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

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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; INTERACTS WITH 1,2-dimethylhydrazine; 6-propyl-2-thiouracil; alpha-Zearalanol.
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: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87136,559,039 - 136,561,299 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl7136,559,039 - 136,561,299 (-)EnsemblGRCr8
mRatBN7.27134,680,588 - 134,682,848 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7134,680,588 - 134,682,848 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx7136,436,461 - 136,438,721 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07138,665,832 - 138,668,092 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07138,651,510 - 138,653,770 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.07145,172,496 - 145,174,756 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7145,172,493 - 145,174,771 (-)Ensemblrn6Rnor6.0
Rnor_5.07142,951,738 - 142,953,998 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.47142,455,642 - 142,457,902 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera7131,104,664 - 131,106,924 (-)NCBICelera
RGSC_v3.17142,535,830 - 142,538,091 (-)NCBI
Cytogenetic Map7q36NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cell adhesion  (IEA,TAS)

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

miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7121393075137014596Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)7132099939137014596Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)798549867137014596Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)7100548246137014596Rat
61397Bw17Body weight QTL 176.3body mass (VT:0001259)body weight (CMO:0000012)795485047137014596Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)792362341137014596Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7135371291137014596Rat

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

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
16 10 9 62 19 28 4 10 4 98 26 1 58 44 13 24

Sequence


Ensembl Acc Id: ENSRNOT00000055270   ⟹   ENSRNOP00000052145
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl7136,559,039 - 136,561,299 (-)Ensembl
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
GenBank Protein Q04807 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_036926   ⟸   NM_012794
- Peptide Label: precursor
- UniProtKB: Q04807 (UniProtKB/Swiss-Prot),   G3V9L4 (UniProtKB/TrEMBL),   A6KD18 (UniProtKB/TrEMBL)
- Sequence:
Ensembl 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
Ensembl Transcript ENSRNOT00000055270 ENTREZGENE
InterPro GLYCAM-1 UniProtKB/Swiss-Prot
KEGG Report rno:25258 UniProtKB/Swiss-Prot
NCBI Gene 25258 ENTREZGENE
Pfam GLYCAM-1 UniProtKB/Swiss-Prot
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