SYNDIG1 (synapse differentiation inducing 1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: SYNDIG1 (synapse differentiation inducing 1) Chlorocebus sabaeus
Analyze
Symbol: SYNDIG1
Name: synapse differentiation inducing 1
RGD ID: 18338795
Description: ENCODES a protein that exhibits glutamate receptor binding (ortholog); protein homodimerization activity (ortholog); INVOLVED IN intracellular protein transport (ortholog); ASSOCIATED WITH genetic disease (ortholog); FOUND IN cell body (ortholog); dendritic shaft (ortholog); early endosome membrane (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: synapse differentiation-inducing gene protein 1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: ChlSab1.1 - Green Monkey 1.1 Assembly
Position:
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1253,532,455 - 53,682,063 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl253,533,174 - 53,682,056 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605092,177,743 - 92,250,156 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
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

Molecular Function

References
Additional References at PubMed
PMID:30032202  


Genomics

Comparative Map Data
SYNDIG1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1253,532,455 - 53,682,063 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl253,533,174 - 53,682,056 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605092,177,743 - 92,250,156 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
SYNDIG1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382024,469,629 - 24,666,616 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2024,469,629 - 24,666,616 (+)EnsemblGRCh38hg38GRCh38
GRCh372024,450,265 - 24,647,252 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362024,397,835 - 24,595,167 (+)NCBINCBI36Build 36hg18NCBI36
Build 342024,397,834 - 24,595,167NCBI
Celera2024,524,151 - 24,721,487 (+)NCBICelera
Cytogenetic Map20p11.21NCBI
HuRef2024,405,607 - 24,604,629 (+)NCBIHuRef
CHM1_12024,450,308 - 24,648,495 (+)NCBICHM1_1
T2T-CHM13v2.02024,531,610 - 24,729,659 (+)NCBIT2T-CHM13v2.0
Syndig1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392149,672,703 - 149,846,312 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2149,671,131 - 149,846,312 (+)EnsemblGRCm39 Ensembl
GRCm382149,830,783 - 150,004,392 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2149,829,211 - 150,004,392 (+)EnsemblGRCm38mm10GRCm38
MGSCv372149,656,519 - 149,830,128 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362149,522,238 - 149,695,833 (+)NCBIMGSCv36mm8
Celera2151,074,984 - 151,248,632 (+)NCBICelera
Cytogenetic Map2G3NCBI
cM Map273.8NCBI
Syndig1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83158,491,474 - 158,695,174 (+)NCBIGRCr8
mRatBN7.23138,030,995 - 138,234,646 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3138,031,769 - 138,198,122 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3141,965,844 - 142,132,031 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03150,549,574 - 150,715,761 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03148,264,722 - 148,431,040 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03145,031,427 - 145,199,273 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3145,032,200 - 145,199,356 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03151,405,855 - 151,571,801 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43139,434,170 - 139,834,916 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13139,339,742 - 139,740,488 (+)NCBI
Celera3136,716,149 - 136,879,658 (+)NCBICelera
Cytogenetic Map3q41NCBI
Syndig1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541530,909,014 - 31,005,533 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541530,909,654 - 31,005,421 (+)NCBIChiLan1.0ChiLan1.0
SYNDIG1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22125,333,573 - 25,559,619 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12025,330,408 - 25,563,465 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02024,402,471 - 24,629,365 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12024,751,062 - 24,947,280 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2024,825,380 - 24,947,370 (+)Ensemblpanpan1.1panPan2
SYNDIG1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.123759,787 - 865,659 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl23685,782 - 865,359 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha23707,338 - 896,758 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.023919,502 - 1,109,045 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl23918,789 - 1,108,951 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.123819,974 - 925,587 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.023859,317 - 1,048,759 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.023848,398 - 1,037,785 (+)NCBIUU_Cfam_GSD_1.0
Syndig1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640147,745,538 - 147,938,240 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366201,165,709 - 1,359,179 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366201,165,312 - 1,359,127 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYNDIG1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1730,638,039 - 30,709,382 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11730,621,622 - 30,709,387 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21734,684,454 - 34,720,447 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Syndig1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624939560,106 - 661,570 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624939560,192 - 698,100 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


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

endocrine system hemolymphoid system nervous system
High
Medium 29
Low 31 16 31
Below cutoff 5 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSCSAT00000009077   ⟹   ENSCSAP00000007209
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1 Ensembl253,533,174 - 53,682,056 (+)Ensembl
RefSeq Acc Id: XM_037982924   ⟹   XP_037838852
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366605092,177,743 - 92,250,156 (-)NCBI
RefSeq Acc Id: XM_037982925   ⟹   XP_037838853
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366605092,177,743 - 92,249,704 (-)NCBI
RefSeq Acc Id: XM_037982926   ⟹   XP_037838854
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366605092,177,743 - 92,249,580 (-)NCBI
RefSeq Acc Id: XM_037982927   ⟹   XP_037838855
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366605092,177,743 - 92,232,176 (-)NCBI
RefSeq Acc Id: XM_037982928   ⟹   XP_037838856
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366605092,177,743 - 92,249,580 (-)NCBI
Protein Sequences
Protein RefSeqs XP_037838852 (Get FASTA)   NCBI Sequence Viewer  
  XP_037838853 (Get FASTA)   NCBI Sequence Viewer  
  XP_037838854 (Get FASTA)   NCBI Sequence Viewer  
  XP_037838855 (Get FASTA)   NCBI Sequence Viewer  
  XP_037838856 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCSAP00000007209.1
Reference Protein Sequences
RefSeq Acc Id: ENSCSAP00000007209   ⟸   ENSCSAT00000009077
RefSeq Acc Id: XP_037838852   ⟸   XM_037982924
RefSeq Acc Id: XP_037838853   ⟸   XM_037982925
RefSeq Acc Id: XP_037838854   ⟸   XM_037982926
RefSeq Acc Id: XP_037838856   ⟸   XM_037982928
RefSeq Acc Id: XP_037838855   ⟸   XM_037982927


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCSAG00000010985 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCSAT00000009077.1 UniProtKB/TrEMBL
InterPro CD225/Dispanin_fam UniProtKB/TrEMBL
KEGG Report csab:103215569 UniProtKB/TrEMBL
NCBI Gene SYNDIG1 ENTREZGENE
PANTHER SYNAPSE DIFFERENTIATION-INDUCING GENE PROTEIN 1 UniProtKB/TrEMBL
  UPF0338 PROTEIN UniProtKB/TrEMBL
Pfam CD225 UniProtKB/TrEMBL
UniProt A0A0D9RF20_CHLSB UniProtKB/TrEMBL