Glycam1 (glycosylation dependent cell adhesion molecule 1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Glycam1 (glycosylation dependent cell adhesion molecule 1) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Glycam1
Name: glycosylation dependent cell adhesion molecule 1
RGD ID: 2712
Description: Predicted to be involved in cell adhesion. Predicted to be located in plasma membrane.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: endothelial ligand FOR L-selectin; glyCAM-1; glycosylation-dependent cell adhesion molecule 1; SGP50; sulfated 50 kDa glycoprotein
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87136,559,039 - 136,561,299 (-)NCBIGRCr8
mRatBN7.27134,680,588 - 134,682,848 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7134,680,588 - 134,682,848 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7136,436,461 - 136,438,721 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07138,665,832 - 138,668,092 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07138,651,510 - 138,653,770 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07145,172,496 - 145,174,756 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7145,172,493 - 145,174,771 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07142,951,738 - 142,953,998 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47142,455,642 - 142,457,902 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.17142,535,830 - 142,538,091 (-)NCBI
Celera7131,104,664 - 131,106,924 (-)NCBICelera
Cytogenetic Map7q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Cloning of a rat homologue of mouse GlyCAM 1 reveals conservation of structural domains. Dowbenko D, etal., J Biol Chem 1993 Jul 5;268(19):14399-403.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data

Genomics

Variants

.
Variants in Glycam1
10 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:39
Count of miRNA genes:34
Interacting mature miRNAs:39
Transcripts:ENSRNOT00000055270
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7119513385135012528Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat

Markers in Region
RH131461  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27134,680,606 - 134,680,802 (+)MAPPERmRatBN7.2
Rnor_6.07145,172,515 - 145,172,710NCBIRnor6.0
Rnor_5.07142,951,757 - 142,951,952UniSTSRnor5.0
RGSC_v3.47142,455,661 - 142,455,856UniSTSRGSC3.4
Celera7131,104,683 - 131,104,878UniSTS
RH 3.4 Map71064.7UniSTS
Cytogenetic Map7q36UniSTS


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 5 1 1 4 1
Low 5 2 3 2 7 7 15 14 2 6 7
Below cutoff 1 4 5 2 1 2 2 14 1 5 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000055270   ⟹   ENSRNOP00000052145
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7134,680,588 - 134,682,848 (-)Ensembl
Rnor_6.0 Ensembl7145,172,493 - 145,174,771 (-)Ensembl
RefSeq Acc Id: NM_012794   ⟹   NP_036926
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87136,559,039 - 136,561,299 (-)NCBI
mRatBN7.27134,680,588 - 134,682,848 (-)NCBI
Rnor_6.07145,172,496 - 145,174,756 (-)NCBI
Rnor_5.07142,951,738 - 142,953,998 (-)NCBI
RGSC_v3.47142,455,642 - 142,457,902 (-)RGD
Celera7131,104,664 - 131,106,924 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_036926 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA41249 (Get FASTA)   NCBI Sequence Viewer  
  EDL86773 (Get FASTA)   NCBI Sequence Viewer  
  EDL86774 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000052145
  ENSRNOP00000052145.2
GenBank Protein Q04807 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_036926   ⟸   NM_012794
- Peptide Label: precursor
- UniProtKB: Q04807 (UniProtKB/Swiss-Prot),   G3V9L4 (UniProtKB/TrEMBL),   A6KD18 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000052145   ⟸   ENSRNOT00000055270

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q04807-F1-model_v2 AlphaFold Q04807 1-146 view protein structure

Transcriptome

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

Promoters
RGD ID:13695721
Promoter ID:EPDNEW_R6246
Type:single initiation site
Name:Glycam1_1
Description:glycosylation dependent cell adhesion molecule 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.07145,174,784 - 145,174,844EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2712 AgrOrtholog
BioCyc Gene G2FUF-31862 BioCyc
Ensembl Genes ENSRNOG00000036826 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000055270 ENTREZGENE
  ENSRNOT00000055270.5 UniProtKB/TrEMBL
InterPro GLYCAM-1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25258 UniProtKB/Swiss-Prot
NCBI Gene 25258 ENTREZGENE
Pfam GLYCAM-1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Glycam1 PhenoGen
RatGTEx ENSRNOG00000036826 RatGTEx
TIGR TC221064
UniProt A6KD18 ENTREZGENE, UniProtKB/TrEMBL
  A6KD19_RAT UniProtKB/TrEMBL
  G3V9L4 ENTREZGENE, UniProtKB/TrEMBL
  GLCM1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Glycam1  Glycosylation dependent cell adhesion molecule 1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains contains clustered 0-linked domains for presenting sulfate-modified carbohydrate side chains to lectin domain of L selectin 728599