Slitrk4 (SLIT and NTRK-like family, member 4) - Rat Genome Database

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Gene: Slitrk4 (SLIT and NTRK-like family, member 4) Rattus norvegicus
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Symbol: Slitrk4
Name: SLIT and NTRK-like family, member 4
RGD ID: 1588563
Description: Predicted to be involved in regulation of synapse organization. Predicted to act upstream of or within axonogenesis and positive regulation of synapse assembly. Predicted to be located in membrane. Predicted to be active in glutamatergic synapse. Orthologous to human SLITRK4 (SLIT and NTRK like family member 4); INTERACTS WITH 17alpha-ethynylestradiol; bisphenol A; Cuprizon.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: hypothetical protein LOC302473; LOC302473; similar to SLIT and NTRK-like family, member 4; SLIT and NTRK-like protein 4; uncharacterized protein LOC302473
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
GRCr8X147,728,163 - 147,755,086 (-)NCBIGRCr8
mRatBN7.2X142,706,495 - 142,718,968 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX142,706,338 - 142,718,575 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX144,906,746 - 144,913,095 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X148,431,708 - 148,438,057 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X145,981,431 - 145,987,780 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X147,582,195 - 147,589,529 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X147,598,020 - 147,605,354 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X150,053,376 - 150,059,675 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX138,589,008 - 138,595,357 (-)NCBICelera
Cytogenetic MapXq36NCBI
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

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. GOA pipeline RGD automated data pipeline
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:14550773   PMID:23345436   PMID:24613359  


Genomics

Comparative Map Data
Slitrk4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X147,728,163 - 147,755,086 (-)NCBIGRCr8
mRatBN7.2X142,706,495 - 142,718,968 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX142,706,338 - 142,718,575 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX144,906,746 - 144,913,095 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X148,431,708 - 148,438,057 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X145,981,431 - 145,987,780 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X147,582,195 - 147,589,529 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X147,598,020 - 147,605,354 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X150,053,376 - 150,059,675 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX138,589,008 - 138,595,357 (-)NCBICelera
Cytogenetic MapXq36NCBI
SLITRK4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X143,622,790 - 143,636,101 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX143,622,790 - 143,636,101 (-)EnsemblGRCh38hg38GRCh38
GRCh37X142,710,595 - 142,723,920 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X142,543,584 - 142,550,685 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X142,441,463 - 142,448,539NCBI
CeleraX142,997,864 - 143,011,197 (-)NCBICelera
Cytogenetic MapXq27.3NCBI
HuRefX131,814,638 - 131,827,586 (-)NCBIHuRef
CHM1_1X142,622,489 - 142,635,821 (-)NCBICHM1_1
T2T-CHM13v2.0X141,932,069 - 141,945,367 (-)NCBIT2T-CHM13v2.0
Slitrk4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X63,308,489 - 63,320,951 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX63,308,491 - 63,320,602 (-)EnsemblGRCm39 Ensembl
GRCm38X64,264,883 - 64,277,345 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX64,264,885 - 64,276,996 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X61,522,619 - 61,530,171 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X60,530,109 - 60,537,661 (-)NCBIMGSCv36mm8
CeleraX50,666,912 - 50,674,468 (-)NCBICelera
Cytogenetic MapXA7.1NCBI
cM MapX34.57NCBI
Slitrk4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555391,929,681 - 1,942,525 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555391,929,681 - 1,942,525 (-)NCBIChiLan1.0ChiLan1.0
SLITRK4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X143,039,708 - 143,053,417 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X143,043,310 - 143,057,016 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X132,750,454 - 132,763,782 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X143,132,733 - 143,146,029 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX143,138,515 - 143,141,028 (-)Ensemblpanpan1.1panPan2
SLITRK4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X112,794,049 - 112,806,710 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX112,799,447 - 112,801,963 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX98,633,819 - 98,646,492 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X114,805,470 - 114,818,159 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX114,809,815 - 114,818,165 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X111,922,592 - 111,935,261 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X114,135,361 - 114,148,018 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X113,786,520 - 113,799,188 (-)NCBIUU_Cfam_GSD_1.0
Slitrk4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X110,858,763 - 110,871,727 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365134,743,661 - 4,750,633 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365134,742,743 - 4,750,633 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLITRK4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX117,148,744 - 117,156,801 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X117,145,647 - 117,157,275 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X133,678,389 - 133,687,860 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SLITRK4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X118,508,790 - 118,518,971 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX118,511,438 - 118,513,951 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606555,904,351 - 55,917,649 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slitrk4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248083,516,092 - 3,523,455 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248083,516,053 - 3,527,915 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Slitrk4
17 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X103312877148312877Rat
1598809Memor15Memory QTL 154.4exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X103312877148312877Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX100567703150256146Rat
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X126975089152453651Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat

