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 enable intermediate filament binding activity and vinculin binding activity. Predicted to be a structural constituent of cytoskeleton and structural constituent of muscle. Predicted to be involved in fast-twitch skeletal muscle fiber contraction. Located in intermediate filament. Orthologous to human SYNM (synemin); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3,7-dihydropurine-6-thione; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: desmuslin; Dmn; LOC308709; synemin, intermediate filament protein
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
mRatBN7.21121,333,712 - 121,363,652 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1121,333,720 - 121,363,652 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1129,331,682 - 129,361,456 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01136,501,760 - 136,531,534 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01129,302,717 - 129,332,493 (-)NCBIRnor_WKY
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,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)
acrolein  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
CGP 52608  (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)
inulin  (ISO)
ivermectin  (ISO)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
mercaptopurine  (EXP)
methylmercury chloride  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-methyl-4-phenylpyridinium  (EXP)
nickel atom  (ISO)
orphenadrine  (EXP)
ozone  (ISO)
paracetamol  (EXP,ISO)
perfluorooctane-1-sulfonic acid  (ISO)
permethrin  (EXP)
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)
temozolomide  (ISO)
tetrachloromethane  (EXP,ISO)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
triptonide  (ISO)
urethane  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Desmuslin, an intermediate filament protein that interacts with alpha -dystrobrevin and desmin. Mizuno Y, etal., Proc Natl Acad Sci U S A 2001 May 22;98(11):6156-61. Epub 2001 May 15.
4. NCBI rat LocusLink and RefSeq merged data October 15, 2003 NCBI rat LocusLink and RefSeq merged data October 15, 2003
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8552632   PMID:11737198   PMID:15265691   PMID:16777071   PMID:16817202   PMID:18028034   PMID:18342854   PMID:21139996   PMID:21982947   PMID:25567810   PMID:35769011  


Genomics

Comparative Map Data
Synm
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21121,333,712 - 121,363,652 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1121,333,720 - 121,363,652 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1129,331,682 - 129,361,456 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01136,501,760 - 136,531,534 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01129,302,717 - 129,332,493 (-)NCBIRnor_WKY
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh381599,105,080 - 99,141,767 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1599,098,217 - 99,135,593 (+)EnsemblGRCh38hg38GRCh38
GRCh371599,645,286 - 99,675,798 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361597,462,809 - 97,493,323 (+)NCBINCBI36Build 36hg18NCBI36
Build 341597,462,808 - 97,493,311NCBI
Celera1576,064,213 - 76,094,750 (+)NCBICelera
Cytogenetic Map15q26.3NCBI
HuRef1575,774,873 - 75,805,361 (+)NCBIHuRef
CHM1_11599,486,672 - 99,517,169 (+)NCBICHM1_1
T2T-CHM13v2.01596,869,529 - 96,908,995 (+)NCBIT2T-CHM13v2.0
Synm
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39767,379,909 - 67,409,490 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl767,379,908 - 67,409,490 (-)EnsemblGRCm39 Ensembl
GRCm38767,730,161 - 67,759,742 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl767,730,160 - 67,759,742 (-)EnsemblGRCm38mm10GRCm38
MGSCv37774,875,047 - 74,904,628 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36767,603,681 - 67,633,206 (-)NCBIMGSCv36mm8
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
NHGRI_mPanPan11592,349,350 - 92,380,230 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01577,790,447 - 77,821,317 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11596,974,351 - 97,004,956 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1596,975,160 - 97,002,412 (+)Ensemblpanpan1.1panPan2
SYNM
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1341,595,218 - 41,623,475 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl341,594,580 - 41,623,627 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha344,293,967 - 44,322,213 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0342,002,473 - 42,030,729 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1341,527,975 - 41,556,222 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0341,758,828 - 41,787,080 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0341,979,463 - 42,007,725 (-)NCBIUU_Cfam_GSD_1.0
Synm
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640141,945,901 - 141,971,595 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364834,365,508 - 4,389,180 (-)EnsemblSpeTri2.0
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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12917,693,148 - 17,723,847 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2917,693,121 - 17,724,387 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605928,842,961 - 28,873,687 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Synm
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247685,195,707 - 5,219,047 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247685,193,075 - 5,219,015 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Synm
159 total Variants
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.


