Slitrk6 (SLIT and NTRK-like family, member 6) - Rat Genome Database

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Gene: Slitrk6 (SLIT and NTRK-like family, member 6) Rattus norvegicus
Analyze
Symbol: Slitrk6
Name: SLIT and NTRK-like family, member 6
RGD ID: 1306550
Description: Predicted to be involved in axonogenesis and positive regulation of synapse assembly. Predicted to act upstream of or within several processes, including auditory behavior; linear vestibuloocular reflex; and nervous system development. Predicted to be located in cell periphery and cell surface. Predicted to be active in plasma membrane. Human ortholog(s) of this gene implicated in high myopia-sensorineural deafness syndrome. Orthologous to human SLITRK6 (SLIT and NTRK like family member 6); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; atrazine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC290467; SLIT and NTRK-like protein 6
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21587,563,506 - 87,570,125 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1587,563,322 - 87,570,393 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1591,506,334 - 91,512,973 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01592,639,255 - 92,645,886 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01589,555,945 - 89,562,571 (-)NCBIRnor_WKY
Rnor_6.01595,507,632 - 95,514,259 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1595,507,640 - 95,514,259 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01598,989,203 - 98,995,830 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41595,106,364 - 95,112,983 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11595,122,135 - 95,128,679 (-)NCBI
Celera1586,576,029 - 86,582,648 (-)NCBICelera
Cytogenetic Map15q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:14550773   PMID:19936227   PMID:21298075   PMID:23543054   PMID:24613359  


Genomics

Comparative Map Data
Slitrk6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21587,563,506 - 87,570,125 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1587,563,322 - 87,570,393 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1591,506,334 - 91,512,973 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01592,639,255 - 92,645,886 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01589,555,945 - 89,562,571 (-)NCBIRnor_WKY
Rnor_6.01595,507,632 - 95,514,259 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1595,507,640 - 95,514,259 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01598,989,203 - 98,995,830 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41595,106,364 - 95,112,983 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11595,122,135 - 95,128,679 (-)NCBI
Celera1586,576,029 - 86,582,648 (-)NCBICelera
Cytogenetic Map15q23NCBI
SLITRK6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381385,792,790 - 85,799,419 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1385,792,790 - 85,806,683 (-)EnsemblGRCh38hg38GRCh38
GRCh371386,366,925 - 86,373,554 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361385,264,923 - 85,271,484 (-)NCBINCBI36Build 36hg18NCBI36
Build 341385,264,922 - 85,271,484NCBI
Celera1367,280,318 - 67,286,879 (-)NCBICelera
Cytogenetic Map13q31.1NCBI
HuRef1367,078,179 - 67,084,734 (-)NCBIHuRef
CHM1_11386,335,513 - 86,342,073 (-)NCBICHM1_1
T2T-CHM13v2.01385,041,234 - 85,047,862 (-)NCBIT2T-CHM13v2.0
Slitrk6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3914110,984,770 - 110,992,640 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl14110,986,012 - 110,992,581 (-)EnsemblGRCm39 Ensembl
GRCm3814110,747,338 - 110,755,204 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl14110,748,580 - 110,755,149 (-)EnsemblGRCm38mm10GRCm38
MGSCv3714111,147,800 - 111,154,371 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3614109,630,422 - 109,636,908 (-)NCBIMGSCv36mm8
Celera14109,332,207 - 109,338,788 (-)NCBICelera
Cytogenetic Map14E3NCBI
Slitrk6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540422,737,974 - 22,745,046 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540422,738,080 - 22,744,601 (+)NCBIChiLan1.0ChiLan1.0
SLITRK6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11386,160,711 - 86,167,332 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1386,161,905 - 86,164,430 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01366,990,025 - 67,003,900 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SLITRK6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12237,911,533 - 37,918,273 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2237,912,612 - 37,925,177 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2237,737,693 - 37,745,442 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02238,283,620 - 38,291,371 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.12237,922,146 - 37,929,894 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02238,028,765 - 38,036,516 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02238,036,205 - 38,043,951 (-)NCBIUU_Cfam_GSD_1.0
Slitrk6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945121,376,350 - 121,383,016 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936866412,818 - 419,381 (+)EnsemblSpeTri2.0
SpeTri2.0NW_004936866412,719 - 419,381 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLITRK6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1156,508,767 - 56,522,197 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11156,508,713 - 56,522,270 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21162,016,419 - 62,023,681 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLITRK6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1364,808,716 - 64,822,519 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl364,809,920 - 64,812,442 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604621,173,421 - 21,180,352 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slitrk6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247797,030,395 - 7,036,108 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247797,030,017 - 7,036,581 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Slitrk6
25 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:559
Count of miRNA genes:275
Interacting mature miRNAs:347
Transcripts:ENSRNOT00000038433
Prediction methods:Microtar, 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
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
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
61477Aia4Adjuvant induced arthritis QTL 43joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)155559608991365858Rat
631516Gluco31Glucose level QTL 317blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)155559608995018120Rat
631655Bp126Blood pressure QTL 1264arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1558156477101769107Rat
731177Uae26Urinary albumin excretion QTL 262.40.025urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1567588667101769107Rat
2300326Plaw1Placental weight QTL 1150.005placenta mass (VT:0004257)placenta wet weight (CMO:0002088)1568327165100062518Rat
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
70182BpQTLcluster12Blood pressure QTL cluster 123.53arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)157369065795018120Rat
2317055Aia10Adjuvant induced arthritis QTL 103.41joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1575788062101769107Rat
1549844Bss7Bone structure and strength QTL 76.4femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1575788062101769107Rat
1581555Eae19Experimental allergic encephalomyelitis QTL 194.7nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)157630609990088744Rat
70155Gcs1Gastric cancer susceptibility QTL13.8stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)1576306099101769107Rat
1300118Bp190Blood pressure QTL 1902.94arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)158226252098288169Rat
1300120Kidm7Kidney mass QTL 73.55kidney mass (VT:0002707)left kidney wet weight to body weight ratio (CMO:0001954)158226252098288169Rat


