Slitrk5 (SLIT and NTRK-like family, member 5) - Rat Genome Database

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Gene: Slitrk5 (SLIT and NTRK-like family, member 5) Rattus norvegicus
Analyze
Symbol: Slitrk5
Name: SLIT and NTRK-like family, member 5
RGD ID: 1310957
Description: Predicted to be involved in axonogenesis and positive regulation of synapse assembly. Predicted to act upstream of or within several processes, including adult behavior; grooming behavior; and nervous system development. Predicted to be located in membrane and synapse. Predicted to be part of receptor complex. Orthologous to human SLITRK5 (SLIT and NTRK like family member 5); INTERACTS WITH 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine; 3,3',4,4',5-pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC306152; SLIT and NTRK-like protein 5
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
GRCr81595,261,397 - 95,270,465 (+)NCBIGRCr8
mRatBN7.21588,848,123 - 88,858,809 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1588,847,535 - 88,856,836 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1592,796,049 - 92,800,870 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01593,928,944 - 93,933,765 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01590,858,691 - 90,863,512 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01596,817,907 - 96,826,760 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1596,821,832 - 96,826,653 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.015100,296,097 - 100,304,915 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41596,407,553 - 96,412,374 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11596,419,582 - 96,427,541 (+)NCBI
Celera1587,847,358 - 87,852,179 (+)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

Molecular Function

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:14550773   PMID:20418887   PMID:23382219   PMID:24613359   PMID:36811190  


Genomics

Comparative Map Data
Slitrk5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81595,261,397 - 95,270,465 (+)NCBIGRCr8
mRatBN7.21588,848,123 - 88,858,809 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1588,847,535 - 88,856,836 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1592,796,049 - 92,800,870 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01593,928,944 - 93,933,765 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01590,858,691 - 90,863,512 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01596,817,907 - 96,826,760 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1596,821,832 - 96,826,653 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.015100,296,097 - 100,304,915 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41596,407,553 - 96,412,374 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11596,419,582 - 96,427,541 (+)NCBI
Celera1587,847,358 - 87,852,179 (+)NCBICelera
Cytogenetic Map15q23NCBI
SLITRK5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381387,671,371 - 87,679,616 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1387,671,371 - 87,696,272 (+)EnsemblGRCh38hg38GRCh38
GRCh371388,323,626 - 88,331,871 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361387,122,871 - 87,129,872 (+)NCBINCBI36Build 36hg18NCBI36
Build 341387,122,870 - 87,129,869NCBI
Celera1369,166,179 - 69,173,176 (+)NCBICelera
Cytogenetic Map13q31.2NCBI
HuRef1368,910,931 - 68,917,930 (+)NCBIHuRef
CHM1_11388,293,198 - 88,300,203 (+)NCBICHM1_1
T2T-CHM13v2.01386,874,975 - 86,899,840 (+)NCBIT2T-CHM13v2.0
Slitrk5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3914111,912,547 - 111,920,576 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl14111,912,529 - 111,920,573 (+)EnsemblGRCm39 Ensembl
GRCm3814111,675,115 - 111,683,144 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl14111,675,097 - 111,683,141 (+)EnsemblGRCm38mm10GRCm38
MGSCv3714112,074,337 - 112,082,357 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3614110,556,952 - 110,564,972 (+)NCBIMGSCv36mm8
Celera14110,285,183 - 110,293,077 (+)NCBICelera
Cytogenetic Map14E4NCBI
cM Map1457.86NCBI
Slitrk5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540421,342,379 - 21,350,464 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540421,342,379 - 21,350,803 (-)NCBIChiLan1.0ChiLan1.0
SLITRK5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21489,167,647 - 89,175,189 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11387,763,651 - 87,771,201 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01368,810,639 - 68,831,189 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11387,979,061 - 87,985,133 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1387,980,905 - 87,983,781 (+)Ensemblpanpan1.1panPan2
SLITRK5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12239,381,201 - 39,390,728 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2239,384,666 - 39,387,542 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2239,212,232 - 39,221,692 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02239,757,760 - 39,767,235 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2239,757,875 - 39,766,340 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12239,427,942 - 39,437,403 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02239,508,055 - 39,517,498 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02239,505,957 - 39,515,412 (+)NCBIUU_Cfam_GSD_1.0
Slitrk5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945175,245,525 - 175,253,697 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647220,698,463 - 20,705,408 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647220,698,334 - 20,706,161 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLITRK5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1157,792,665 - 57,800,846 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11157,792,576 - 57,800,852 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21163,658,233 - 63,669,168 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SLITRK5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1366,566,718 - 66,574,096 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl366,569,866 - 66,572,742 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604622,928,682 - 22,936,945 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slitrk5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247795,382,466 - 5,390,079 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247795,382,712 - 5,390,490 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Slitrk5
24 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:652
Count of miRNA genes:277
Interacting mature miRNAs:352
Transcripts:ENSRNOT00000012785
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
1581519Cm59Cardiac mass QTL 592.80.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)158885347095840528Rat

Markers in Region
BF405158  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21588,855,935 - 88,856,059 (+)MAPPERmRatBN7.2
Rnor_6.01596,826,364 - 96,826,487NCBIRnor6.0
Rnor_5.015100,304,519 - 100,304,642UniSTSRnor5.0
RGSC_v3.41596,412,085 - 96,412,208UniSTSRGSC3.4
Celera1587,851,890 - 87,852,013UniSTS
RH 3.4 Map15619.09UniSTS
Cytogenetic Map15q23UniSTS


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 2 70
Low 24 8 8 8 1 1 4 12 23 1
Below cutoff 3 10 20 15 7 15 6 7 6 12 5 6

Sequence


RefSeq Acc Id: ENSRNOT00000012785   ⟹   ENSRNOP00000066274
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1588,847,535 - 88,856,836 (+)Ensembl
Rnor_6.0 Ensembl1596,821,832 - 96,826,653 (+)Ensembl
RefSeq Acc Id: NM_001107284   ⟹   NP_001100754
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81595,265,644 - 95,270,465 (+)NCBI
mRatBN7.21588,851,404 - 88,856,225 (+)NCBI
Rnor_6.01596,821,832 - 96,826,653 (+)NCBI
Rnor_5.015100,296,097 - 100,304,915 (+)NCBI
RGSC_v3.41596,407,553 - 96,412,374 (+)RGD
Celera1587,847,358 - 87,852,179 (+)RGD
Sequence:
RefSeq Acc Id: XM_006252445   ⟹   XP_006252507
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81595,262,449 - 95,269,858 (+)NCBI
mRatBN7.21588,848,123 - 88,858,809 (+)NCBI
Rnor_6.01596,817,908 - 96,826,760 (+)NCBI
Rnor_5.015100,296,097 - 100,304,915 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006252446   ⟹   XP_006252508
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81595,262,985 - 95,269,858 (+)NCBI
mRatBN7.21588,848,745 - 88,858,809 (+)NCBI
Rnor_6.01596,819,179 - 96,826,760 (+)NCBI
Rnor_5.015100,296,097 - 100,304,915 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006252447   ⟹   XP_006252509
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81595,263,802 - 95,269,858 (+)NCBI
mRatBN7.21588,849,562 - 88,858,809 (+)NCBI
Rnor_6.01596,819,644 - 96,826,760 (+)NCBI
Rnor_5.015100,296,097 - 100,304,915 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063274343   ⟹   XP_063130413
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81595,261,397 - 95,269,858 (+)NCBI
RefSeq Acc Id: NP_001100754   ⟸   NM_001107284
- UniProtKB: M0R9U3 (UniProtKB/TrEMBL),   A6HUD7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252507   ⟸   XM_006252445
- Peptide Label: isoform X2
- UniProtKB: M0R9U3 (UniProtKB/TrEMBL),   A6HUD7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252508   ⟸   XM_006252446
- Peptide Label: isoform X2
- UniProtKB: M0R9U3 (UniProtKB/TrEMBL),   A6HUD7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252509   ⟸   XM_006252447
- Peptide Label: isoform X2
- UniProtKB: M0R9U3 (UniProtKB/TrEMBL),   A6HUD7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000066274   ⟸   ENSRNOT00000012785
RefSeq Acc Id: XP_063130413   ⟸   XM_063274343
- Peptide Label: isoform X1
Protein Domains
LRRCT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R9U3-F1-model_v2 AlphaFold M0R9U3 1-958 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:1310957 AgrOrtholog
BioCyc Gene G2FUF-12559 BioCyc
Ensembl Genes ENSRNOG00000009649 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012785.6 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:306152 UniProtKB/TrEMBL
NCBI Gene 306152 ENTREZGENE
PANTHER PTHR45773 UniProtKB/TrEMBL
  SLIT AND NTRK-LIKE PROTEIN 5 UniProtKB/TrEMBL
Pfam LRR_8 UniProtKB/TrEMBL
PhenoGen Slitrk5 PhenoGen
PROSITE LRR UniProtKB/TrEMBL
RatGTEx ENSRNOG00000009649 RatGTEx
SMART LRR_TYP UniProtKB/TrEMBL
  LRRCT UniProtKB/TrEMBL
Superfamily-SCOP L domain-like UniProtKB/TrEMBL
UniProt A6HUD7 ENTREZGENE, UniProtKB/TrEMBL
  M0R9U3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Slitrk5  SLIT and NTRK-like family, member 5   Slitrk5_predicted  SLIT and NTRK-like family, member 5 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Slitrk5_predicted  SLIT and NTRK-like family, member 5 (predicted)      Symbol and Name status set to approved 70820 APPROVED