365 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY325213 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC085701 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB586797 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474014 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211812 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000374 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000050819   ⟹   ENSRNOP00000042259
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX23,481,380 - 23,530,003 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000059431   ⟹   ENSRNOP00000056187
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX23,478,871 - 23,649,466 (-)Ensembl
RefSeq Acc Id: NM_001047893   ⟹   NP_001041358
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X21,812,469 - 21,983,499 (-)NCBI
Rnor_6.0X23,478,869 - 23,649,330 (-)NCBI
Rnor_5.0X23,895,809 - 24,066,198 (-)NCBI
RGSC_v3.4X42,290,709 - 42,462,067 (-)RGD
CeleraX22,219,215 - 22,383,703 (-)RGD
Sequence:
RefSeq Acc Id: XM_006256816   ⟹   XP_006256878
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X21,814,980 - 21,983,724 (-)NCBI
Rnor_6.0X23,481,380 - 23,649,424 (-)NCBI
Rnor_5.0X23,895,809 - 24,066,198 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006256817   ⟹   XP_006256879
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X21,814,980 - 21,983,499 (-)NCBI
Rnor_6.0X23,481,380 - 23,649,330 (-)NCBI
Rnor_5.0X23,895,809 - 24,066,198 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008773126   ⟹   XP_008771348
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X21,814,980 - 21,983,724 (-)NCBI
Rnor_6.0X23,481,380 - 23,649,424 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008773127   ⟹   XP_008771349
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X21,814,980 - 21,839,930 (-)NCBI
Rnor_6.0X23,481,380 - 23,506,434 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008773128   ⟹   XP_008771350
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X21,814,980 - 21,840,470 (-)NCBI
Rnor_6.0X23,481,380 - 23,508,656 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008773129   ⟹   XP_008771351
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X21,814,980 - 21,840,470 (-)NCBI
Rnor_6.0X23,481,380 - 23,508,656 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008773130   ⟹   XP_008771352
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X21,814,980 - 21,840,470 (-)NCBI
Rnor_6.0X23,481,380 - 23,508,656 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008773131   ⟹   XP_008771353
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X21,812,474 - 21,839,603 (-)NCBI
Rnor_6.0X23,478,874 - 23,506,001 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008773132   ⟹   XP_008771354
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X21,814,980 - 21,839,930 (-)NCBI
Rnor_6.0X23,481,380 - 23,506,434 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001041358   ⟸   NM_001047893
- Sequence:
RefSeq Acc Id: XP_006256879   ⟸   XM_006256817
- Peptide Label: isoform X2
- UniProtKB: D4A053 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256878   ⟸   XM_006256816
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008771348   ⟸   XM_008773126
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008771351   ⟸   XM_008773129
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008771352   ⟸   XM_008773130
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008771350   ⟸   XM_008773128
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008771353   ⟸   XM_008773131
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008771354   ⟸   XM_008773132
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008771349   ⟸   XM_008773127
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000056187   ⟸   ENSRNOT00000059431
RefSeq Acc Id: ENSRNOP00000042259   ⟸   ENSRNOT00000050819
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)
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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)
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
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)
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
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)
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
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)
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
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)
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
WKY/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
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)
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
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565163 AgrOrtholog
Ensembl Genes ENSRNOG00000024322 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000042259 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000056187 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000050819 UniProtKB/Swiss-Prot
  ENSRNOT00000059431 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.30.42.10 UniProtKB/TrEMBL
InterPro ASD1_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ASD2_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ/DHR/GLGF UniProtKB/TrEMBL
  PDZ_sf UniProtKB/TrEMBL
  Shroom2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Shroom_fam UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 317435 ENTREZGENE
PANTHER PTHR15012 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR15012:SF8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam ASD1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ASD2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/TrEMBL
PhenoGen Shroom2 PhenoGen
PROSITE ASD1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ASD2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/TrEMBL
SMART PDZ UniProtKB/TrEMBL
Superfamily-SCOP PDZ UniProtKB/TrEMBL
UniProt D4A053 ENTREZGENE, UniProtKB/TrEMBL
  Q7TP36 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-03 Shroom2  shroom family member 2  Apxl  apical protein-like (Xenopus laevis)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Apxl  apical protein-like (Xenopus laevis)  LOC317435  similar to apical protein, Xenopus laevis-like  Symbol and Name updated 1299863 APPROVED
2006-02-09 LOC317435  similar to apical protein, Xenopus laevis-like      Symbol and Name status set to provisional 70820 PROVISIONAL