Slitrk3 (SLIT and NTRK-like family, member 3) - Rat Genome Database

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Gene: Slitrk3 (SLIT and NTRK-like family, member 3) Mus musculus
Analyze
Symbol: Slitrk3
Name: SLIT and NTRK-like family, member 3
RGD ID: 1558493
MGI Page MGI
Description: Involved in regulation of presynapse assembly. Acts upstream of or within axonogenesis and positive regulation of synapse assembly. Located in GABA-ergic synapse. Is integral component of postsynaptic membrane. Is expressed in alimentary system; bladder; central nervous system; neural retina; and peripheral nervous system. Orthologous to human SLITRK3 (SLIT and NTRK like family member 3); INTERACTS WITH pirinixic acid; 2,3,7,8-tetrachlorodibenzodioxine (ortholog); 2,3,7,8-Tetrachlorodibenzofuran (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: SLIT and NTRK-like protein 3; slit and trk like gene 3; ST; ST3
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39372,954,399 - 72,965,298 (-)NCBIGRCm39mm39
GRCm39 Ensembl372,954,598 - 72,965,136 (-)Ensembl
GRCm38373,047,066 - 73,057,953 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl373,047,265 - 73,057,803 (-)EnsemblGRCm38mm10GRCm38
MGSCv37372,852,047 - 72,860,865 (-)NCBIGRCm37mm9NCBIm37
MGSCv36373,134,051 - 73,142,869 (-)NCBImm8
Celera373,161,163 - 73,169,943 (-)NCBICelera
Cytogenetic Map3E3NCBI
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

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:14550773   PMID:14557068   PMID:16141072   PMID:16141073   PMID:16602821  
PMID:17145500   PMID:19924824   PMID:21267068   PMID:21677750   PMID:21862448   PMID:21873635   PMID:22286174   PMID:24613359   PMID:29031500   PMID:29107521  


Genomics

Comparative Map Data
Slitrk3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39372,954,399 - 72,965,298 (-)NCBIGRCm39mm39
GRCm39 Ensembl372,954,598 - 72,965,136 (-)Ensembl
GRCm38373,047,066 - 73,057,953 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl373,047,265 - 73,057,803 (-)EnsemblGRCm38mm10GRCm38
MGSCv37372,852,047 - 72,860,865 (-)NCBIGRCm37mm9NCBIm37
MGSCv36373,134,051 - 73,142,869 (-)NCBImm8
Celera373,161,163 - 73,169,943 (-)NCBICelera
Cytogenetic Map3E3NCBI
SLITRK3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3165,186,720 - 165,197,109 (-)EnsemblGRCh38hg38GRCh38
GRCh383165,186,720 - 165,197,109 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh373164,904,508 - 164,914,897 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363166,387,202 - 166,397,163 (-)NCBINCBI36hg18NCBI36
Build 343166,387,211 - 166,397,171NCBI
Celera3163,303,200 - 163,313,157 (-)NCBI
Cytogenetic Map3q26.1NCBI
HuRef3162,274,102 - 162,284,057 (-)NCBIHuRef
CHM1_13164,867,392 - 164,877,350 (-)NCBICHM1_1
Slitrk3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22157,680,067 - 157,697,404 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl2157,687,535 - 157,696,709 (-)Ensembl
Rnor_6.02170,446,582 - 170,461,513 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2170,452,702 - 170,460,754 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02189,791,839 - 189,803,411 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42163,703,843 - 163,711,895 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12163,653,847 - 163,658,733 (-)NCBI
Celera2151,947,474 - 151,955,526 (-)NCBICelera
Cytogenetic Map2q32NCBI
Slitrk3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544814,846,976 - 14,852,612 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495544814,846,976 - 14,852,612 (-)NCBIChiLan1.0ChiLan1.0
SLITRK3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13170,263,109 - 170,274,217 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3170,265,342 - 170,268,275 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03162,207,530 - 162,223,830 (-)NCBIMhudiblu_PPA_v0panPan3
SLITRK3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13430,447,606 - 30,456,444 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3430,447,659 - 30,450,598 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3439,508,350 - 39,517,571 (-)NCBI
ROS_Cfam_1.03430,508,728 - 30,517,972 (-)NCBI
UMICH_Zoey_3.13430,452,470 - 30,461,687 (-)NCBI
UNSW_CanFamBas_1.03430,403,986 - 30,413,213 (-)NCBI
UU_Cfam_GSD_1.03430,673,215 - 30,682,473 (-)NCBI
Slitrk3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560296,524,602 - 96,539,253 (-)NCBI
SpeTri2.0NW_0049367071,315,267 - 1,324,793 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLITRK3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13104,449,973 - 104,461,119 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113104,443,610 - 104,461,850 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213112,883,358 - 112,893,492 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLITRK3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11524,361,523 - 24,374,865 (+)NCBI
ChlSab1.1 Ensembl1524,367,287 - 24,370,226 (+)Ensembl
Vero_WHO_p1.0NW_02366606333,329,965 - 33,345,375 (+)NCBI
Slitrk3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473043,175,690 - 43,191,689 (-)NCBI