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 4 4 7 4 3 5
Low 3 37 26 12 12 12 6 6 74 22 28 6 6
Below cutoff 6 20 18 18 2 4 11 4 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000038433   ⟹   ENSRNOP00000034471
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1587,563,322 - 87,570,393 (-)Ensembl
Rnor_6.0 Ensembl1595,507,640 - 95,514,259 (-)Ensembl
RefSeq Acc Id: NM_001106057   ⟹   NP_001099527
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21587,563,506 - 87,570,125 (-)NCBI
Rnor_6.01595,507,640 - 95,514,259 (-)NCBI
Rnor_5.01598,989,203 - 98,995,830 (-)NCBI
RGSC_v3.41595,106,364 - 95,112,983 (-)RGD
Celera1586,576,029 - 86,582,648 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001099527 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM02496 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001099527   ⟸   NM_001106057
- Peptide Label: precursor
- UniProtKB: D3ZP44 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000034471   ⟸   ENSRNOT00000038433
Protein Domains
LRRCT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZP44-F1-model_v2 AlphaFold D3ZP44 1-840 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:1306550 AgrOrtholog
BioCyc Gene G2FUF-12579 BioCyc
Ensembl Genes ENSRNOG00000022337 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000034471 ENTREZGENE
  ENSRNOP00000034471.4 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000038433 ENTREZGENE
  ENSRNOT00000038433.5 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:290467 UniProtKB/TrEMBL
NCBI Gene 290467 ENTREZGENE
PANTHER PTHR45773 UniProtKB/TrEMBL
Pfam LRR_8 UniProtKB/TrEMBL
PhenoGen Slitrk6 PhenoGen
PROSITE LRR UniProtKB/TrEMBL
SMART LRR_TYP UniProtKB/TrEMBL
  LRRCT UniProtKB/TrEMBL
UniProt D3ZP44 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Slitrk6  SLIT and NTRK-like family, member 6   Slitrk6_predicted  SLIT and NTRK-like family, member 6 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Slitrk6_predicted  SLIT and NTRK-like family, member 6 (predicted)      Symbol and Name status set to approved 70820 APPROVED