Matr3 (matrin 3) - Rat Genome Database
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Gene: Matr3 (matrin 3) Rattus norvegicus
Analyze
Symbol: Matr3
Name: matrin 3
RGD ID: 3052
Description: Predicted to have identical protein binding activity and miRNA binding activity. Predicted to be involved in several processes, including activation of innate immune response; blastocyst formation; and heart development. Localizes to cytoplasm and nuclear matrix. Human ortholog(s) of this gene implicated in amyotrophic lateral sclerosis type 21. Orthologous to human MATR3 (matrin 3); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: matrin-3; nuclear scaffold protein P130/MAT3; P130/MAT3; snhg4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: LOC100360347   Matr3-ps1  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21827,154,098 - 27,193,212 (+)NCBI
Rnor_6.0 Ensembl1828,361,283 - 28,390,717 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01828,351,691 - 28,390,764 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01828,074,345 - 28,103,874 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41828,171,639 - 28,215,659 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11828,221,884 - 28,242,302 (+)NCBI
Celera1826,897,382 - 26,926,742 (+)NCBICelera
Cytogenetic Map18p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,6-dinitrotoluene  (EXP)
2-methylcholine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-chloropropane-1,2-diol  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4-hydroxyphenyl retinamide  (ISO)
acrolein  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
Aroclor 1254  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP)
Brodifacoum  (EXP)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
chlorpyrifos  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
DDT  (EXP)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
enzyme inhibitor  (ISO)
ethyl methanesulfonate  (ISO)
flavonoids  (EXP)
fulvestrant  (ISO)
geldanamycin  (ISO)
genistein  (ISO)
gentamycin  (EXP)
irinotecan  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
ozone  (ISO)
PCB138  (EXP)
pentachlorophenol  (ISO)
phenethyl isothiocyanate  (EXP)
phenobarbital  (ISO)
PhIP  (EXP)
raloxifene  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
succimer  (ISO)
tamoxifen  (ISO)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
tolcapone  (EXP)
Tributyltin oxide  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vincristine  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IDA)
nuclear matrix  (IDA)
nucleus  (IBA,IDA,IEA,ISO)

Molecular Function

References

Additional References at PubMed
PMID:1575753   PMID:8250943   PMID:8357833   PMID:9111204   PMID:9524232   PMID:10860485   PMID:11112453   PMID:16396499   PMID:16641100   PMID:19946888   PMID:21771347   PMID:22082260  
PMID:22658674   PMID:22681889   PMID:22871113   PMID:24625528   PMID:25416956   PMID:25574029   PMID:27869233   PMID:28431233   PMID:28712728   PMID:28755400   PMID:29476059   PMID:30597036  