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
26884436Zlq3_mzygomatic length QTL 3, 10 week (mouse)33200000142700000Mouse
4142399Aec1_mautoimmune exocrinopathy 1 (mouse)Not determined7521114102782718Mouse
4141563Lgq3_mlate growth QTL 3 (mouse)Not determined1018416183277639Mouse
1357440Hrtpq1_mheart weight percentage QTL 1 (mouse)Not determined31018416183277639Mouse
1357857Lvrq5_mliver weight QTL 5 (mouse)Not determined31018416183277639Mouse
1357584Splq6_mspleen weight QTL 6 (mouse)Not determined31018416183277639Mouse
4141116Lgaq4_mlate growth adjusted QTL 4 (mouse)Not determined1018416183277639Mouse
4141255W10q3_mweight 10 weeks QTL 3 (mouse)Not determined1018416183277639Mouse
39128206Lwq18_mliver weight QTL 18 (mouse)31018416183277639Mouse
26884427Cvht4_mcranial vault height 4, 10 week (mouse)316000000109800000Mouse
13207570Tcq12_mtotal cholesterol QTL 12 (mouse)316450000130370000Mouse
26884422Cvht7_mcranial vault height 7, 16 week (mouse)328900000119100000Mouse
1302056Orgwq4_morgan weight QTL 4 (mouse)Not determined330013439147599053Mouse
1301705Sles3_msystemic lupus erythmatosus suppressor 3 (mouse)Not determined337120713143647422Mouse
1301585Cd4ts1_mCD4 T cell subset 1 (mouse)Not determined33979668173796810Mouse
10755516Amzn1_manatomical modifier of Zfp423 1 (mouse)33979668173796810Mouse
11039513Ltpr3a_mLeishmania tropica response 3a (mouse)33979668173796810Mouse
11041901Lmr11b_mleishmaniasis resistance 11b (mouse)33979668173796810Mouse
13208566Bmiq5_mbody mass index QTL 5 (mouse)341000000116000000Mouse
26884380Skwq1_mskull length QTL 1, 5 week (mouse)344000000101700000Mouse
4141079Ath23_matherosclerosis 23 (mouse)Not determined4945016083450160Mouse
1301824Susp_msuppressor of superoxide production (mouse)Not determined34958758483587697Mouse
1300895Hdl5_mHDL level 5 (mouse)Not determined34958758483587697Mouse
26884378Skwq6_mskull length QTL 6, 10 week (mouse)352000000102400000Mouse
26884382Bzwq1_mbi-zygomatic width QTL 1, 5 week (mouse)352300000137500000Mouse
1301917Tshp4_mtooth shape 4 (mouse)Not determined35271817686718412Mouse
1357585Manln3_mmandible length 3 (mouse)Not determined35271817686718412Mouse
1300593Skull4_mskull morphology 4 (mouse)Not determined35271817686718412Mouse
13464139Nhdlq17_mnon-HDL QTL 17 (mouse)35301585087015850Mouse
11039519Ltpr3_mLeishmania tropica response 3 (mouse)356796681100556821Mouse
12880419V125Dq4_mvitamin D active form serum level QTL 4 (mouse)35900000093000000Mouse
4141294Bmd24_mbone mineral density 24 (mouse)Not determined36183275495832934Mouse
1301971Cia5_mcollagen induced arthritis QTL 5 (mouse)Not determined366139351100139488Mouse
25314313Syncl1_msynaptonemal complex length 1 (mouse)368000000128600000Mouse
11251721Ewc3_methanol withdrawal and consumption 3 (mouse)369661247103661247Mouse
1301791Char4_mP. chabaudi malaria resistance QTL 4 (mouse)Not determined369718176100747974Mouse
1301422Sle11_msystematic lupus erythematosus susceptibility 11 (mouse)Not determined370301597104301735Mouse
1300982Lmr11_mleishmaniasis resistance 11 (mouse)Not determined372232660106232787Mouse
11049572Lmr11c_mleishmaniasis resistance 11c (mouse)372232660106232787Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:136
Count of miRNA genes:113
Interacting mature miRNAs:125
Transcripts:ENSMUST00000059407
Prediction methods: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.