QTLs in Region (mRatBN7.2)
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)130882023123479925Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132356093162846471Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)148963584144267916Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149393172159356837Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149393289199050459Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)157336763151090257Rat
1358192Ept13Estrogen-induced pituitary tumorigenesis QTL 133.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)177494165122494165Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)177857876122857876Rat
61344Bp29Blood pressure QTL 297.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)178350581123350581Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)178430536123430536Rat
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)178479925123479925Rat
4889494Scort2Serum corticosterone level QTL 24.2blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)180592172125592172Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)181591954219808434Rat
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)183547917128547917Rat
724529Cm16Cardiac mass QTL 162.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)187580395150700247Rat
724521Uae1Urinary albumin excretion QTL 13.80.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)190508614173018436Rat
1358902Bw47Body weight QTL 471.67body mass (VT:0001259)body weight (CMO:0000012)190508614180359386Rat
1302788Scl19Serum cholesterol QTL 194.60.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)190532338123479925Rat
1300153Bp171Blood pressure QTL 1713.37arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)190664883143200202Rat
2293142Bp314Blood pressure QTL 314arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192184926137184926Rat
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)192948896144267916Rat
1331793Bp200Blood pressure QTL 2003.71601arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)194494440172949803Rat
1331751Bp199Blood pressure QTL 1993.60022arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)194494440181830018Rat
1331749Hrtrt11Heart rate QTL 112.973heart pumping trait (VT:2000009)heart rate (CMO:0000002)194494440198211706Rat
70209Niddm23Non-insulin dependent diabetes mellitus QTL 232.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)194494440198324465Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)194642722214537671Rat
61346Rf2Renal disease susceptibility QTL 23.7urine protein amount (VT:0005160)urine protein level (CMO:0000591)199267916144267916Rat
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)199267916144267916Rat
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)1100357752183970443Rat
2317833Alcrsp19Alcohol response QTL 1912.40.001response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1100979852145979852Rat
1641897Alcrsp1Alcohol response QTL 1response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1100979852145979852Rat
2303591Gluco41Glucose level QTL 412blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1102168504147168504Rat
61370Mcs3Mammary carcinoma susceptibility QTL 32.15mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1102268556147268556Rat
1354623Rf46Renal function QTL 463.8blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)1102813953151162766Rat
1354591Cm36Cardiac mass QTL 364.1heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1102813953201278233Rat
1354615Cm32Cardiac mass QTL 325.2heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1102813953201278233Rat
1354606Bp246Blood pressure QTL 2463.6arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)1102813953218753816Rat
9590300Scort16Serum corticosterone level QTL 164.390.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1103111621148111621Rat
8694370Bw154Body weight QTL 1548.910.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)1103111621148111621Rat
631569Bp93Blood pressure QTL 930.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1106047847121834139Rat
631496Bp97Blood pressure QTL 973.08arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1106047847151047847Rat
1300158Bp173Blood pressure QTL 1733.48arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1115540693185145286Rat
7794788Mcs32Mammary carcinoma susceptibility QTL 322.61mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)1115540693238914717Rat
631199Cm23Cardiac mass QTL 234.60.0004heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1115585465172949803Rat
7421630Bp362Blood pressure QTL 3620.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1118608292241799120Rat
2313060Bss71Bone structure and strength QTL 712.60.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)1118944747163944747Rat
631205Bp196Blood pressure QTL 19640.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1118944897199050459Rat
1598850Bp297Blood pressure QTL 2972.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1121006655166006655Rat
1598866Bp287Blood pressure QTL 2875.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1121006655166006655Rat

Markers in Region
RH137882  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21121,333,925 - 121,334,093 (+)MAPPERmRatBN7.2
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
RH 3.4 Map11450.39UniSTS
Cytogenetic Map1q22UniSTS
RH143655  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21121,363,802 - 121,363,913 (+)MAPPERmRatBN7.2
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
RH 3.4 Map11447.29UniSTS
Cytogenetic Map1q22UniSTS


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
mRatBN7.2 Ensembl1121,333,720 - 121,363,652 (-)Ensembl
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
mRatBN7.2 Ensembl1121,333,720 - 121,363,560 (-)Ensembl
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
mRatBN7.21121,333,714 - 121,363,652 (-)NCBI
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
mRatBN7.21121,333,712 - 121,363,652 (-)NCBI
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

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V9G5-F1-model_v2 AlphaFold G3V9G5 1-1557 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:727872 AgrOrtholog
BioCyc Gene G2FUF-58978 BioCyc
Ensembl Genes ENSRNOG00000014030 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000046923 ENTREZGENE
  ENSRNOP00000046923.3 UniProtKB/TrEMBL
  ENSRNOP00000068384 ENTREZGENE
  ENSRNOP00000068384.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000050832 ENTREZGENE
  ENSRNOT00000050832.5 UniProtKB/TrEMBL
  ENSRNOT00000076511 ENTREZGENE
  ENSRNOT00000076511.3 UniProtKB/TrEMBL
Gene3D-CATH 1.20.5.170 UniProtKB/TrEMBL
  Vasodilator-stimulated phosphoprotein UniProtKB/TrEMBL
InterPro IF_rod_dom UniProtKB/TrEMBL
  Intermediate_filament_CS UniProtKB/TrEMBL
  SYNM UniProtKB/TrEMBL
KEGG Report rno:308709 UniProtKB/TrEMBL
NCBI Gene 308709 ENTREZGENE
PANTHER PTHR47136 UniProtKB/TrEMBL
  SYNEMIN UniProtKB/TrEMBL
Pfam Filament UniProtKB/TrEMBL
PhenoGen Synm PhenoGen
PROSITE IF_ROD_2 UniProtKB/TrEMBL
  PS00226 UniProtKB/TrEMBL
SMART Filament UniProtKB/TrEMBL
Superfamily-SCOP Intermediate filament protein, coiled coil region UniProtKB/TrEMBL
UniProt A0A096MK54 ENTREZGENE, 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