Synm (synemin) - Rat Genome Database

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Gene: Synm (synemin) Ictidomys tridecemlineatus
Analyze
Symbol: Synm
Name: synemin
RGD ID: 12735208
Description: ENCODES a protein that exhibits intermediate filament binding (inferred); structural constituent of cytoskeleton (inferred); structural constituent of muscle (inferred); INVOLVED IN fast-twitch skeletal muscle fiber contraction (ortholog); ASSOCIATED WITH chromosome 15q26-qter deletion syndrome (ortholog); genetic disease (ortholog); FOUND IN intermediate filament (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: synemin, transcript variant X1; synemin, transcript variant X2
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: SpeTri2.0 - Squirrel SpeTri2.0 Assembly
Position:
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 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364834,362,891 - 4,388,558 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:30032202  


Genomics

Comparative Map Data
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 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364834,362,891 - 4,388,558 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
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 (+)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
cM Map737.12NCBI
Synm
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81130,743,891 - 130,774,254 (-)NCBIGRCr8
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_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01136,501,760 - 136,531,534 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01129,302,717 - 129,332,493 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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
(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_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 (+)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
(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


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSSTOT00000024579   ⟹   ENSSTOP00000021455
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_0049364834,365,508 - 4,389,180 (-)Ensembl
RefSeq Acc Id: ENSSTOT00000042070   ⟹   ENSSTOP00000030461
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_0049364834,365,508 - 4,389,180 (-)Ensembl
RefSeq Acc Id: XM_005320092   ⟹   XP_005320149
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_024408640141,945,901 - 141,971,595 (+)NCBI
SpeTri2.0NW_0049364834,362,891 - 4,388,558 (-)NCBI
Sequence:
RefSeq Acc Id: XM_005320093   ⟹   XP_005320150
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_024408640141,945,903 - 141,971,595 (+)NCBI
SpeTri2.0NW_0049364834,362,891 - 4,388,555 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_005320149 (Get FASTA)   NCBI Sequence Viewer  
  XP_005320150 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSTOP00000021455.1
  ENSSTOP00000030461.1
GenBank Protein KAG3262645 (Get FASTA)   NCBI Sequence Viewer  
  KAG3262646 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: XP_005320150   ⟸   XM_005320093
- Peptide Label: isoform X2
- UniProtKB: A0A287DAD6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005320149   ⟸   XM_005320092
- Peptide Label: isoform X1
- UniProtKB: I3NAQ8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSTOP00000021455   ⟸   ENSSTOT00000024579
RefSeq Acc Id: ENSSTOP00000030461   ⟸   ENSSTOT00000042070
Protein Domains
IF rod


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000022419 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000024579.2 UniProtKB/TrEMBL
  ENSSTOT00000042070.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.5.170 UniProtKB/TrEMBL
  Vasodilator-stimulated phosphoprotein UniProtKB/TrEMBL
InterPro IF_conserved UniProtKB/TrEMBL
  IF_rod_dom UniProtKB/TrEMBL
  SYNM UniProtKB/TrEMBL
NCBI Gene Synm ENTREZGENE
PANTHER PTHR47136 UniProtKB/TrEMBL
  SYNEMIN UniProtKB/TrEMBL
Pfam Filament UniProtKB/TrEMBL
PROSITE IF_ROD_1 UniProtKB/TrEMBL
  IF_ROD_2 UniProtKB/TrEMBL
SMART Filament UniProtKB/TrEMBL
Superfamily-SCOP Intermediate filament protein, coiled coil region UniProtKB/TrEMBL
UniProt A0A287DAD6 ENTREZGENE, UniProtKB/TrEMBL
  I3NAQ8 ENTREZGENE, UniProtKB/TrEMBL