Genomics

Comparative Map Data
Matr3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21827,154,098 - 27,193,212 (+)NCBI
Rnor_6.0 Ensembl1828,361,283 - 28,390,717 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01828,351,691 - 28,390,764 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01828,074,345 - 28,103,874 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41828,171,639 - 28,215,659 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11828,221,884 - 28,242,302 (+)NCBI
Celera1826,897,382 - 26,926,742 (+)NCBICelera
Cytogenetic Map18p11NCBI
MATR3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl5139,293,674 - 139,331,677 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl5139,273,752 - 139,331,671 (+)EnsemblGRCh38hg38GRCh38
GRCh385139,274,101 - 139,331,677 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh375138,609,790 - 138,667,366 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365138,637,691 - 138,694,029 (+)NCBINCBI36hg18NCBI36
Build 345138,657,253 - 138,694,023NCBI
Celera5134,731,161 - 134,789,067 (+)NCBI
Cytogenetic Map5q31.2NCBI
HuRef5133,798,796 - 133,857,165 (+)NCBIHuRef
CHM1_15138,042,040 - 138,099,954 (+)NCBICHM1_1
Matr3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391835,695,211 - 35,725,098 (+)NCBIGRCm39mm39
GRCm39 Ensembl1835,695,191 - 35,726,888 (+)Ensembl
GRCm381835,562,158 - 35,592,045 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1835,562,138 - 35,593,835 (+)EnsemblGRCm38mm10GRCm38
MGSCv371835,721,812 - 35,751,699 (+)NCBIGRCm37mm9NCBIm37
MGSCv361835,688,242 - 35,717,383 (+)NCBImm8
Celera1836,018,404 - 36,048,039 (+)NCBICelera
Cytogenetic Map18B2NCBI
cM Map1819.14NCBI
Matr3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554181,213,503 - 1,269,755 (-)NCBIChiLan1.0ChiLan1.0
MATR3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15140,788,667 - 140,825,064 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v05134,664,893 - 134,702,566 (+)NCBIMhudiblu_PPA_v0panPan3
MATR3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11126,736,728 - 26,790,449 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1126,758,261 - 26,790,449 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1125,527,245 - 25,559,143 (+)NCBI
ROS_Cfam_1.01127,616,211 - 27,648,180 (+)NCBI
UMICH_Zoey_3.11126,323,723 - 26,355,841 (+)NCBI
UNSW_CanFamBas_1.01126,145,651 - 26,177,531 (+)NCBI
UU_Cfam_GSD_1.01126,810,878 - 26,842,761 (+)NCBI
Matr3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_ltri_2NW_024407213153,192,756 - 153,239,429 (-)NCBI
SpeTri2.0NW_0049365318,385,919 - 8,418,753 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MATR3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.12141,179,515 - 141,230,259 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22147,010,375 - 147,060,861 (+)NCBISscrofa10.2Sscrofa10.2susScr3
MATR3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12341,955,451 - 41,992,280 (+)NCBI
Vero_WHO_p1.0NW_02366603435,898,083 - 35,935,039 (-)NCBI
Matr3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474332,086,821 - 32,147,079 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631264Scl22Serum cholesterol level QTL 226.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)181553296332704022Rat
1331733Bp233Blood pressure QTL 2333.97196arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182596102681761656Rat
1331735Rf44Renal function QTL 442.981total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)181925171732670473Rat
1331741Bp232Blood pressure QTL 2323.59112arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)182260373687074531Rat
1331753Bp231Blood pressure QTL 2313.643arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181553942753861431Rat
1331766Bp236Blood pressure QTL 2363.022arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181553942732670473Rat
1331775Bp235Blood pressure QTL 2353.201arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181925171732670473Rat
2312598Bp340Blood pressure QTL 3400.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)18371954732487870Rat
2325839Bp348Blood pressure QTL 3480.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182674340443659626Rat
1641923Colcr8Colorectal carcinoma resistance QTL 83.10.0014intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)182318422753861431Rat
2300180Bmd67Bone mineral density QTL 674.80.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)18138195967Rat
2301413Bp318Blood pressure QTL 3180.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182774302448499517Rat
2293661Bss50Bone structure and strength QTL 504.640.0003lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)18138195967Rat
1600373Mamtr6Mammary tumor resistance QTL 6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)182028575887080053Rat
1578661Bss20Bone structure and strength QTL 203.7femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)181569587287080053Rat
1578667Bss21Bone structure and strength QTL 213.5femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)181569587287080053Rat
2293708Bss46Bone structure and strength QTL 468.80.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)181569587268524999Rat
2299160Iddm35Insulin dependent diabetes mellitus QTL 352.79blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)18440751362570466Rat
1358193Emca2Estrogen-induced mammary cancer QTL 21.6mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)181903103068436105Rat
1358358Sradr6Stress Responsive Adrenal Weight QTL 62.49adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)181553942761499684Rat
2312568Glom21Glomerulus QTL 2120.005kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)18543013441781619Rat
2313082Bss85Bone structure and strength QTL 850.80.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)181467885259678852Rat
61375Bp41Blood pressure QTL 412.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)181553967129530300Rat
61382Bp46Blood pressure QTL 4618.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181553296332704022Rat
61388Bp2Blood pressure QTL 23.23arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)18135097280Rat
6903353Bp353Blood pressure QTL 3532.8arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)182260476461985648Rat
6903359Bp355Blood pressure QTL 3553.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181553967161985648Rat
7387267Uae42Urinary albumin excretion QTL 420.61urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)142163949166639491Rat
9589153Insul31Insulin level QTL 317.150.05blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)18138753381Rat
12904670Cm126Cardiac mass QTL 1260.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)182774302448499517Rat
12904669Cm125Cardiac mass QTL 1250.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)182774302448499517Rat
12904677Kidm72Kidney mass QTL 720.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)182774302448499517Rat
12904668Bw188Body weight QTL 1880.03body mass (VT:0001259)body weight (CMO:0000012)182774302448499517Rat
12904673Cm127Cardiac mass QTL 1270.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)182774302448499517Rat
12904675Am19Aortic mass QTL 190.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)182774302448499517Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:107
Count of miRNA genes:88
Interacting mature miRNAs:97
Transcripts:ENSRNOT00000026949
Prediction methods:Miranda
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 3 42 57 41 19 41 8 10 74 35 41 11 8
Low 1 1
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_019149 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006254534 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006254535 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600886 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600887 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039096649 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB205483 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC135285 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC062231 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC168723 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473974 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213524 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225101 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227851 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230646 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233097 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234052 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234627 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ235016 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000299 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  LC420149 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M63485 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000026949   ⟹   ENSRNOP00000026949
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1828,361,283 - 28,390,696 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000083993   ⟹   ENSRNOP00000073436
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1828,370,085 - 28,390,717 (+)Ensembl
RefSeq Acc Id: NM_019149   ⟹   NP_062022
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21827,163,729 - 27,193,164 (+)NCBI
Rnor_6.01828,361,283 - 28,390,716 (+)NCBI
Rnor_5.01828,074,345 - 28,103,874 (+)NCBI
RGSC_v3.41828,171,639 - 28,215,659 (+)RGD
Celera1826,897,382 - 26,926,742 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006254534   ⟹   XP_006254596
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21827,163,644 - 27,193,212 (+)NCBI
Rnor_6.01828,361,227 - 28,390,764 (+)NCBI
Rnor_5.01828,074,345 - 28,103,874 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006254535   ⟹   XP_006254597
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21827,163,636 - 27,193,212 (+)NCBI
Rnor_6.01828,361,239 - 28,390,764 (+)NCBI
Rnor_5.01828,074,345 - 28,103,874 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600886   ⟹   XP_017456375
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21827,154,098 - 27,193,212 (+)NCBI
Rnor_6.01828,351,691 - 28,390,764 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600887   ⟹   XP_017456376
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21827,163,891 - 27,193,212 (+)NCBI
Rnor_6.01828,361,365 - 28,390,764 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039096649   ⟹   XP_038952577
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21827,163,636 - 27,185,032 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_062022   ⟸   NM_019149
- UniProtKB: P43244 (UniProtKB/Swiss-Prot),   A0A0G2JSR7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006254596   ⟸   XM_006254534
- Peptide Label: isoform X1
- UniProtKB: P43244 (UniProtKB/Swiss-Prot),   A0A0G2JSR7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006254597   ⟸   XM_006254535
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017456375   ⟸   XM_017600886
- Peptide Label: isoform X1
- UniProtKB: P43244 (UniProtKB/Swiss-Prot),   A0A0G2JSR7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456376   ⟸   XM_017600887
- Peptide Label: isoform X1
- UniProtKB: P43244 (UniProtKB/Swiss-Prot),   A0A0G2JSR7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000026949   ⟸   ENSRNOT00000026949
RefSeq Acc Id: ENSRNOP00000073436   ⟸   ENSRNOT00000083993
RefSeq Acc Id: XP_038952577   ⟸   XM_039096649
- Peptide Label: isoform X3
Protein Domains
Matrin-type   RRM   U1-type

Transcriptome

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

Promoters
RGD ID:13700708
Promoter ID:EPDNEW_R11231
Type:initiation region
Name:Matr3_1
Description:matrin 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_6.01828,361,286 - 28,361,346EPDNEW

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)
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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
BN/SsN (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
Buf/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
COP/CrCrl (MCW & UW)
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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)
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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
F344/NRrrc (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
FHH/EurMcwi (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)
FHH/EurMcwi (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
FHL/EurMcwi (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)
FHL/EurMcwi (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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
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
18 28084396 28084397 G T snv RCS/Kyo (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3052 AgrOrtholog
Ensembl Genes ENSRNOG00000019875 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000026949 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073436 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000026949 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000083993 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.330 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:6921221 IMAGE-MGC_LOAD
InterPro MATR3_RRM1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MATR3_RRM2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Matrin/U1-C_Znf_C2H2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Matrin/U1-like-C_Znf_C2H2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucleotide-bd_a/b_plait_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RRM_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29150 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:72856 IMAGE-MGC_LOAD
NCBI Gene 29150 ENTREZGENE
PhenoGen Matr3 PhenoGen
PROSITE RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_MATRIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZnF_U1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54928 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC217434
UniProt A0A0G2JSR7 ENTREZGENE, UniProtKB/TrEMBL
  B5DEM0_RAT UniProtKB/TrEMBL
  MATR3_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q6P6H1_RAT UniProtKB/TrEMBL
UniProt Secondary O35833 UniProtKB/Swiss-Prot
  Q5DVW1 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Matr3  matrin 3      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains contains a highly acidic domain and a putative nuclear targeting signal sequence 69882