Slitrk1 (SLIT and NTRK-like family, member 1) - Rat Genome Database

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Gene: Slitrk1 (SLIT and NTRK-like family, member 1) Rattus norvegicus
Analyze
Symbol: Slitrk1
Name: SLIT and NTRK-like family, member 1
RGD ID: 1308858
Description: Involved in regulation of synapse organization. Is active in GABA-ergic synapse; glutamatergic synapse; and postsynaptic density membrane. Human ortholog(s) of this gene implicated in Gilles de la Tourette syndrome and trichotillomania. Orthologous to human SLITRK1 (SLIT and NTRK like family member 1); INTERACTS WITH 17alpha-ethynylestradiol; alpha-Zearalanol; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC306147; SLIT and NTRK-like protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81592,137,703 - 92,141,741 (-)NCBIGRCr8
mRatBN7.21585,723,252 - 85,727,290 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1585,724,475 - 85,727,509 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1589,666,140 - 89,670,177 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01590,783,409 - 90,787,447 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01587,714,550 - 87,718,588 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01593,303,382 - 93,307,420 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1593,303,382 - 93,307,420 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01596,793,133 - 96,797,171 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41593,205,850 - 93,209,888 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11593,220,490 - 93,225,771 (-)NCBI
Celera1584,748,071 - 84,752,109 (-)NCBICelera
Cytogenetic Map15q23NCBI
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

Cellular Component
GABA-ergic synapse  (IBA,IDA,IMP,ISO)
glutamatergic synapse  (IBA,IDA,IMP,ISO)
postsynaptic density membrane  (IBA,IDA,IEP,ISO)
postsynaptic membrane  (IDA)
synapse  (ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Slitrk1 is localized to excitatory synapses and promotes their development. Beaubien F, etal., Sci Rep. 2016 Jun 7;6:27343. doi: 10.1038/srep27343.
2. 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.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. A Modular Organization of LRR Protein-Mediated Synaptic Adhesion Defines Synapse Identity. Schroeder A, etal., Neuron. 2018 Jul 25;99(2):329-344.e7. doi: 10.1016/j.neuron.2018.06.026. Epub 2018 Jul 5.
8. Slitrks control excitatory and inhibitory synapse formation with LAR receptor protein tyrosine phosphatases. Yim YS, etal., Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):4057-62. doi: 10.1073/pnas.1209881110. Epub 2013 Jan 23.
Additional References at PubMed
PMID:14550773   PMID:18794888   PMID:23990902   PMID:24613359  


Genomics

Comparative Map Data
Slitrk1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81592,137,703 - 92,141,741 (-)NCBIGRCr8
mRatBN7.21585,723,252 - 85,727,290 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1585,724,475 - 85,727,509 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1589,666,140 - 89,670,177 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01590,783,409 - 90,787,447 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01587,714,550 - 87,718,588 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01593,303,382 - 93,307,420 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1593,303,382 - 93,307,420 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01596,793,133 - 96,797,171 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41593,205,850 - 93,209,888 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11593,220,490 - 93,225,771 (-)NCBI
Celera1584,748,071 - 84,752,109 (-)NCBICelera
Cytogenetic Map15q23NCBI
SLITRK1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381383,877,205 - 83,882,474 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1383,877,205 - 83,882,474 (-)EnsemblGRCh38hg38GRCh38
GRCh371384,451,340 - 84,456,609 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361383,349,344 - 83,354,529 (-)NCBINCBI36Build 36hg18NCBI36
Build 341383,349,344 - 83,354,529NCBI
Celera1365,348,921 - 65,354,105 (-)NCBICelera
Cytogenetic Map13q31.1NCBI
HuRef1365,151,246 - 65,156,419 (-)NCBIHuRef
CHM1_11384,418,864 - 84,424,052 (-)NCBICHM1_1
T2T-CHM13v2.01383,110,000 - 83,115,269 (-)NCBIT2T-CHM13v2.0
Slitrk1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3914109,147,420 - 109,151,671 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl14109,146,232 - 109,151,590 (-)EnsemblGRCm39 Ensembl
GRCm3814108,909,988 - 108,914,239 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl14108,908,800 - 108,914,158 (-)EnsemblGRCm38mm10GRCm38
MGSCv3714109,309,205 - 109,313,456 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3614107,794,000 - 107,796,090 (-)NCBIMGSCv36mm8
Celera14107,460,480 - 107,464,780 (-)NCBICelera
Cytogenetic Map14E3NCBI
cM Map1456.78NCBI
Slitrk1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540424,437,299 - 24,439,389 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540424,436,394 - 24,439,749 (+)NCBIChiLan1.0ChiLan1.0
SLITRK1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21485,431,417 - 85,436,813 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11384,029,703 - 84,034,980 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01365,081,844 - 65,087,135 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11384,251,713 - 84,256,899 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1384,253,287 - 84,256,069 (-)Ensemblpanpan1.1panPan2
SLITRK1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12236,325,548 - 36,329,784 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2236,326,751 - 36,328,841 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2236,153,354 - 36,157,576 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02236,686,513 - 36,690,728 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2236,685,446 - 36,690,833 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12236,332,182 - 36,336,404 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02236,441,629 - 36,445,848 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02236,443,335 - 36,447,558 (-)NCBIUU_Cfam_GSD_1.0
Slitrk1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945123,124,522 - 123,128,770 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366961,449,687 - 1,451,777 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366961,447,644 - 1,452,612 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLITRK1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1154,950,676 - 54,955,949 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11154,950,669 - 54,955,768 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21160,164,538 - 60,169,641 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLITRK1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1362,912,035 - 62,917,774 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl362,914,244 - 62,916,331 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604619,250,084 - 19,255,988 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slitrk1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475116,636,183 - 16,638,273 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475116,635,950 - 16,638,771 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Slitrk1
13 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:209
Count of miRNA genes:127
Interacting mature miRNAs:167
Transcripts:ENSRNOT00000012195
Prediction methods:Miranda, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731177Uae26Urinary albumin excretion QTL 262.40.025urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1567588667101769107Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)154063126898288169Rat
1576315Schws6Schwannoma susceptibility QTL 60.0069nervous system integrity trait (VT:0010566)post-insult time of death (CMO:0002005)155380615298806152Rat
1549844Bss7Bone structure and strength QTL 76.4femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1575788062101769107Rat
61477Aia4Adjuvant induced arthritis QTL 43joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)155559608991365858Rat
2300326Plaw1Placental weight QTL 1150.005placenta mass (VT:0004257)placenta wet weight (CMO:0002088)1568327165100062518Rat
1300118Bp190Blood pressure QTL 1902.94arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)158226252098288169Rat
70182BpQTLcluster12Blood pressure QTL cluster 123.53arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)157369065795018120Rat
152025253Hrtrt24Heart rate QTL 243.82heart pumping trait (VT:2000009)152788577486257085Rat
70155Gcs1Gastric cancer susceptibility QTL13.8stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)1576306099101769107Rat
1581555Eae19Experimental allergic encephalomyelitis QTL 194.7nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)157630609990088744Rat
1300120Kidm7Kidney mass QTL 73.55kidney mass (VT:0002707)left kidney wet weight to body weight ratio (CMO:0001954)158226252098288169Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
631655Bp126Blood pressure QTL 1264arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1558156477101769107Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
631516Gluco31Glucose level QTL 317blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)155559608995018120Rat
1331724Bp223Blood pressure QTL 2233.53715arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)157369051895018228Rat
1641889Colcr6Colorectal carcinoma resistance QTL 62.90.0126intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)157369051899794247Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
2317055Aia10Adjuvant induced arthritis QTL 103.41joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1575788062101769107Rat

