Smlr1 (small leucine-rich protein 1) - Rat Genome Database

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Gene: Smlr1 (small leucine-rich protein 1) Rattus norvegicus
Analyze
Symbol: Smlr1
Name: small leucine-rich protein 1
RGD ID: 1586664
Description: Orthologous to human SMLR1 (small leucine rich protein 1); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical protein LOC686032; LOC686032; uncharacterized protein LOC686032
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8121,656,720 - 21,678,232 (+)NCBIGRCr8
mRatBN7.2119,837,390 - 19,858,906 (+)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx119,614,118 - 19,635,631 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0125,614,091 - 25,628,680 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0119,813,989 - 19,835,503 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0120,856,187 - 20,877,716 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl120,856,187 - 20,877,716 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0122,337,121 - 22,358,779 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4120,302,433 - 20,339,166 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera118,316,279 - 18,337,152 (-)NCBICelera
Cytogenetic Map1p12NCBI
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

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548  


Genomics

Comparative Map Data
Smlr1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8121,656,720 - 21,678,232 (+)NCBIGRCr8
mRatBN7.2119,837,390 - 19,858,906 (+)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx119,614,118 - 19,635,631 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0125,614,091 - 25,628,680 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0119,813,989 - 19,835,503 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0120,856,187 - 20,877,716 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl120,856,187 - 20,877,716 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0122,337,121 - 22,358,779 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4120,302,433 - 20,339,166 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera118,316,279 - 18,337,152 (-)NCBICelera
Cytogenetic Map1p12NCBI
SMLR1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386130,827,406 - 130,837,135 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6130,827,406 - 130,837,135 (+)EnsemblGRCh38hg38GRCh38
GRCh376131,148,546 - 131,158,275 (+)NCBIGRCh37GRCh37hg19GRCh37
Celera6131,894,658 - 131,904,609 (+)NCBICelera
Cytogenetic Map6q23.1NCBI
HuRef6128,729,834 - 128,739,564 (+)NCBIHuRef
CHM1_16131,411,603 - 131,421,333 (+)NCBICHM1_1
T2T-CHM13v2.06132,022,469 - 132,032,200 (+)NCBIT2T-CHM13v2.0
Smlr1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391025,403,841 - 25,412,170 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1025,403,841 - 25,412,165 (-)EnsemblGRCm39 Ensembl
GRCm381025,527,943 - 25,536,272 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1025,527,943 - 25,536,267 (-)EnsemblGRCm38mm10GRCm38
MGSCv371025,247,749 - 25,256,078 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361025,247,749 - 25,256,078 (-)NCBIMGSCv36mm8
Celera1026,464,631 - 26,473,154 (-)NCBICelera
Cytogenetic Map10A4NCBI
cM Map1012.26NCBI
Smlr1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495543611,639,564 - 11,647,131 (+)NCBIChiLan1.0ChiLan1.0
SMLR1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25150,834,837 - 150,844,609 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16148,741,601 - 148,751,371 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06128,628,887 - 128,636,684 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16132,735,376 - 132,743,272 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6132,735,376 - 132,743,272 (+)Ensemblpanpan1.1panPan2
Smlr1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946119,354,391 - 119,368,017 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936790595,284 - 602,433 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SMLR1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl132,635,744 - 32,645,093 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1132,638,169 - 32,708,198 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2136,034,943 - 36,104,959 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SMLR1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11342,724,017 - 42,734,873 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1342,723,703 - 42,733,959 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604014,862,377 - 14,870,531 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Smlr1
188 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:29
Count of miRNA genes:23
Interacting mature miRNAs:27
Transcripts:ENSRNOT00000071726
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354647Despr8Despair related QTL 80.0000341locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1124744506Rat
2298546Neuinf4Neuroinflammation QTL 45.1nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1128736750Rat
2313053Bss51Bone structure and strength QTL 513.80.0001tibia length (VT:0004357)tibia length (CMO:0000450)1132356093Rat
2313070Bss52Bone structure and strength QTL 524.40.0001body length (VT:0001256)body length (CMO:0000013)1132356093Rat
2313090Bmd69Bone mineral density QTL 694.40.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)1132356093Rat
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1165833076Rat
1578650Bmd6Bone mineral density QTL 612.2femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)150910843284926Rat
1578651Bmd7Bone mineral density QTL 714.2femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)150910843284926Rat
1578669Bss9Bone structure and strength QTL 96.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)150910843284926Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
1600360Mcs16Mammary carcinoma susceptibility QTL 162.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1224439043433040Rat
7421626Bp360Blood pressure QTL 3600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1439328949393289Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
4889451Eae29Experimental allergic encephalomyelitis QTL 295.51nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1592587724697545Rat
631508Sald1Serum aldosterone level QTL 13.7blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)1985600154856001Rat
2302038Pia31Pristane induced arthritis QTL 315.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)11099206555992065Rat
1300167Hrtrt2Heart rate QTL 24.35heart pumping trait (VT:2000009)heart rate (CMO:0000002)11148131275088344Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)11148131282174945Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11148131282174945Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11148131282174945Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11148131282174945Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2317755Glom22Glomerulus QTL 223.8urine protein amount (VT:0005160)urine protein level (CMO:0000591)11148148232355910Rat
1578756Iddm22Insulin dependent diabetes mellitus QTL 222.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)11183518156835181Rat
5684998Bss101Bone structure and strength QTL 1013.6tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)11543162149361612Rat
5684999Bss102Bone structure and strength QTL 1025.50.00000072tibia strength trait (VT:1000284)tibia stiffness (CMO:0001735)11543162149361612Rat
631494Bp95Blood pressure QTL 95400.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)11620621049268520Rat
634353Rends2Renal damage susceptibility QTL 20.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)11933357156983283Rat

