Syndig1l (synapse differentiation inducing 1-like) - Rat Genome Database

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Gene: Syndig1l (synapse differentiation inducing 1-like) Rattus norvegicus
Analyze
Symbol: Syndig1l
Name: synapse differentiation inducing 1-like
RGD ID: 1589004
Description: Predicted to be located in Golgi apparatus. Predicted to be active in membrane. Orthologous to human SYNDIG1L (synapse differentiation inducing 1 like); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; amitrole.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: capucin; hypothetical protein LOC685882; LOC685882; synapse differentiation-inducing gene protein 1-like; Tmem90a; transmembrane protein 90A
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
GRCr86110,053,713 - 110,076,058 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl6110,054,504 - 110,075,969 (-)EnsemblGRCr8
mRatBN7.26104,318,096 - 104,344,989 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl6104,323,424 - 104,344,891 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx6104,492,018 - 104,513,444 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.06104,791,108 - 104,812,538 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.06104,160,676 - 104,182,100 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.06108,392,837 - 108,415,187 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6108,393,628 - 108,415,093 (-)Ensemblrn6Rnor6.0
Rnor_5.06117,134,046 - 117,156,622 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.46108,719,898 - 108,741,367 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera6102,148,305 - 102,169,778 (-)NCBICelera
Cytogenetic Map6q31NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
Golgi apparatus  (IEA,ISO)
membrane  (IBA,IEA)

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16359841  


Genomics

Comparative Map Data
Syndig1l
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr86110,053,713 - 110,076,058 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl6110,054,504 - 110,075,969 (-)EnsemblGRCr8
mRatBN7.26104,318,096 - 104,344,989 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl6104,323,424 - 104,344,891 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx6104,492,018 - 104,513,444 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.06104,791,108 - 104,812,538 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.06104,160,676 - 104,182,100 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.06108,392,837 - 108,415,187 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6108,393,628 - 108,415,093 (-)Ensemblrn6Rnor6.0
Rnor_5.06117,134,046 - 117,156,622 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.46108,719,898 - 108,741,367 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera6102,148,305 - 102,169,778 (-)NCBICelera
Cytogenetic Map6q31NCBI
SYNDIG1L
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381474,405,899 - 74,480,143 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1474,405,894 - 74,426,210 (-)Ensemblhg38GRCh38
GRCh371474,872,602 - 74,892,913 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361473,942,349 - 73,962,558 (-)NCBIBuild 36Build 36hg18NCBI36
Celera1454,909,910 - 54,930,122 (-)NCBICelera
Cytogenetic Map14q24.3NCBI
HuRef1455,039,931 - 55,060,036 (-)NCBIHuRef
CHM1_11474,812,136 - 74,832,341 (-)NCBICHM1_1
T2T-CHM13v2.01468,613,779 - 68,683,890 (-)NCBIT2T-CHM13v2.0
Syndig1l
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391284,724,051 - 84,745,720 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1284,724,051 - 84,745,605 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381284,677,277 - 84,698,947 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1284,677,277 - 84,698,831 (-)Ensemblmm10GRCm38
MGSCv371286,018,228 - 86,039,757 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361285,567,026 - 85,588,555 (-)NCBIMGSCv36mm8
Celera1286,132,908 - 86,154,460 (-)NCBICelera
Cytogenetic Map12D1NCBI
cM Map1239.33NCBI
Syndig1l
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555231,091,744 - 1,095,652 (+)Ensembl
ChiLan1.0NW_0049555231,092,463 - 1,095,567 (+)NCBIChiLan1.0ChiLan1.0
SYNDIG1L
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21575,488,574 - 75,509,250 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11474,705,080 - 74,725,756 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01454,957,901 - 54,978,582 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11473,805,990 - 73,826,055 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1473,805,990 - 73,826,055 (-)EnsemblpanPan2panpan1.1
SYNDIG1L
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1847,570,289 - 47,583,571 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl847,570,275 - 47,573,836 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha847,254,518 - 47,272,820 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0847,797,441 - 47,815,702 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl847,797,427 - 47,800,988 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1847,466,524 - 47,484,678 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0847,487,616 - 47,505,866 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0847,874,989 - 47,893,149 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Syndig1l
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864028,447,926 - 28,470,920 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364883,599,572 - 3,601,356 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049364883,598,050 - 3,621,049 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYNDIG1L
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl797,658,301 - 97,679,795 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1797,658,299 - 97,679,796 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.27103,500,823 - 103,522,298 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SYNDIG1L
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12451,617,631 - 51,638,382 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2451,617,437 - 51,638,659 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605339,854,428 - 39,875,304 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Syndig1l
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473427,221,116 - 27,241,879 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462473427,221,110 - 27,242,657 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Syndig1l
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1798,784,625 - 98,806,869 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Syndig1l
108 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:232
Count of miRNA genes:146
Interacting mature miRNAs:168
Transcripts:ENSRNOT00000031650
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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
2293088Iddm28Insulin dependent diabetes mellitus QTL 285.21blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)668767270135411972Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)688019181136741135Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6106095977147156653Rat
61329Eae9Experimental allergic encephalomyelitis QTL 93.7body mass (VT:0001259)change in body weight (CMO:0002045)684490437129490437Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6101593607138161926Rat
1331725Bp212Blood pressure QTL 2123.52475arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)699437079125323237Rat
1331789Rf37Renal function QTL 373.224kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)686494122112380234Rat
1331722Thshl1Thyroid stimulating hormone level QTL 111.70.0001blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)699708426112483760Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)671278722116278722Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)693560258136550638Rat
10054138Gmadr3Adrenal mass QTL 33.680.00045adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)690871046135871046Rat
1641917Colcr5Colorectal carcinoma resistance QTL 53.180.0009intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)698944780143944780Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)6100704576136029228Rat
724524Uae2Urinary albumin excretion QTL 22.70.0005urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)679198463144254945Rat
737827Hcar11Hepatocarcinoma resistance QTL 114.4liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)646050607116278722Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (CMO:0000132)693778632138778632Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)620859430113082285Rat
2293837Kiddil1Kidney dilation QTL 13.7kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)686867923110125012Rat
2293842Kiddil3Kidney dilation QTL 34.3kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)686867923110125012Rat
10054123Srcrt6Stress Responsive Cort QTL 62.50.0043blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)690871046135871046Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)693560258136550638Rat
1576302Schws4Schwannoma susceptibility QTL 40.0078nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)678204640123204640Rat
1581550Pur8Proteinuria QTL 8urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)693560258136550638Rat
1300075Glom7Glomerulus QTL 75.60.0000002kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)676937178121937178Rat
12801471Schws9Schwannoma susceptibility QTL 9nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)6101593607146593607Rat


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
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
8 3 12 142 33 29 15 16 15 6 97 41 130 31 59 14 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000031650   ⟹   ENSRNOP00000030389
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl6110,054,504 - 110,075,969 (-)Ensembl
mRatBN7.2 Ensembl6104,323,424 - 104,344,891 (-)Ensembl
Rnor_6.0 Ensembl6108,393,628 - 108,415,093 (-)Ensembl
RefSeq Acc Id: NM_001109485   ⟹   NP_001102955
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr86110,054,504 - 110,075,969 (-)NCBI
mRatBN7.26104,323,424 - 104,344,891 (-)NCBI
Rnor_6.06108,393,628 - 108,415,093 (-)NCBI
Rnor_5.06117,134,046 - 117,156,622 (+)NCBI
RGSC_v3.46108,719,898 - 108,741,367 (-)RGD
Celera6102,148,305 - 102,169,778 (-)RGD
Sequence:
RefSeq Acc Id: XM_006240353   ⟹   XP_006240415
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr86110,053,713 - 110,076,058 (-)NCBI
mRatBN7.26104,318,096 - 104,344,989 (-)NCBI
Rnor_6.06108,392,837 - 108,415,187 (-)NCBI
Rnor_5.06117,134,046 - 117,156,622 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594357   ⟹   XP_017449846
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr86110,053,713 - 110,057,273 (-)NCBI
mRatBN7.26104,318,096 - 104,326,193 (-)NCBI
Rnor_6.06108,392,837 - 108,396,397 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001102955 (Get FASTA)   NCBI Sequence Viewer  
  XP_006240415 (Get FASTA)   NCBI Sequence Viewer  
  XP_017449846 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL81524 (Get FASTA)   NCBI Sequence Viewer  
  EDL81525 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000030389
  ENSRNOP00000030389.4
RefSeq Acc Id: NP_001102955   ⟸   NM_001109485
- UniProtKB: D4A4K5 (UniProtKB/TrEMBL),   A6JDY1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006240415   ⟸   XM_006240353
- Peptide Label: isoform X1
- UniProtKB: D4A4K5 (UniProtKB/TrEMBL),   A6JDY1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017449846   ⟸   XM_017594357
- Peptide Label: isoform X1
- UniProtKB: D4A4K5 (UniProtKB/TrEMBL),   A6JDY1 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000030389   ⟸   ENSRNOT00000031650

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A4K5-F1-model_v2 AlphaFold D4A4K5 1-237 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1589004 AgrOrtholog
BioCyc Gene G2FUF-36811 BioCyc
Ensembl Genes ENSRNOG00000027645 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000031650 ENTREZGENE
  ENSRNOT00000031650.6 UniProtKB/TrEMBL
InterPro Interferon-induced_TM_protein UniProtKB/TrEMBL
KEGG Report rno:685882 UniProtKB/TrEMBL
NCBI Gene 685882 ENTREZGENE
PANTHER SYNAPSE DIFFERENTIATION-INDUCING GENE PROTEIN 1-LIKE UniProtKB/TrEMBL
  UPF0338 PROTEIN UniProtKB/TrEMBL
Pfam CD225 UniProtKB/TrEMBL
PhenoGen Syndig1l PhenoGen
RatGTEx ENSRNOG00000027645 RatGTEx
UniProt A6JDY1 ENTREZGENE, UniProtKB/TrEMBL
  D4A4K5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-01 Syndig1l  synapse differentiation inducing 1-like  Tmem90a  transmembrane protein 90A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Tmem90a  transmembrane protein 90A  LOC685882  hypothetical protein LOC685882  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC685882  hypothetical protein LOC685882  LOC681439  hypothetical protein LOC681439  Data merged from RGD:1595387 1643240 APPROVED
2006-11-20 LOC681439  hypothetical protein LOC681439      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC685882  hypothetical protein LOC685882      Symbol and Name status set to provisional 70820 PROVISIONAL