Markers in Region
RH137671  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21585,724,014 - 85,724,159 (+)MAPPERmRatBN7.2
Rnor_6.01593,304,145 - 93,304,289NCBIRnor6.0
Rnor_5.01596,793,896 - 96,794,040UniSTSRnor5.0
RGSC_v3.41593,206,613 - 93,206,757UniSTSRGSC3.4
Celera1584,748,834 - 84,748,978UniSTS
Cytogenetic Map15q23UniSTS
D13S865E  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21585,723,836 - 85,724,043 (+)MAPPERmRatBN7.2
Rnor_6.01593,303,967 - 93,304,173NCBIRnor6.0
Rnor_5.01596,793,718 - 96,793,924UniSTSRnor5.0
RGSC_v3.41593,206,435 - 93,206,641UniSTSRGSC3.4
Celera1584,748,656 - 84,748,862UniSTS
Cytogenetic Map15q23UniSTS


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
9 8 37 112 53 46 24 20 24 5 160 77 93 42 43 22

Sequence


Ensembl Acc Id: ENSRNOT00000012195   ⟹   ENSRNOP00000012195
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1585,724,475 - 85,727,509 (-)Ensembl
Rnor_6.0 Ensembl1593,303,382 - 93,307,420 (-)Ensembl
RefSeq Acc Id: NM_001107283   ⟹   NP_001100753
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81592,137,703 - 92,141,741 (-)NCBI
mRatBN7.21585,723,252 - 85,727,290 (-)NCBI
Rnor_6.01593,303,382 - 93,307,420 (-)NCBI
Rnor_5.01596,793,133 - 96,797,171 (-)NCBI
RGSC_v3.41593,205,850 - 93,209,888 (-)RGD
Celera1584,748,071 - 84,752,109 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001100753 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM02494 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000012195.5
RefSeq Acc Id: NP_001100753   ⟸   NM_001107283
- Peptide Label: precursor
- UniProtKB: D3Z8D8 (UniProtKB/TrEMBL),   A6HUD1 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000012195   ⟸   ENSRNOT00000012195
Protein Domains
LRRCT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3Z8D8-F1-model_v2 AlphaFold D3Z8D8 1-696 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:1308858 AgrOrtholog
BioCyc Gene G2FUF-12583 BioCyc
Ensembl Genes ENSRNOG00000009209 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012195.6 UniProtKB/TrEMBL
Gene3D-CATH 3.80.10.10 UniProtKB/TrEMBL
InterPro Cys-rich_flank_reg_C UniProtKB/TrEMBL
  L_dom-like UniProtKB/TrEMBL
  Leu-rich_rpt UniProtKB/TrEMBL
  Leu-rich_rpt_typical-subtyp UniProtKB/TrEMBL
  Slitrk UniProtKB/TrEMBL
KEGG Report rno:306147 UniProtKB/TrEMBL
NCBI Gene 306147 ENTREZGENE
PANTHER PTHR45773 UniProtKB/TrEMBL
  SLIT AND NTRK-LIKE PROTEIN 1 UniProtKB/TrEMBL
Pfam LRR_8 UniProtKB/TrEMBL
PhenoGen Slitrk1 PhenoGen
PROSITE LRR UniProtKB/TrEMBL
RatGTEx ENSRNOG00000009209 RatGTEx
SMART LRR_TYP UniProtKB/TrEMBL
  LRRCT UniProtKB/TrEMBL
Superfamily-SCOP L domain-like UniProtKB/TrEMBL
UniProt A6HUD1 ENTREZGENE, UniProtKB/TrEMBL
  D3Z8D8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Slitrk1  SLIT and NTRK-like family, member 1   Slitrk1_predicted  SLIT and NTRK-like family, member 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Slitrk1_predicted  SLIT and NTRK-like family, member 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED