Madcam1 (mucosal vascular addressin cell adhesion molecule 1) - Rat Genome Database

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Gene: Madcam1 (mucosal vascular addressin cell adhesion molecule 1) Rattus norvegicus
Analyze
Symbol: Madcam1
Name: mucosal vascular addressin cell adhesion molecule 1
RGD ID: 3029
Description: Predicted to enable integrin binding activity involved in cell-matrix adhesion. Involved in cell adhesion and positive regulation of leukocyte migration. Predicted to be located in plasma membrane. Used to study Crohn's disease and food allergy. Orthologous to human MADCAM1 (mucosal vascular addressin cell adhesion molecule 1); INTERACTS WITH 1,2-dimethylhydrazine; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: MAdCAM-1; mucosal addressin cell adhesion molecule 1; rMAdCAM-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2710,036,301 - 10,039,703 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl710,036,301 - 10,039,703 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx712,917,270 - 12,920,672 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0714,795,349 - 14,798,751 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0712,654,653 - 12,658,055 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0712,918,352 - 12,922,509 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl712,918,710 - 12,922,112 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0713,087,337 - 13,092,220 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4711,553,219 - 11,556,621 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1711,553,218 - 11,556,621 (-)NCBI
Celera78,209,542 - 8,212,944 (-)NCBICelera
Cytogenetic Map7q11NCBI
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

References - curated
# Reference Title Reference Citation
1. Aberrant endometrial features of pregnancy in diabetic NOD mice. Burke SD, etal., Diabetes. 2007 Dec;56(12):2919-26. Epub 2007 Sep 7.
2. Treatment with an antibody to VLA-1 integrin reduces glomerular and tubulointerstitial scarring in a rat model of crescentic glomerulonephritis. Cook HT, etal., Am J Pathol 2002 Oct;161(4):1265-72.
3. Immunohistochemical analysis of MAdCAM-1 expression during acute rejection on small bowel grafts in rats. Fujisaki S, etal., Transplant Proc 2002 May;34(3):1045-6.
4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. Involvement of mucosal addressin cell adhesion molecule-1 (MAdCAM-1) in the pathogenesis of granulomatous colitis in rats. Hokari R, etal., Clin Exp Immunol. 2001 Nov;126(2):259-65.
6. Expression of adhesion molecules in the rectum-associated lymph nodules of pre- and postnatal specific pathogen-free rats. Ichikawa S and Yamashita A, J Gastroenterol Hepatol 2003 Aug;18(8):970-979.
7. Cloning and characterization of the rat MAdCAM-1 cDNA and gene. Iizuka T, etal., Biochim Biophys Acta 1998 Feb 11;1395(3):266-70.
8. Stage-specific expression of mucosal addressin cell adhesion molecule-1 during embryogenesis in rats. Iizuka T, etal., J Immunol. 2000 Mar 1;164(5):2463-71.
9. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
10. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
11. Chronic allergy to dietary ovalbumin induces lymphocyte migration to rat small intestinal mucosa that is inhibited by MAdCAM-1. Ogawa T, etal., Am J Physiol Gastrointest Liver Physiol. 2004 May;286(5):G702-10. Epub 2003 Dec 11.
12. GOA pipeline RGD automated data pipeline
13. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
14. Comprehensive gene review and curation RGD comprehensive gene curation
15. Basis for the age-related decline in intestinal mucosal immunity. Schmucker DL, etal., Clin Dev Immunol. 2003 Jun-Dec;10(2-4):167-72.
16. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
17. Involvement of beta 7 integrin and mucosal addressin cell adhesion molecule-1 (MAdCAM-1) in the development of diabetes in obese diabetic mice. Yang XD, etal., Diabetes. 1997 Oct;46(10):1542-7.
Additional References at PubMed
PMID:12230506   PMID:15484189   PMID:16387148   PMID:18308860   PMID:23986478  


Genomics

Comparative Map Data
Madcam1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2710,036,301 - 10,039,703 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl710,036,301 - 10,039,703 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx712,917,270 - 12,920,672 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0714,795,349 - 14,798,751 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0712,654,653 - 12,658,055 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0712,918,352 - 12,922,509 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl712,918,710 - 12,922,112 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0713,087,337 - 13,092,220 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4711,553,219 - 11,556,621 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1711,553,218 - 11,556,621 (-)NCBI
Celera78,209,542 - 8,212,944 (-)NCBICelera
Cytogenetic Map7q11NCBI
MADCAM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3819496,486 - 505,343 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl19489,176 - 505,343 (+)EnsemblGRCh38hg38GRCh38
GRCh3719496,486 - 505,343 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3619447,490 - 456,343 (+)NCBINCBI36Build 36hg18NCBI36
Build 3419447,489 - 456,342NCBI
Celera19312,275 - 321,128 (-)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef19266,619 - 275,499 (+)NCBIHuRef
CHM1_119496,085 - 504,846 (+)NCBICHM1_1
T2T-CHM13v2.019448,988 - 457,915 (+)NCBIT2T-CHM13v2.0
Madcam1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391079,500,393 - 79,504,376 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1079,500,393 - 79,504,371 (+)EnsemblGRCm39 Ensembl
GRCm381079,664,559 - 79,668,542 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1079,664,559 - 79,668,537 (+)EnsemblGRCm38mm10GRCm38
MGSCv371079,127,319 - 79,131,281 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361079,067,712 - 79,071,665 (+)NCBIMGSCv36mm8
Celera1080,678,309 - 80,682,271 (+)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.72NCBI
Madcam1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554957,190,009 - 7,194,966 (-)NCBIChiLan1.0ChiLan1.0
MADCAM1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1194,063,146 - 4,074,931 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v019627,526 - 636,684 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.119467,651 - 478,208 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl19468,026 - 477,830 (+)Ensemblpanpan1.1panPan2
MADCAM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12057,978,189 - 57,981,966 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2057,978,185 - 57,981,966 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2057,780,967 - 57,784,744 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02058,721,763 - 58,725,542 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2058,721,759 - 58,725,542 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12057,775,339 - 57,779,116 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02058,255,185 - 58,258,962 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02058,458,457 - 58,462,234 (-)NCBIUU_Cfam_GSD_1.0
Madcam1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118217,685,617 - 217,689,136 (-)NCBIHiC_Itri_2
SpeTri2.0NW_004936588145,696 - 149,158 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MADCAM1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl277,784,612 - 77,789,067 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1277,784,610 - 77,789,036 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
LOC103233562
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.16222,795 - 235,198 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660818,890,323 - 8,901,527 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Madcam1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248287,954,745 - 7,958,398 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248287,953,693 - 7,959,518 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Madcam1
5 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:67
Count of miRNA genes:56
Interacting mature miRNAs:62
Transcripts:ENSRNOT00000010938
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
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat


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 6 16
Low 1 20 6 6 7 6 1 1 61 12 20 1
Below cutoff 17 21 6 11 6 4 7 9 11 5 11 4

Sequence


RefSeq Acc Id: ENSRNOT00000010938   ⟹   ENSRNOP00000010939
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl710,036,301 - 10,039,703 (-)Ensembl
Rnor_6.0 Ensembl712,918,710 - 12,922,112 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000096335   ⟹   ENSRNOP00000089873
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl710,036,382 - 10,039,703 (-)Ensembl
RefSeq Acc Id: NM_019317   ⟹   NP_062190
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2710,036,301 - 10,039,703 (-)NCBI
Rnor_6.0712,918,710 - 12,922,112 (-)NCBI
Rnor_5.0713,087,337 - 13,092,220 (-)NCBI
RGSC_v3.4711,553,219 - 11,556,621 (-)RGD
Celera78,209,542 - 8,212,944 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_062190 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAA25260 (Get FASTA)   NCBI Sequence Viewer  
  EDL89413 (Get FASTA)   NCBI Sequence Viewer  
  EDL89414 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000010939
  ENSRNOP00000010939.1
  ENSRNOP00000089873.1
  ENSRNOP00055045535
  ENSRNOP00060040987
  ENSRNOP00065027928
GenBank Protein O70540 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_062190   ⟸   NM_019317
- Peptide Label: precursor
- UniProtKB: O70540 (UniProtKB/Swiss-Prot),   A6K8Z4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000010939   ⟸   ENSRNOT00000010938
RefSeq Acc Id: ENSRNOP00000089873   ⟸   ENSRNOT00000096335
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O70540-F1-model_v2 AlphaFold O70540 1-394 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3029 AgrOrtholog
BioCyc Gene G2FUF-34879 BioCyc
Ensembl Genes ENSRNOG00000008217 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00055031831 UniProtKB/Swiss-Prot
  ENSRNOG00060028258 UniProtKB/Swiss-Prot
  ENSRNOG00065020543 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000010938 ENTREZGENE
  ENSRNOT00000010938.3 UniProtKB/Swiss-Prot
  ENSRNOT00000096335.1 UniProtKB/TrEMBL
  ENSRNOT00055055091 UniProtKB/Swiss-Prot
  ENSRNOT00060049107 UniProtKB/Swiss-Prot
  ENSRNOT00065034786 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Adhes-Ig-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ICAM_VCAM_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MADCAM1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:54266 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 54266 ENTREZGENE
PANTHER MUCOSAL ADDRESSIN CELL ADHESION MOLECULE 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR14162 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Adhes-Ig_like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Madcam1 PhenoGen
PRINTS ICAMVCAM1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000008217 RatGTEx
  ENSRNOG00055031831 RatGTEx
  ENSRNOG00060028258 RatGTEx
  ENSRNOG00065020543 RatGTEx
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC211744
UniProt A0A8I6AAQ2_RAT UniProtKB/TrEMBL
  A6K8Z3_RAT UniProtKB/TrEMBL
  A6K8Z4 ENTREZGENE, UniProtKB/TrEMBL
  MADCA_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Madcam1  Mucosal vascular addressin cell adhesion molecule 1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in endothelial cells of blood vessels in the entire colonic mucosa until day 7 after birth 724402