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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81130,743,891 - 130,774,254 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1130,743,897 - 130,773,824 (-)EnsemblGRCr8
mRatBN7.21121,333,712 - 121,363,652 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1121,333,720 - 121,363,652 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1129,331,682 - 129,361,456 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01136,501,760 - 136,531,534 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01129,302,717 - 129,332,493 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01128,692,112 - 128,722,048 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1128,692,112 - 128,722,048 (-)Ensemblrn6Rnor6.0
Rnor_5.01129,757,882 - 129,788,008 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41122,474,205 - 122,504,176 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1113,533,990 - 113,563,954 (-)NCBICelera
RGSC_v3.11122,552,553 - 122,582,427 (-)NCBI
Cytogenetic Map1q22NCBI
JBrowse:




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)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (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)
7,12-dimethyltetraphene  (ISO)
acetamide  (EXP)
acrolein  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
alpha-Zearalanol  (EXP)
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 AF  (ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
corticosterone  (EXP)
cyclosporin A  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
diallyl trisulfide  (ISO)
dicrotophos  (ISO)
dioxygen  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
entinostat  (ISO)
ethanol  (ISO)
folic acid  (ISO)
FR900359  (ISO)
GW 4064  (ISO)
indometacin  (ISO)
inulin  (ISO)
ivermectin  (ISO)
L-methionine  (ISO)
lead(0)  (ISO)
mercaptopurine  (EXP)
methylmercury chloride  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-methyl-4-phenylpyridinium  (EXP)
nickel atom  (ISO)
okadaic acid  (ISO)
orphenadrine  (EXP)
ozone  (ISO)
paracetamol  (EXP,ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP)
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)
triphenyl phosphate  (ISO)
triptonide  (ISO)
urethane  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
costamere  (IBA,IEA,ISO)
intermediate filament  (IBA,IDA,IEA,ISO)
intermediate filament cytoskeleton  (IEA,ISO)
membrane  (IEA,ISO)
neurofilament cytoskeleton  (IBA,IEA,ISO)
sarcolemma  (IBA,IEA,ISO)

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:35352799   PMID:35769011  


Genomics

Comparative Map Data
Synm
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81130,743,891 - 130,774,254 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1130,743,897 - 130,773,824 (-)EnsemblGRCr8
mRatBN7.21121,333,712 - 121,363,652 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1121,333,720 - 121,363,652 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1129,331,682 - 129,361,456 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01136,501,760 - 136,531,534 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01129,302,717 - 129,332,493 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01128,692,112 - 128,722,048 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1128,692,112 - 128,722,048 (-)Ensemblrn6Rnor6.0
Rnor_5.01129,757,882 - 129,788,008 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41122,474,205 - 122,504,176 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1113,533,990 - 113,563,954 (-)NCBICelera
RGSC_v3.11122,552,553 - 122,582,427 (-)NCBI
Cytogenetic Map1q22NCBI
SYNM
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381599,105,080 - 99,141,767 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1599,098,217 - 99,135,593 (+)Ensemblhg38GRCh38
GRCh371599,645,286 - 99,675,798 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361597,462,809 - 97,493,323 (+)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm38767,730,161 - 67,759,742 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl767,730,160 - 67,759,742 (-)Ensemblmm10GRCm38
MGSCv37774,875,047 - 74,904,628 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36767,603,681 - 67,633,206 (-)NCBIMGSCv36mm8
Celera765,184,111 - 65,213,801 (-)NCBICelera
Cytogenetic Map7CNCBI
cM Map737.12NCBI
Synm
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541626,554,703 - 26,578,761 (+)Ensembl
ChiLan1.0NW_00495541626,554,074 - 26,579,804 (+)NCBIChiLan1.0ChiLan1.0
SYNM
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21688,652,427 - 88,683,309 (+)NCBINHGRI_mPanPan1-v2
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 (+)EnsemblpanPan2panpan1.1
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 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha344,293,967 - 44,322,213 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0342,002,473 - 42,030,729 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl341,968,310 - 42,030,628 (-)EnsemblROS_Cfam_1.0 Ensembl
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_1.0UU_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 Ensembl
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 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247685,193,075 - 5,219,015 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Synm
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v12132,578,005 - 132,607,259 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Synm
364 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)187889942132889942Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)139728272132889942Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)151940904168768703Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1101228864146228864Rat
1598866Bp287Blood pressure QTL 2875.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1130419227175419227Rat
631684Bp117Blood pressure QTL 1178.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1120082258165082258Rat
9590300Scort16Serum corticosterone level QTL 164.390.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1112521556157521556Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)166009857160501508Rat
1302788Scl19Serum cholesterol QTL 194.60.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)166400974132889942Rat
631569Bp93Blood pressure QTL 930.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1115183611131244255Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)151511344153680016Rat
1598850Bp297Blood pressure QTL 2972.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1130419227175419227Rat
152025232Bw192Body weight QTL 1923.93body mass (VT:0001259)1127329268206393015Rat
724521Uae1Urinary albumin excretion QTL 13.80.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)199645382182701046Rat
1358902Bw47Body weight QTL 471.67body mass (VT:0001259)body weight (CMO:0000012)199645382221502378Rat
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)1109493780193400781Rat
2317833Alcrsp19Alcohol response QTL 1912.40.001response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1110389869155389869Rat
1300153Bp171Blood pressure QTL 1713.37arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1124975316152612788Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1103779152223964440Rat
631205Bp196Blood pressure QTL 19640.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)198879955208479939Rat
1641897Alcrsp1Alcohol response QTL 1response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1110389869155389869Rat
1331749Hrtrt11Heart rate QTL 112.973heart pumping trait (VT:2000009)heart rate (CMO:0000002)192683681137683681Rat
737977Bp160Blood pressure QTL 1600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)197582336142582336Rat
1331751Bp199Blood pressure QTL 1993.60022arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1116099376191260518Rat
2293142Bp314Blood pressure QTL 314arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1101594089146594089Rat
724529Cm16Cardiac mass QTL 162.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)196717367160111531Rat
61370Mcs3Mammary carcinoma susceptibility QTL 32.15mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1111404407142582336Rat
737974Bp161Blood pressure QTL 1610.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1129182274174182274Rat
631496Bp97Blood pressure QTL 973.08arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1115183611176289080Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151941022208479811Rat
1331793Bp200Blood pressure QTL 2003.71601arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1102780511182384005Rat
1354591Cm36Cardiac mass QTL 364.1heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1111949780210707719Rat
1331800Scl25Serum cholesterol level QTL 253.013blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)187785026142582336Rat
7421630Bp362Blood pressure QTL 3620.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1128019551173019551Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134184556172281316Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134565911208798288Rat
631519Pia11Pristane induced arthritis QTL 115.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)193903998191260518Rat
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)1108680016153680016Rat
2313083Bmd74Bone mineral density QTL 7440.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)191302413136302413Rat
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)1102359314153680016Rat
1354615Cm32Cardiac mass QTL 325.2heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1111949780210707719Rat
1358192Ept13Estrogen-induced pituitary tumorigenesis QTL 133.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)186622262131622262Rat
8694370Bw154Body weight QTL 1548.910.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)1112521556157521556Rat
1354623Rf46Renal function QTL 463.8blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)1111949780160574007Rat
738022Anxrr13Anxiety related response QTL 134.60.00039locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of, or within a discrete space in an open field apparatus (CMO:0001514)192683681137683681Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)186993904131993904Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)187558587132558587Rat
61433Cia2Collagen induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1100345976145345976Rat
1354606Bp246Blood pressure QTL 2463.6arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)1111949780228180370Rat

