Tamalin (trafficking regulator and scaffold protein tamalin) - Rat Genome Database

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Gene: Tamalin (trafficking regulator and scaffold protein tamalin) Rattus norvegicus
Analyze
Symbol: Tamalin
Name: trafficking regulator and scaffold protein tamalin
RGD ID: 70554
Description: Exhibits PDZ domain binding activity; identical protein binding activity; and small GTPase binding activity. Involved in protein localization. Localizes to glutamatergic synapse; plasma membrane; and postsynaptic density. Orthologous to human TAMALIN (trafficking regulator and scaffold protein tamalin); INTERACTS WITH 2,2',5,5'-tetrachlorobiphenyl; 3,3',4,4',5-pentachlorobiphenyl; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: 95 kDa postsynaptic density protein discs-large ZO-1 domain-containing protein; general receptor for phosphoinositides 1 associated scaffold protein; general receptor for phosphoinositides 1-associated scaffold protein; Grasp; GRP1 (general receptor for phosphoinositides 1)-associated scaffold protein; Grp1 (general receptor for phosphoinositides)-associated scaffold protein; GRP1-associated scaffold protein; LOC102556412; PSD-95 PDZ domain-containing protein; uncharacterized LOC102556412
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
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
mRatBN7.27132,338,900 - 132,359,519 (+)NCBI
Rnor_6.0 Ensembl7142,869,752 - 142,878,347 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07142,869,785 - 142,877,551 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07140,670,666 - 140,678,432 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47139,970,173 - 139,977,939 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17140,046,609 - 140,054,376 (+)NCBI
Celera7128,804,534 - 128,812,273 (+)NCBICelera
Cytogenetic Map7q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:10828067   PMID:15173175   PMID:22569042   PMID:22980744   PMID:28285821  


Genomics

Comparative Map Data
Tamalin
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27132,338,900 - 132,359,519 (+)NCBI
Rnor_6.0 Ensembl7142,869,752 - 142,878,347 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07142,869,785 - 142,877,551 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07140,670,666 - 140,678,432 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47139,970,173 - 139,977,939 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17140,046,609 - 140,054,376 (+)NCBI
Celera7128,804,534 - 128,812,273 (+)NCBICelera
Cytogenetic Map7q36NCBI
TAMALIN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1252,006,946 - 52,015,889 (+)EnsemblGRCh38hg38GRCh38
GRCh381252,006,946 - 52,015,889 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371252,400,730 - 52,409,673 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361250,687,015 - 50,695,938 (+)NCBINCBI36hg18NCBI36
Build 341250,687,014 - 50,695,938NCBI
Celera1251,203,041 - 51,211,963 (+)NCBI
Cytogenetic Map12q13.13NCBI
HuRef1249,433,882 - 49,442,831 (+)NCBIHuRef
CHM1_11252,367,010 - 52,375,941 (+)NCBICHM1_1
Tamalin
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3915101,122,088 - 101,130,637 (+)NCBIGRCm39mm39
GRCm39 Ensembl15101,122,069 - 101,130,637 (+)Ensembl
GRCm3815101,224,207 - 101,232,756 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl15101,224,188 - 101,232,756 (+)EnsemblGRCm38mm10GRCm38
MGSCv3715101,054,638 - 101,063,187 (+)NCBIGRCm37mm9NCBIm37
MGSCv3615101,052,243 - 101,066,427 (+)NCBImm8
Celera15103,372,533 - 103,381,084 (+)NCBICelera
Cytogenetic Map15F1NCBI
Tamalin
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555472,377,702 - 2,385,277 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555472,377,612 - 2,385,918 (+)NCBIChiLan1.0ChiLan1.0
TAMALIN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11237,523,542 - 37,531,996 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1237,524,232 - 37,531,927 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01236,747,159 - 36,755,812 (-)NCBIMhudiblu_PPA_v0panPan3
Tamalin
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494563,697,480 - 63,706,368 (-)NCBI
SpeTri2.0NW_0049365129,458,549 - 9,467,350 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TAMALIN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl517,357,866 - 17,367,453 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1517,357,625 - 17,366,033 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2517,942,982 - 17,953,496 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TAMALIN
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11148,176,394 - 48,184,985 (+)NCBI
ChlSab1.1 Ensembl1148,176,413 - 48,184,981 (+)Ensembl
Tamalin
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624816314,841 - 322,696 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)751251919145729302Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)771448715145729302Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)7100028953145729302Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)7100192194145192194Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)7106564316145729302Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7111519266143965591Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7114825174145729302Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7115922628145729302Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7120746024145692398Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7121654760145729302Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7121986439143965591Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7122421276143965415Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7129412003145729302Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:49
Count of miRNA genes:47
Interacting mature miRNAs:47
Transcripts:ENSRNOT00000009979
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 10 3 10 18 25 11
Low 3 33 57 41 16 41 8 11 64 17 16 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_138894 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078372 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078373 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078374 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078375 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078376 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078377 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078380 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078381 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078382 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078383 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078384 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC119007 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF374272 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474035 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000187 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000009979   ⟹   ENSRNOP00000009979
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7142,869,752 - 142,878,012 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000088730   ⟹   ENSRNOP00000069285
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7142,877,086 - 142,878,347 (+)Ensembl
RefSeq Acc Id: NM_138894   ⟹   NP_620249
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27132,338,900 - 132,346,666 (+)NCBI
Rnor_6.07142,869,785 - 142,877,551 (+)NCBI
Rnor_5.07140,670,666 - 140,678,432 (+)NCBI
RGSC_v3.47139,970,173 - 139,977,939 (+)RGD
Celera7128,804,534 - 128,812,273 (+)RGD
Sequence:
RefSeq Acc Id: XM_039078372   ⟹   XP_038934300
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27132,338,906 - 132,359,519 (+)NCBI
RefSeq Acc Id: XM_039078373   ⟹   XP_038934301
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27132,338,906 - 132,359,519 (+)NCBI
RefSeq Acc Id: XM_039078374   ⟹   XP_038934302
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27132,338,906 - 132,359,519 (+)NCBI
RefSeq Acc Id: XM_039078375   ⟹   XP_038934303
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27132,338,906 - 132,359,519 (+)NCBI
RefSeq Acc Id: XM_039078376   ⟹   XP_038934304
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27132,338,906 - 132,359,519 (+)NCBI
RefSeq Acc Id: XM_039078377   ⟹   XP_038934305
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27132,338,906 - 132,359,519 (+)NCBI
RefSeq Acc Id: XM_039078380   ⟹   XP_038934308
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27132,338,906 - 132,359,519 (+)NCBI
RefSeq Acc Id: XM_039078381   ⟹   XP_038934309
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27132,338,906 - 132,359,519 (+)NCBI
RefSeq Acc Id: XM_039078382   ⟹   XP_038934310
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27132,338,906 - 132,359,519 (+)NCBI
RefSeq Acc Id: XM_039078383   ⟹   XP_038934311
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27132,338,906 - 132,359,519 (+)NCBI
RefSeq Acc Id: XM_039078384   ⟹   XP_038934312
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27132,338,906 - 132,359,519 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_620249   ⟸   NM_138894
- UniProtKB: Q8R4T5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009979   ⟸   ENSRNOT00000009979
RefSeq Acc Id: ENSRNOP00000069285   ⟸   ENSRNOT00000088730
RefSeq Acc Id: XP_038934300   ⟸   XM_039078372
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934304   ⟸   XM_039078376
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934303   ⟸   XM_039078375
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934308   ⟸   XM_039078380
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934309   ⟸   XM_039078381
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934302   ⟸   XM_039078374
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934305   ⟸   XM_039078377
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934310   ⟸   XM_039078382
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934311   ⟸   XM_039078383
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934312   ⟸   XM_039078384
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934301   ⟸   XM_039078373
- Peptide Label: isoform X1
Protein Domains
PDZ

Transcriptome

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

Promoters
RGD ID:13695666
Promoter ID:EPDNEW_R6190
Type:single initiation site
Name:Grasp_1
Description:general receptor for phosphoinositides 1 associated scaffoldprotein
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_6.07142,869,768 - 142,869,828EPDNEW

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_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 140670858 140670859 G A snv IS-Tlk/Kyo (KyushuU), IS/Kyo (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:70554 AgrOrtholog
BIND 144392
  144395
  144396
  144397
  144399
Ensembl Genes ENSRNOG00000007346 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009979 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000069285 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009979 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000088730 UniProtKB/TrEMBL
Gene3D-CATH 2.30.42.10 UniProtKB/Swiss-Prot
InterPro PDZ UniProtKB/Swiss-Prot
  PDZ_sf UniProtKB/Swiss-Prot
KEGG Report rno:192254 UniProtKB/Swiss-Prot
NCBI Gene 192254 ENTREZGENE
Pfam PDZ UniProtKB/Swiss-Prot
PhenoGen Tamalin PhenoGen
PROSITE PDZ UniProtKB/Swiss-Prot
SMART PDZ UniProtKB/Swiss-Prot
Superfamily-SCOP SSF50156 UniProtKB/Swiss-Prot
UniProt A0A0G2JUZ1_RAT UniProtKB/TrEMBL
  GRASP_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Tamalin  trafficking regulator and scaffold protein tamalin  LOC102556412  uncharacterized LOC102556412  Data Merged 737654 PROVISIONAL
2020-02-24 Tamalin  trafficking regulator and scaffold protein tamalin  Grasp  general receptor for phosphoinositides 1 associated scaffold protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-06-22 Grasp  general receptor for phosphoinositides 1 associated scaffold protein  Grasp  GRP1 (general receptor for phosphoinositides 1)-associated scaffold protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-12-18 LOC102556412  uncharacterized LOC102556412      Symbol and Name status set to provisional 70820 PROVISIONAL
2004-09-10 Grasp  GRP1 (general receptor for phosphoinositides 1)-associated scaffold protein    Grp1 (general receptor for phosphoinositides)-associated scaffold protein  Name updated 1299863 APPROVED
2002-06-10 Grasp  Grp1 (general receptor for phosphoinositides)-associated scaffold protein      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains contains a 95-kDa postsynaptic density protein (PSD-95)/discs-large/ZO-1 (PDZ) domain, a leucine-zipper region, and a carboxyl-terminal PDZ binding motif 1299234
gene_function scaffold protein that binds group 1 metabotropic glutamate receptors at its amino-terminal PDZ domain and ARF-specific GEF protein at its C-terminus 70394
gene_function forms a complex with PSD-95 and Mint2/X11beta/X11L 1299234
gene_process has a role in associating group 1 metabotropic glutamate receptors and ARF-specific GEF proteins to mediate intracellular trafficking 70394