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000059407   ⟹   ENSMUSP00000088561
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl372,955,458 - 72,965,136 (-)Ensembl
GRCm38.p6 Ensembl373,048,125 - 73,057,803 (-)Ensembl
RefSeq Acc Id: ENSMUST00000192477   ⟹   ENSMUSP00000141236
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl372,954,598 - 72,964,276 (-)Ensembl
GRCm38.p6 Ensembl373,047,265 - 73,056,943 (-)Ensembl
RefSeq Acc Id: NM_001357851   ⟹   NP_001344780
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39372,954,602 - 72,965,136 (-)NCBI
GRCm38373,047,269 - 73,057,803 (-)NCBI
Sequence:
RefSeq Acc Id: NM_198864   ⟹   NP_942564
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39372,954,602 - 72,964,399 (-)NCBI
GRCm38373,047,269 - 73,057,066 (-)NCBI
MGSCv37372,852,047 - 72,860,865 (-)RGD
Celera373,161,163 - 73,169,943 (-)RGD
cM Map3 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006501638   ⟹   XP_006501701
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39372,954,399 - 72,965,298 (-)NCBI
GRCm38373,047,066 - 73,057,881 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006501639   ⟹   XP_006501702
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39372,954,399 - 72,965,214 (-)NCBI
GRCm38373,047,066 - 73,057,881 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006501640   ⟹   XP_006501703
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39372,954,399 - 72,965,214 (-)NCBI
GRCm38373,047,066 - 73,057,881 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006501641   ⟹   XP_006501704
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39372,954,399 - 72,965,286 (-)NCBI
GRCm38373,047,066 - 73,057,953 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_942564   ⟸   NM_198864
- Peptide Label: precursor
- UniProtKB: Q810B9 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006501704   ⟸   XM_006501641
- Peptide Label: isoform X1
- UniProtKB: Q810B9 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006501703   ⟸   XM_006501640
- Peptide Label: isoform X1
- UniProtKB: Q810B9 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006501701   ⟸   XM_006501638
- Peptide Label: isoform X1
- UniProtKB: Q810B9 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006501702   ⟸   XM_006501639
- Peptide Label: isoform X1
- UniProtKB: Q810B9 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001344780   ⟸   NM_001357851
- Peptide Label: precursor
RefSeq Acc Id: ENSMUSP00000088561   ⟸   ENSMUST00000059407
RefSeq Acc Id: ENSMUSP00000141236   ⟸   ENSMUST00000192477
Protein Domains
LRRCT   LRRNT

Promoters
RGD ID:6880886
Promoter ID:EPDNEW_M3894
Type:single initiation site
Name:Slitrk3_2
Description:Mus musculus SLIT and NTRK-like family, member 3 , transcriptvariant 2, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M3895  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38373,057,038 - 73,057,098EPDNEW
RGD ID:6880888
Promoter ID:EPDNEW_M3895
Type:multiple initiation site
Name:Slitrk3_1
Description:Mus musculus SLIT and NTRK-like family, member 3 , transcriptvariant 2, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M3894  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38373,057,820 - 73,057,880EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2679447 AgrOrtholog
Ensembl Genes ENSMUSG00000048304 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSMUSP00000088561 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000141236 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000059407 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000192477 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.80.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Cys-rich_flank_reg_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  L_dom-like UniProtKB/Swiss-Prot
  Leu-rich_rpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Leu-rich_rpt_typical-subtyp UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR_dom_sf UniProtKB/TrEMBL
  Slitrk UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:386750 UniProtKB/Swiss-Prot
MGD MGI:2679447 ENTREZGENE
NCBI Gene 386750 ENTREZGENE
PANTHER PTHR45773 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam LRR_8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slitrk3 PhenoGen
SMART LRR_TYP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRRCT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt Q3UTG8_MOUSE UniProtKB/TrEMBL
  Q810B9 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q6NZM5 UniProtKB/Swiss-Prot