Matn3 (matrilin 3) - Rat Genome Database

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Gene: Matn3 (matrilin 3) Rattus norvegicus
Analyze
Symbol: Matn3
Name: matrilin 3
RGD ID: 1305085
Description: Predicted to enable calcium ion binding activity. Predicted to be involved in extracellular matrix organization. Predicted to act upstream of or within cartilage development. Predicted to be located in extracellular matrix. Predicted to be part of matrilin complex. Predicted to be active in collagen-containing extracellular matrix. Human ortholog(s) of this gene implicated in multiple epiphyseal dysplasia 5; osteoarthritis; and osteochondrodysplasia. Orthologous to human MATN3 (matrilin 3); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; acrylamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC313954; matrilin-3
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
mRatBN7.2631,748,383 - 31,768,101 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl631,748,474 - 31,768,101 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx632,040,513 - 32,060,559 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0632,356,375 - 32,376,426 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0631,830,987 - 31,851,031 (+)NCBIRnor_WKY
Rnor_6.0634,071,428 - 34,091,048 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl634,071,428 - 34,091,048 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0643,852,755 - 43,872,213 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4632,439,372 - 32,459,031 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1632,442,437 - 32,460,463 (+)NCBI
Celera631,196,790 - 31,216,533 (+)NCBICelera
Cytogenetic Map6q14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Spondylo-epi-metaphyseal dysplasia (SEMD) matrilin 3 type: homozygote matrilin 3 mutation in a novel form of SEMD. Borochowitz ZU, etal., J Med Genet. 2004 May;41(5):366-72.
2. Mutations in the region encoding the von Willebrand factor A domain of matrilin-3 are associated with multiple epiphyseal dysplasia. Chapman KL, etal., Nat Genet. 2001 Aug;28(4):393-6.
3. 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.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
6. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
7. GOA pipeline RGD automated data pipeline
8. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
10. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:11102754   PMID:23951406  


Genomics

Comparative Map Data
Matn3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2631,748,383 - 31,768,101 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl631,748,474 - 31,768,101 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx632,040,513 - 32,060,559 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0632,356,375 - 32,376,426 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0631,830,987 - 31,851,031 (+)NCBIRnor_WKY
Rnor_6.0634,071,428 - 34,091,048 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl634,071,428 - 34,091,048 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0643,852,755 - 43,872,213 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4632,439,372 - 32,459,031 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1632,442,437 - 32,460,463 (+)NCBI
Celera631,196,790 - 31,216,533 (+)NCBICelera
Cytogenetic Map6q14NCBI
MATN3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38219,992,052 - 20,012,668 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl219,992,052 - 20,012,668 (-)EnsemblGRCh38hg38GRCh38
GRCh37220,191,813 - 20,212,429 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36220,055,294 - 20,075,936 (-)NCBINCBI36Build 36hg18NCBI36
Build 34220,113,441 - 20,134,083NCBI
Celera220,054,150 - 20,074,788 (-)NCBICelera
Cytogenetic Map2p24.1NCBI
HuRef219,949,096 - 19,969,718 (-)NCBIHuRef
CHM1_1220,121,147 - 20,141,790 (-)NCBICHM1_1
T2T-CHM13v2.0220,025,556 - 20,046,168 (-)NCBIT2T-CHM13v2.0
Matn3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39128,997,929 - 9,022,028 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl128,997,929 - 9,022,028 (+)EnsemblGRCm39 Ensembl
GRCm38128,947,929 - 8,972,028 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl128,947,929 - 8,972,028 (+)EnsemblGRCm38mm10GRCm38
MGSCv37128,954,735 - 8,978,299 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36128,974,004 - 8,997,501 (+)NCBIMGSCv36mm8
Celera129,331,285 - 9,357,948 (+)NCBICelera
Cytogenetic Map12A1.1NCBI
cM Map123.96NCBI
Matn3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554692,548,443 - 2,568,497 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554692,548,443 - 2,568,497 (-)NCBIChiLan1.0ChiLan1.0
MATN3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A20,095,710 - 20,116,015 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A20,095,710 - 20,116,015 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A19,979,188 - 20,000,733 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
MATN3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11715,037,175 - 15,054,451 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1715,037,995 - 15,054,436 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1714,997,345 - 15,014,511 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01715,184,967 - 15,202,146 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1715,185,696 - 15,202,146 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11715,038,650 - 15,055,806 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01715,045,148 - 15,062,297 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01715,076,833 - 15,093,993 (-)NCBIUU_Cfam_GSD_1.0
Matn3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629259,467,323 - 59,487,466 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493649311,352,206 - 11,371,349 (+)EnsemblSpeTri2.0
SpeTri2.0NW_00493649311,352,206 - 11,371,596 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MATN3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3118,185,975 - 118,205,558 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13118,185,928 - 118,206,465 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23126,216,838 - 126,237,778 (+)NCBISscrofa10.2Sscrofa10.2susScr3
MATN3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11487,707,293 - 87,729,793 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1487,707,380 - 87,728,800 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604524,499,588 - 24,520,604 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Matn3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247382,723,038 - 2,743,572 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247382,722,247 - 2,740,153 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Matn3
20 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:7
Count of miRNA genes:7
Interacting mature miRNAs:7
Transcripts:ENSRNOT00000067962
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6134235784Rat
1578758Tcas9Tongue tumor susceptibility QTL 93.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)6137618905Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6139036266Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6141223769Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6141223769Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6141223769Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6141223769Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6141223769Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6142487980Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6142487980Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6142487980Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142838846Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6143394190Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449734434305Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449754641141Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)61173566972593685Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)61173566972593685Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)61653614061536140Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)61653614071636405Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62033877762613667Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat

Markers in Region
RH134255  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2631,768,247 - 31,768,494 (+)MAPPERmRatBN7.2
Rnor_6.0634,091,195 - 34,091,441NCBIRnor6.0
Rnor_5.0643,872,360 - 43,872,606UniSTSRnor5.0
RGSC_v3.4632,459,178 - 32,459,424UniSTSRGSC3.4
Celera631,216,680 - 31,216,926UniSTS
Cytogenetic Map6q14UniSTS
AU047958  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2631,752,033 - 31,752,182 (+)MAPPERmRatBN7.2
Rnor_6.0634,074,988 - 34,075,136NCBIRnor6.0
Rnor_5.0643,856,315 - 43,856,463UniSTSRnor5.0
RGSC_v3.4632,442,932 - 32,443,080UniSTSRGSC3.4
Celera631,200,351 - 31,200,489UniSTS
Cytogenetic Map6q14UniSTS
MARC_9961-9962:996688712:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2631,753,245 - 31,753,642 (+)MAPPERmRatBN7.2
Rnor_6.0634,076,200 - 34,076,596NCBIRnor6.0
Rnor_5.0643,857,527 - 43,857,923UniSTSRnor5.0
RGSC_v3.4632,444,144 - 32,444,540UniSTSRGSC3.4
Celera631,201,553 - 31,201,949UniSTS
Cytogenetic Map6q14UniSTS


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
Low 14 20 20 20 12 8 19 3
Below cutoff 1 10 19 9 6 9 3 4 57 21 17 6 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000084212   ⟹   ENSRNOP00000070640
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl631,748,474 - 31,768,101 (+)Ensembl
Rnor_6.0 Ensembl634,071,428 - 34,091,048 (+)Ensembl
RefSeq Acc Id: NM_001108013   ⟹   NP_001101483
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2631,748,474 - 31,768,101 (+)NCBI
Rnor_6.0634,071,428 - 34,091,048 (+)NCBI
Rnor_5.0643,852,755 - 43,872,213 (+)NCBI
RGSC_v3.4632,439,372 - 32,459,031 (+)RGD
Celera631,196,790 - 31,216,533 (+)RGD
Sequence:
RefSeq Acc Id: XM_039112187   ⟹   XP_038968115
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2631,748,383 - 31,767,656 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001101483 (Get FASTA)   NCBI Sequence Viewer  
  NP_001382499 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968115 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM03083 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001101483   ⟸   NM_001108013
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000070640   ⟸   ENSRNOT00000084212
RefSeq Acc Id: XP_038968115   ⟸   XM_039112187
- Peptide Label: isoform X1
Protein Domains
EGF-like   VWFA

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2JYF9-F1-model_v2 AlphaFold A0A0G2JYF9 1-463 view protein structure

Transcriptome

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

Promoters
RGD ID:13694487
Promoter ID:EPDNEW_R5012
Type:single initiation site
Name:Matn3_1
Description:matrilin 3
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_6.0634,071,471 - 34,071,531EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305085 AgrOrtholog
BioCyc Gene G2FUF-38172 BioCyc
Ensembl Genes ENSRNOG00000056141 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000070640.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000084212.2 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.410 UniProtKB/TrEMBL
InterPro cEGF UniProtKB/TrEMBL
  EGF-like_Ca-bd_dom UniProtKB/TrEMBL
  EGF_3 UniProtKB/TrEMBL
  Growth_fac_rcpt_N_dom UniProtKB/TrEMBL
  Matrilin-3/4 UniProtKB/TrEMBL
  Matrilin_coiled-coil_trimer UniProtKB/TrEMBL
  VWF_A UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
NCBI Gene 313954 ENTREZGENE
PANTHER PTHR24034:SF105 UniProtKB/TrEMBL
Pfam cEGF UniProtKB/TrEMBL
  Matrilin_ccoil UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
PhenoGen Matn3 PhenoGen
PROSITE EGF_2 UniProtKB/TrEMBL
  EGF_3 UniProtKB/TrEMBL
  VWFA UniProtKB/TrEMBL
SMART EGF UniProtKB/TrEMBL
  EGF_CA UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
Superfamily-SCOP SSF53300 UniProtKB/TrEMBL
  SSF57184 UniProtKB/TrEMBL
UniProt A0A0G2JYF9_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Matn3  matrilin 3   Matn3_predicted  matrilin 3 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Matn3_predicted  matrilin 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED