Synm (synemin) - Rat Genome Database
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Gene: Synm (synemin) Rattus norvegicus
Analyze
Symbol: Synm
Name: synemin
RGD ID: 727872
Description: Predicted to have intermediate filament binding activity and vinculin binding activity. Predicted to be involved in fast-twitch skeletal muscle fiber contraction. Localizes to intermediate filament. Orthologous to human SYNM (synemin); INTERACTS WITH 3,7-dihydropurine-6-thione; acetamide; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: desmuslin; Dmn; LOC308709; synemin, intermediate filament protein
Orthologs:
Homo sapiens (human) : SYNM (synemin)  HGNC  Alliance
Mus musculus (house mouse) : Synm (synemin, intermediate filament protein)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Synm (synemin)
Pan paniscus (bonobo/pygmy chimpanzee) : SYNM (synemin)
Canis lupus familiaris (dog) : SYNM (synemin)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Synm (synemin)
Sus scrofa (pig) : SYNM (synemin)
Chlorocebus sabaeus (African green monkey) : SYNM (synemin)
Heterocephalus glaber (naked mole-rat) : Synm (synemin)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01128,692,112 - 128,722,048 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1128,692,112 - 128,722,048 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01129,757,882 - 129,788,008 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41122,474,205 - 122,504,176 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11122,552,553 - 122,582,427 (-)NCBI
Celera1113,533,990 - 113,563,954 (-)NCBICelera
Cytogenetic Map1q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-hydroxypropanoic acid  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,7-dihydropurine-6-thione  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
acetamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
calcitriol  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
choline  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
corticosterone  (EXP)
cyclosporin A  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
dicrotophos  (ISO)
dioxygen  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
entinostat  (ISO)
ethanol  (ISO)
folic acid  (ISO)
GW 4064  (ISO)
indometacin  (ISO)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
mercaptopurine  (EXP)
methylmercury chloride  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
nickel atom  (ISO)
orphenadrine  (EXP)
paracetamol  (ISO)
phenylmercury acetate  (ISO)
potassium chromate  (ISO)
progesterone  (ISO)
purine-6-thiol  (EXP)
rac-lactic acid  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
sodium fluoride  (ISO)
Soman  (EXP)
sulforaphane  (ISO)
tetrachloromethane  (EXP,ISO)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
urethane  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:8552632   PMID:11737198   PMID:15265691   PMID:16777071   PMID:16817202   PMID:18028034   PMID:18342854   PMID:21139996   PMID:21982947   PMID:25567810  


Genomics

Comparative Map Data
Synm
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01128,692,112 - 128,722,048 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1128,692,112 - 128,722,048 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01129,757,882 - 129,788,008 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41122,474,205 - 122,504,176 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11122,552,553 - 122,582,427 (-)NCBI
Celera1113,533,990 - 113,563,954 (-)NCBICelera
Cytogenetic Map1q22NCBI
SYNM
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1599,098,217 - 99,135,593 (+)EnsemblGRCh38hg38GRCh38
GRCh381599,105,069 - 99,136,586 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371599,645,286 - 99,675,800 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361597,462,809 - 97,493,323 (+)NCBINCBI36hg18NCBI36
Build 341597,462,808 - 97,493,311NCBI
Celera1576,064,213 - 76,094,750 (+)NCBI
Cytogenetic Map15q26.3NCBI
HuRef1575,774,873 - 75,805,361 (+)NCBIHuRef
CHM1_11599,486,672 - 99,517,169 (+)NCBICHM1_1
Synm
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39767,379,909 - 67,409,490 (-)NCBI
GRCm38767,730,161 - 67,759,742 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl767,730,160 - 67,759,742 (-)EnsemblGRCm38mm10GRCm38
MGSCv37774,875,047 - 74,904,628 (-)NCBIGRCm37mm9NCBIm37
MGSCv36767,603,681 - 67,633,206 (-)NCBImm8
Celera765,184,111 - 65,213,801 (-)NCBICelera
Cytogenetic Map7CNCBI
Synm
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541626,554,703 - 26,578,761 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541626,554,074 - 26,579,804 (+)NCBIChiLan1.0ChiLan1.0
SYNM
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11596,974,351 - 97,004,956 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1596,975,160 - 97,002,412 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01577,790,447 - 77,821,317 (+)NCBI
SYNM
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl341,594,580 - 41,623,627 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1341,595,218 - 41,623,475 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Synm
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364834,362,891 - 4,388,558 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYNM
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11137,855,644 - 137,883,914 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21154,019,589 - 154,047,542 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SYNM
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl2917,693,121 - 17,724,387 (+)Ensembl
ChlSab1.12917,693,148 - 17,723,847 (+)NCBI
Synm
(Heterocephalus glaber - naked mole-rat)
No map positions available.

Position Markers
RH137882  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01128,692,326 - 128,692,493NCBIRnor6.0
Rnor_5.01129,758,094 - 129,758,261UniSTSRnor5.0
RGSC_v3.41122,474,417 - 122,474,584UniSTSRGSC3.4
Celera1113,534,202 - 113,534,369UniSTS
Cytogenetic Map1q22UniSTS
RH 3.4 Map11450.39UniSTS
RH143655  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01128,722,199 - 128,722,309NCBIRnor6.0
Rnor_5.01129,788,009 - 129,788,119UniSTSRnor5.0
RGSC_v3.41122,504,327 - 122,504,437UniSTSRGSC3.4
Celera1113,564,105 - 113,564,215UniSTS
Cytogenetic Map1q22UniSTS
RH 3.4 Map11447.29UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)125951907130917265Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134993530173445086Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135377692217372257Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)149147799156446783Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149578577169852184Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149578693217054291Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)158354072161711996Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)182788437239853971Rat
61344Bp29Blood pressure QTL 297.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)185779320130779320Rat
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)185917265130917265Rat
4889494Scort2Serum corticosterone level QTL 24.2blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)186776571131776571Rat
724529Cm16Cardiac mass QTL 162.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)190804143161321256Rat
738022Anxrr13Anxiety related response QTL 134.60.00039locomotor behavior trait (VT:0001392)number of 20 x 20 cm floor squares crossed into, out of or within a discrete space in an experimental apparatus (CMO:0001514)191093646136093646Rat
724521Uae1Urinary albumin excretion QTL 13.80.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)194201400184846632Rat
1358902Bw47Body weight QTL 471.67body mass (VT:0001259)body weight (CMO:0000012)194201400197187904Rat
1302788Scl19Serum cholesterol QTL 194.60.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)194225372130917265Rat
1300153Bp171Blood pressure QTL 1713.37arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)194364073153076991Rat
724567Tcas6Tongue tumor susceptibility QTL 66.85tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)195304961156446783Rat
1331793Bp200Blood pressure QTL 2003.71601arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)199983293188289386Rat
1331751Bp199Blood pressure QTL 1993.60022arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)199983293198656062Rat
1331749Hrtrt11Heart rate QTL 112.973heart pumping trait (VT:2000009)heart rate (CMO:0000002)199983293216213510Rat
70209Niddm23Non-insulin dependent diabetes mellitus QTL 232.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)199983293216325819Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1100131562236763528Rat
2293142Bp314Blood pressure QTL 314arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1100354344145354344Rat
8655649Arrd1Age-related retinal degeneration QTL 14.89retinal layer morphology trait (VT:0003727)percentage of study population developing retinopathy during a period of time (CMO:0002453)1106002252202571904Rat
61370Mcs3Mammary carcinoma susceptibility QTL 32.15mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1108057233167517487Rat
1641897Alcrsp1Alcohol response QTL 1response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1108417193153417193Rat
2317833Alcrsp19Alcohol response QTL 1912.40.001response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1108417193153417193Rat
1354623Rf46Renal function QTL 463.8blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)1108986301161784422Rat
1354591Cm36Cardiac mass QTL 364.1heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1108986301219232156Rat
1354615Cm32Cardiac mass QTL 325.2heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1108986301219232156Rat
1354606Bp246Blood pressure QTL 2463.6arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)1108986301238830534Rat
2303591Gluco41Glucose level QTL 412blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1109634374154634374Rat
9590300Scort16Serum corticosterone level QTL 164.390.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1110620749155620749Rat
8694370Bw154Body weight QTL 1548.910.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)1110620749155620749Rat
61399Tcat1Tongue tumor resistance QTL 13.3tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 5 mm (CMO:0001879)1111446783156446783Rat
61346Rf2Renal disease susceptibility QTL 23.7urine protein amount (VT:0005160)urine protein level (CMO:0000591)1111446783156446783Rat
631569Bp93Blood pressure QTL 930.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1113593576129209407Rat
631496Bp97Blood pressure QTL 973.08arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1113593576158593576Rat
1300158Bp173Blood pressure QTL 1733.48arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1122614824201146953Rat
7794788Mcs32Mammary carcinoma susceptibility QTL 322.61mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)1122614824262664716Rat
2313060Bss71Bone structure and strength QTL 712.60.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)1124090312169090312Rat
631199Cm23Cardiac mass QTL 234.60.0004heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1124603592188289386Rat
7421630Bp362Blood pressure QTL 3620.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1125875758262433692Rat
631205Bp196Blood pressure QTL 19640.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1126240667217054291Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:39
Count of miRNA genes:37
Interacting mature miRNAs:39
Transcripts:ENSRNOT00000050832
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.


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 16 8 4 8 11 19 8 11 8
Low 27 41 33 15 33 53 35 33
Below cutoff 8 8 8 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000050832   ⟹   ENSRNOP00000046923
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1128,692,120 - 128,722,048 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076329   ⟹   ENSRNOP00000068488
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1128,694,735 - 128,695,796 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076511   ⟹   ENSRNOP00000068384
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1128,692,112 - 128,721,956 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000077020   ⟹   ENSRNOP00000068230
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1128,695,213 - 128,695,995 (-)Ensembl
RefSeq Acc Id: NM_001134858   ⟹   NP_001128330
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01128,692,114 - 128,722,048 (-)NCBI
Rnor_5.01129,757,882 - 129,788,008 (-)NCBI
RGSC_v3.41122,474,205 - 122,504,176 (-)RGD
Celera1113,533,990 - 113,563,954 (-)RGD
Sequence:
RefSeq Acc Id: XM_006229337   ⟹   XP_006229399
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01128,692,112 - 128,722,043 (-)NCBI
Rnor_5.01129,757,882 - 129,788,008 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001128330 (Get FASTA)   NCBI Sequence Viewer  
  XP_006229399 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAC66620 (Get FASTA)   NCBI Sequence Viewer  
  EDM08464 (Get FASTA)   NCBI Sequence Viewer  
  EDM08467 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001128330   ⟸   NM_001134858
- UniProtKB: G3V9G5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229399   ⟸   XM_006229337
- Peptide Label: isoform X1
- UniProtKB: A0A096MK54 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000068230   ⟸   ENSRNOT00000077020
RefSeq Acc Id: ENSRNOP00000046923   ⟸   ENSRNOT00000050832
RefSeq Acc Id: ENSRNOP00000068488   ⟸   ENSRNOT00000076329
RefSeq Acc Id: ENSRNOP00000068384   ⟸   ENSRNOT00000076511
Protein Domains
IF rod

Transcriptome

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

Promoters
RGD ID:13690110
Promoter ID:EPDNEW_R634
Type:single initiation site
Name:Synm_1
Description:synemin
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_6.01128,721,940 - 128,722,000EPDNEW

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)
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
BN/SsN (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
Buf/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
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
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)
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
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
1 129762631 129762632 G A snv WKY/N (KNAW), WKY/NCrl (KNAW), GK/Ox (KNAW), WKY/NHsd (KNAW), DOB/Oda (KyushuU)
1 129763709 129763710 G A snv SBN/Ygl (MCW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), F344/Jcl (KyushuU), F344/Stm (KyushuU), F344/NSlc (KyushuU), F344/DuCrlCrlj (KyushuU), Crl:SD (UDEL), MNS/Gib (KNAW), M520/N (KNAW), F344/NHsd (KNAW), F344/NCrl (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NRrrc (Illumina) (KNAW), SBN/Ygl (KNAW), SBH/Ygl (KNAW), BBDP/WorN (KNAW)
1 129763742 129763743 G T snv SR/JrHsd (MCW), SR/JrHsd (KNAW), BUF/N (KNAW), DOB/Oda (KyushuU), LE/Stm (KyushuU), BDIX/NemOda (KyushuU), FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), FHH/EurMcwi (MCW), LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), BDIX.Cg-Tal/NemOda (KyushuU), HWY/Slc (KyushuU), WN/N (KNAW), SS/JrHsdMcwi (MCW), WKY/Gcrc (KNAW), FHL/EurMcwi (MCW), SHRSP/Gcrc (KNAW), SHR/OlaIpcvPrin (KNAW), SHR/OlaIpcv (KNAW), SHR/NHsd (KNAW), SHR/NCrlPrin (KNAW), Crl:SD (UDEL), LEC/Tj (KyushuU), SDLEF7/Barth (UDEL), WAG/Rij (KNAW), SS/JrHsdMcwi (KNAW), SS/Jr (KNAW)
1 129763766 129763767 G T snv NIG-III/Hok (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 128696863 128696864 G A snv WKY/NCrl (RGD), WKY/N (MCW), GK/Ox (RGD)
1 128697941 128697942 G A snv SBN/Ygl (MCW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), SBN/Ygl (RGD), SBH/Ygl (RGD), MNS/Gib (RGD), F344/NCrl (RGD), BBDP/Wor (RGD), M520/N (MCW), F344/NRrrc (MCW), CDS
1 128697974 128697975 G T snv FHL/EurMcwi (RGD), SR/JrHsd (MCW), SS/Jr (RGD), FHH/EurMcwi (RGD), FHH/EurMcwi (MCW), LE/Stm (RGD), SS/JrHsdMcwi (RGD), WAG/Rij (RGD), WN/N (MCW), FHL/EurMcwi (MCW), SHRSP/Gcrc (RGD), SHR/NHsd (RGD), Buf/N (MCW), WKY/Gcrc (RGD), CDR, SS/JrHsdMcwi (MCW), SR/JrHsd (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 122478954 122478955 G A snv WKY/N (KNAW), WKY/NCrl (ICL), GK/Ox (ICL), WKY/NHsd (ICL)
1 122480032 122480033 G A snv M520/N (KNAW), F344/NCrl (ICL), BBDP/WorN (ICL), GH/OmrMcwi (MCW), F344/NHsd (ICAHN), MNS/Gib (ICL), SBH/Ygl (ICL), SBN/Ygl (ICL), F344/NRrrc (KNAW)
1 122480065 122480066 G T snv FHL/EurMcwi (ICL), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), SR/JrHsd (ICL), SS/Jr (ICL), SS/JrHsdMcwi (ICL), WAG/Rij (ICL), WKY/Gcrc (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), LCR/2Mco (UMich), FHH/EurMcwi (ICL), LE/Stm (ICL), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), SHR/OlaIpcv (KNAW), WN/N (KNAW), LE/Stm (KNAW), BUF/N (KNAW), SS/JrHsdMcwi (MDC), SHRSP/Gcrc (MDC), SHR/OlaIpcv (ICL), FHH/EurMcwi (MDC)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:727872 AgrOrtholog
Ensembl Genes ENSRNOG00000014030 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000046923 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068230 UniProtKB/TrEMBL
  ENSRNOP00000068384 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068488 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000050832 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000076329 UniProtKB/TrEMBL
  ENSRNOT00000076511 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000077020 UniProtKB/TrEMBL
Gene3D-CATH 1.20.5.1160 UniProtKB/TrEMBL
InterPro IF_rod_dom UniProtKB/TrEMBL
  IF_rod_dom_coil1B UniProtKB/TrEMBL
  Intermediate_filament_CS UniProtKB/TrEMBL
  SYNM UniProtKB/TrEMBL
KEGG Report rno:308709 UniProtKB/TrEMBL
NCBI Gene 308709 ENTREZGENE
PANTHER PTHR47136 UniProtKB/TrEMBL
Pfam Filament UniProtKB/TrEMBL
PhenoGen Synm PhenoGen
PROSITE IF_ROD_2 UniProtKB/TrEMBL
  PS00226 UniProtKB/TrEMBL
SMART Filament UniProtKB/TrEMBL
UniGene Rn.46362 ENTREZGENE
UniProt A0A096MJR2_RAT UniProtKB/TrEMBL
  A0A096MK54 ENTREZGENE, UniProtKB/TrEMBL
  A0A096MKE8_RAT UniProtKB/TrEMBL
  G3V9G5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-02 Synm  synemin  Synm  synemin, intermediate filament protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-10-16 Synm  synemin, intermediate filament protein  Dmn  desmuslin  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Dmn  desmuslin  LOC308709    Symbol updated 1299863 APPROVED

 



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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.