Markers in Region
SLITRK4__5446  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X142,711,642 - 142,712,205 (+)MAPPERmRatBN7.2
Rnor_6.0X147,583,803 - 147,584,365NCBIRnor6.0
Rnor_5.0X147,599,628 - 147,600,190UniSTSRnor5.0
RGSC_v3.4X150,053,949 - 150,054,511UniSTSRGSC3.4
CeleraX138,589,630 - 138,590,192UniSTS
Cytogenetic MapXq37UniSTS


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSRNOT00000003664   ⟹   ENSRNOP00000092913
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX142,711,031 - 142,717,370 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000100348   ⟹   ENSRNOP00000078621
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX142,706,338 - 142,717,269 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000107855   ⟹   ENSRNOP00000093272
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX142,706,338 - 142,718,575 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000114305   ⟹   ENSRNOP00000093668
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX142,706,338 - 142,718,143 (-)Ensembl
RefSeq Acc Id: NM_001106947   ⟹   NP_001100417
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X147,747,449 - 147,753,798 (-)NCBI
mRatBN7.2X142,711,021 - 142,717,370 (-)NCBI
Rnor_6.0X147,582,195 - 147,589,529 (-)NCBI
Rnor_5.0X147,598,020 - 147,605,354 (-)NCBI
RGSC_v3.4X150,053,376 - 150,059,675 (-)RGD
CeleraX138,589,008 - 138,595,357 (-)RGD
Sequence:
RefSeq Acc Id: XM_039099600   ⟹   XP_038955528
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X147,742,925 - 147,755,066 (-)NCBI
mRatBN7.2X142,706,495 - 142,718,641 (-)NCBI
RefSeq Acc Id: XM_039099601   ⟹   XP_038955529
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X147,742,925 - 147,754,229 (-)NCBI
mRatBN7.2X142,706,495 - 142,717,807 (-)NCBI
RefSeq Acc Id: XM_063279903   ⟹   XP_063135973
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X147,728,163 - 147,755,086 (-)NCBI
RefSeq Acc Id: NP_001100417   ⟸   NM_001106947
- Peptide Label: precursor
- UniProtKB: A0A8I6AET5 (UniProtKB/TrEMBL),   A6K517 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_038955528   ⟸   XM_039099600
- Peptide Label: isoform X1
- UniProtKB: A0A8I6AET5 (UniProtKB/TrEMBL),   A6K517 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038955529   ⟸   XM_039099601
- Peptide Label: isoform X1
- UniProtKB: A0A8I6AET5 (UniProtKB/TrEMBL),   A6K517 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000093668   ⟸   ENSRNOT00000114305
Ensembl Acc Id: ENSRNOP00000078621   ⟸   ENSRNOT00000100348
Ensembl Acc Id: ENSRNOP00000093272   ⟸   ENSRNOT00000107855
Ensembl Acc Id: ENSRNOP00000092913   ⟸   ENSRNOT00000003664
RefSeq Acc Id: XP_063135973   ⟸   XM_063279903
- Peptide Label: isoform X2
Protein Domains
LRRCT

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:1588563 AgrOrtholog
BioCyc Gene G2FUF-840 BioCyc
Ensembl Genes ENSRNOG00000062783 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003664.5 UniProtKB/TrEMBL
  ENSRNOT00000100348.1 UniProtKB/TrEMBL
  ENSRNOT00000107855.1 UniProtKB/TrEMBL
  ENSRNOT00000114305.1 UniProtKB/TrEMBL
Gene3D-CATH 3.80.10.10 UniProtKB/TrEMBL
InterPro Cys-rich_flank_reg_C UniProtKB/TrEMBL
  Leu-rich_rpt UniProtKB/TrEMBL
  Leu-rich_rpt_typical-subtyp UniProtKB/TrEMBL
  LRR_dom_sf UniProtKB/TrEMBL
  Slitrk UniProtKB/TrEMBL
KEGG Report rno:302473 UniProtKB/TrEMBL
NCBI Gene 302473 ENTREZGENE
PANTHER PTHR45773 UniProtKB/TrEMBL
  SLIT AND NTRK-LIKE PROTEIN 4 UniProtKB/TrEMBL
Pfam LRR_8 UniProtKB/TrEMBL
PhenoGen Slitrk4 PhenoGen
PROSITE LRR UniProtKB/TrEMBL
RatGTEx ENSRNOG00000062783 RatGTEx
SMART LRR_SD22 UniProtKB/TrEMBL
  LRR_TYP UniProtKB/TrEMBL
  LRRCT UniProtKB/TrEMBL
Superfamily-SCOP L domain-like UniProtKB/TrEMBL
UniProt A0A8I6AET5 ENTREZGENE, UniProtKB/TrEMBL
  A6K517 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-09-17 Slitrk4  SLIT and NTRK-like family, member 4  LOC302473  similar to SLIT and NTRK-like family, member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC302473  similar to SLIT and NTRK-like family, member 4      Symbol and Name status set to provisional 70820 PROVISIONAL