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

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 160 91 90 59 57 59 6 321 157 11 139 81 92 31 14 14

Sequence


Ensembl Acc Id: ENSRNOT00000050832   ⟹   ENSRNOP00000046923
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1130,743,897 - 130,773,824 (-)Ensembl
mRatBN7.2 Ensembl1121,333,720 - 121,363,652 (-)Ensembl
Rnor_6.0 Ensembl1128,692,120 - 128,722,048 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000076329   ⟹   ENSRNOP00000068488
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1128,694,735 - 128,695,796 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000076511   ⟹   ENSRNOP00000068384
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1130,743,897 - 130,773,732 (-)Ensembl
mRatBN7.2 Ensembl1121,333,720 - 121,363,560 (-)Ensembl
Rnor_6.0 Ensembl1128,692,112 - 128,721,956 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000077020   ⟹   ENSRNOP00000068230
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
GRCr81130,743,891 - 130,773,824 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81130,746,112 - 130,774,254 (-)NCBI
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:
RefSeq Acc Id: NP_001128330   ⟸   NM_001134858
- UniProtKB: G3V9G5 (UniProtKB/TrEMBL),   A6JBT8 (UniProtKB/TrEMBL),   A6JBU1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229399   ⟸   XM_006229337
- Peptide Label: isoform X1
- UniProtKB: A0A096MK54 (UniProtKB/TrEMBL),   A6JBT7 (UniProtKB/TrEMBL),   Q810D0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000068230   ⟸   ENSRNOT00000077020
Ensembl Acc Id: ENSRNOP00000046923   ⟸   ENSRNOT00000050832
Ensembl Acc Id: ENSRNOP00000068488   ⟸   ENSRNOT00000076329
Ensembl 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 Transcript ENSRNOT00000050832 ENTREZGENE
  ENSRNOT00000050832.6 UniProtKB/TrEMBL
  ENSRNOT00000076511 ENTREZGENE
  ENSRNOT00000076511.4 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
RatGTEx ENSRNOG00000014030 RatGTEx
SMART Filament UniProtKB/TrEMBL
Superfamily-SCOP Intermediate filament protein, coiled coil region UniProtKB/TrEMBL
UniProt A0A096MK54 ENTREZGENE, UniProtKB/TrEMBL
  A6JBT7 ENTREZGENE, UniProtKB/TrEMBL
  A6JBT8 ENTREZGENE, UniProtKB/TrEMBL
  A6JBU1 ENTREZGENE, UniProtKB/TrEMBL
  G3V9G5 ENTREZGENE, UniProtKB/TrEMBL
  Q810D0 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