Markers in Region
AU047178  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2119,857,559 - 19,857,711 (+)MAPPERmRatBN7.2
Rnor_6.0120,876,372 - 20,876,521NCBIRnor6.0
Rnor_5.0122,357,435 - 22,357,584UniSTSRnor5.0
RGSC_v3.4120,337,821 - 20,337,970UniSTSRGSC3.4
Celera118,317,474 - 18,317,623UniSTS
Cytogenetic Map1p12UniSTS


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 1 37 37 37 5
Low 1 1 14 4 14 4 3 3 2 24 14 8 3
Below cutoff 1 18 5 3 5 5 9 4 18 2 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000071726   ⟹   ENSRNOP00000065596
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl120,856,187 - 20,877,716 (+)Ensembl
RefSeq Acc Id: NM_001195606   ⟹   NP_001182535
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8121,656,720 - 21,678,232 (+)NCBI
mRatBN7.2119,837,390 - 19,858,906 (+)NCBI
Rnor_6.0120,856,187 - 20,877,716 (+)NCBI
Rnor_5.0122,337,121 - 22,358,779 (+)NCBI
Celera118,316,279 - 18,337,152 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001182535 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL82924 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001182535   ⟸   NM_001195606
- UniProtKB: A6KU07 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000065596   ⟸   ENSRNOT00000071726

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R807-F1-model_v2 AlphaFold M0R807 1-68 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13689523
Promoter ID:EPDNEW_R47
Type:initiation region
Name:Smlr1_1
Description:small leucine-rich protein 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0120,856,170 - 20,856,230EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1586664 AgrOrtholog
BioCyc Gene G2FUF-62138 BioCyc
Ensembl Genes ENSRNOG00000047821 Ensembl
KEGG Report rno:686032 UniProtKB/TrEMBL
NCBI Gene 686032 ENTREZGENE
PhenoGen Smlr1 PhenoGen
RatGTEx ENSRNOG00000047821 RatGTEx
UniProt A6KU07 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-01-22 Smlr1  small leucine-rich protein 1  LOC686032  hypothetical protein LOC686032  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC686032  hypothetical protein LOC686032      Symbol and Name status set to provisional 70820 PROVISIONAL