SMLR1 (small leucine rich protein 1) - Rat Genome Database

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Gene: SMLR1 (small leucine rich protein 1) Homo sapiens
Analyze
Symbol: SMLR1
Name: small leucine rich protein 1
RGD ID: 7205347
HGNC Page HGNC:44670
Description: Predicted to be located in membrane.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: small leucine-rich protein 1; uncharacterized protein LOC100507203
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
membrane  (IEA)

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:8889549   PMID:12477932   PMID:14702039   PMID:25416956   PMID:31741433   PMID:36053190  


Genomics

Comparative Map Data
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
(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
(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
7 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 6q21-23.2(chr6:108944899-132067720)x1 copy number loss See cases [RCV000051196] Chr6:108944899..132067720 [GRCh38]
Chr6:109266102..132388860 [GRCh37]
Chr6:109372795..132430553 [NCBI36]
Chr6:6q21-23.2		 pathogenic
GRCh38/hg38 6q23.1(chr6:130169549-130850911)x3 copy number gain See cases [RCV000136643] Chr6:130169549..130850911 [GRCh38]
Chr6:130490694..131172051 [GRCh37]
Chr6:130532387..131213744 [NCBI36]
Chr6:6q23.1		 uncertain significance
GRCh38/hg38 6q13-24.1(chr6:74382807-142040500)x3 copy number gain See cases [RCV000139729] Chr6:74382807..142040500 [GRCh38]
Chr6:75092523..142361637 [GRCh37]
Chr6:75149243..142403330 [NCBI36]
Chr6:6q13-24.1		 pathogenic
GRCh38/hg38 6q22.33-23.2(chr6:129191313-132131620)x1 copy number loss See cases [RCV000142349] Chr6:129191313..132131620 [GRCh38]
Chr6:129512458..132452760 [GRCh37]
Chr6:129554151..132494453 [NCBI36]
Chr6:6q22.33-23.2		 likely pathogenic
GRCh38/hg38 6q22.32-23.2(chr6:126494533-132497855)x1 copy number loss See cases [RCV000142805] Chr6:126494533..132497855 [GRCh38]
Chr6:126815679..132818994 [GRCh37]
Chr6:126857372..132860687 [NCBI36]
Chr6:6q22.32-23.2		 likely pathogenic
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482)x3 copy number gain See cases [RCV000512067] Chr6:156975..170919482 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482) copy number gain See cases [RCV000510595] Chr6:156975..170919482 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6q22.31-23.2(chr6:122612641-131564463)x1 copy number loss See cases [RCV000511386] Chr6:122612641..131564463 [GRCh37]
Chr6:6q22.31-23.2		 pathogenic
GRCh37/hg19 6q21-23.2(chr6:112939290-132327952)x1 copy number loss Poly (ADP-Ribose) polymerase inhibitor response [RCV000626432] Chr6:112939290..132327952 [GRCh37]
Chr6:6q21-23.2		 drug response
GRCh37/hg19 6p25.3-q27(chr6:60107-171054786)x3 copy number gain not provided [RCV000745400] Chr6:60107..171054786 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:165632-170919470)x3 copy number gain not provided [RCV000745404] Chr6:165632..170919470 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:108666-170980171)x3 copy number gain not provided [RCV000745403] Chr6:108666..170980171 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6q22.33-23.2(chr6:129513837-132618991) copy number loss not provided [RCV000767715] Chr6:129513837..132618991 [GRCh37]
Chr6:6q22.33-23.2		 likely pathogenic
Single allele deletion Interstitial 6q microdeletion syndrome [RCV002280353] Chr6:115941808..133892653 [GRCh38]
Chr6:6q22.1-23.2		 pathogenic
GRCh37/hg19 6q23.1-23.3(chr6:130769034-136009217)x1 copy number loss not provided [RCV001829086] Chr6:130769034..136009217 [GRCh37]
Chr6:6q23.1-23.3		 pathogenic
GRCh37/hg19 6q23.1-23.2(chr6:130949600-131924268) copy number gain not specified [RCV002053622] Chr6:130949600..131924268 [GRCh37]
Chr6:6q23.1-23.2		 uncertain significance
NM_001195597.2(SMLR1):c.268C>T (p.Arg90Cys) single nucleotide variant Inborn genetic diseases [RCV003260647] Chr6:130834899 [GRCh38]
Chr6:131156039 [GRCh37]
Chr6:6q23.1		 uncertain significance
NM_001195597.2(SMLR1):c.146T>C (p.Leu49Pro) single nucleotide variant Inborn genetic diseases [RCV002752761] Chr6:130827559 [GRCh38]
Chr6:131148699 [GRCh37]
Chr6:6q23.1		 uncertain significance
NM_001195597.2(SMLR1):c.114G>A (p.Met38Ile) single nucleotide variant Inborn genetic diseases [RCV002707804] Chr6:130827527 [GRCh38]
Chr6:131148667 [GRCh37]
Chr6:6q23.1		 uncertain significance
NM_001195597.2(SMLR1):c.273A>T (p.Gln91His) single nucleotide variant Inborn genetic diseases [RCV002797973] Chr6:130834904 [GRCh38]
Chr6:131156044 [GRCh37]
Chr6:6q23.1		 uncertain significance
NM_001195597.2(SMLR1):c.308G>T (p.Arg103Ile) single nucleotide variant Inborn genetic diseases [RCV002759619] Chr6:130834939 [GRCh38]
Chr6:131156079 [GRCh37]
Chr6:6q23.1		 uncertain significance
GRCh37/hg19 6q22.31-23.3(chr6:120218852-137160850)x1 copy number loss not provided [RCV003482930] Chr6:120218852..137160850 [GRCh37]
Chr6:6q22.31-23.3		 pathogenic
NM_001195597.2(SMLR1):c.301del (p.Tyr101fs) deletion not provided [RCV003432045] Chr6:130834932 [GRCh38]
Chr6:131156072 [GRCh37]
Chr6:6q23.1		 likely benign
GRCh37/hg19 6q22.31-25.3(chr6:119840686-156623091)x3 copy number gain not specified [RCV003986631] Chr6:119840686..156623091 [GRCh37]
Chr6:6q22.31-25.3		 pathogenic
GRCh37/hg19 6q21-23.2(chr6:110546061-131896074)x3 copy number gain not specified [RCV003986625] Chr6:110546061..131896074 [GRCh37]
Chr6:6q21-23.2		 likely pathogenic
GRCh37/hg19 6q23.1-23.2(chr6:130983223-132108647)x3 copy number gain not specified [RCV003986670] Chr6:130983223..132108647 [GRCh37]
Chr6:6q23.1-23.2		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:800
Count of miRNA genes:593
Interacting mature miRNAs:649
Transcripts:ENST00000541421
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.

Markers in Region
D6S1156E  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh376131,148,366 - 131,148,487UniSTSGRCh37
Build 366131,190,059 - 131,190,180RGDNCBI36
Celera6131,894,700 - 131,894,821RGD
Cytogenetic Map6q23.1UniSTS
HuRef6128,729,655 - 128,729,776UniSTS
GeneMap99-GB4 RH Map6521.49UniSTS
NCBI RH Map61527.4UniSTS
D6S1877  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh376131,156,079 - 131,156,404UniSTSGRCh37
Build 366131,197,772 - 131,198,097RGDNCBI36
Celera6131,902,413 - 131,902,738RGD
Cytogenetic Map6q23.1UniSTS
HuRef6128,737,368 - 128,737,693UniSTS
GeneMap99-GB4 RH Map6521.49UniSTS
GeneMap99-GB4 RH Map6521.73UniSTS
Whitehead-RH Map6744.8UniSTS
Whitehead-YAC Contig Map6 UniSTS
NCBI RH Map61527.4UniSTS
D6S2129  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh376131,156,262 - 131,156,404UniSTSGRCh37
Build 366131,197,955 - 131,198,097RGDNCBI36
Celera6131,902,596 - 131,902,738RGD
Cytogenetic Map6q23.1UniSTS
HuRef6128,737,551 - 128,737,693UniSTS
RH64862  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh376131,156,163 - 131,156,290UniSTSGRCh37
Build 366131,197,856 - 131,197,983RGDNCBI36
Celera6131,902,497 - 131,902,624RGD
Cytogenetic Map6q23.1UniSTS
HuRef6128,737,452 - 128,737,579UniSTS
A005Q25  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh376131,149,504 - 131,149,708UniSTSGRCh37
Build 366131,191,197 - 131,191,401RGDNCBI36
Celera6131,895,838 - 131,896,042RGD
Cytogenetic Map6q23.1UniSTS
HuRef6128,730,793 - 128,730,997UniSTS
GeneMap99-GB4 RH Map6521.73UniSTS
NCBI RH Map61527.4UniSTS
WI-18727  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh376131,156,291 - 131,156,421UniSTSGRCh37
Build 366131,197,984 - 131,198,114RGDNCBI36
Celera6131,902,625 - 131,902,755RGD
Cytogenetic Map6q23.1UniSTS
HuRef6128,737,580 - 128,737,710UniSTS
GeneMap99-GB4 RH Map6521.73UniSTS
Whitehead-RH Map6744.8UniSTS
NCBI RH Map61527.4UniSTS
STS-H49563  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh376131,158,129 - 131,158,262UniSTSGRCh37
Build 366131,199,822 - 131,199,955RGDNCBI36
Celera6131,904,463 - 131,904,596RGD
Cytogenetic Map6q23.1UniSTS
HuRef6128,739,418 - 128,739,551UniSTS
GeneMap99-GB4 RH Map6521.73UniSTS
NCBI RH Map61527.4UniSTS
G32271  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh376131,149,504 - 131,149,708UniSTSGRCh37
Celera6131,895,838 - 131,896,042UniSTS
Cytogenetic Map6q23.1UniSTS
HuRef6128,730,793 - 128,730,997UniSTS


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 sensory system adipose tissue appendage
High
Medium 26 2 399 399 18 399 15 1
Low 127 36 130 42 126 43 130 3 123 208 438 6 4 124
Below cutoff 1737 1692 879 111 641 12 2409 1232 2737 89 637 1012 100 977 1488

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000541421   ⟹   ENSP00000456026
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl6130,827,406 - 130,837,135 (+)Ensembl
RefSeq Acc Id: NM_001195597   ⟹   NP_001182526
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh386130,827,406 - 130,837,135 (+)NCBI
GRCh376131,148,545 - 131,158,275 (+)NCBI
HuRef6128,729,834 - 128,739,564 (+)NCBI
CHM1_16131,411,603 - 131,421,333 (+)NCBI
T2T-CHM13v2.06132,022,469 - 132,032,200 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001182526 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000456026
  ENSP00000456026.1
GenBank Protein H3BR10 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001182526   ⟸   NM_001195597
- UniProtKB: H3BR10 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000456026   ⟸   ENST00000541421

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-H3BR10-F1-model_v2 AlphaFold H3BR10 1-107 view protein structure

Promoters
RGD ID:7209141
Promoter ID:EPDNEW_H10317
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:
Human AssemblyChrPosition (strand)Source
GRCh386130,827,438 - 130,827,498EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:44670 AgrOrtholog
COSMIC SMLR1 COSMIC
Ensembl Genes ENSG00000256162 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000541421 ENTREZGENE
  ENST00000541421.2 UniProtKB/Swiss-Prot
GTEx ENSG00000256162 GTEx
HGNC ID HGNC:44670 ENTREZGENE
Human Proteome Map SMLR1 Human Proteome Map
KEGG Report hsa:100507203 UniProtKB/Swiss-Prot
NCBI Gene SMLR1 ENTREZGENE
PharmGKB PA166049154 PharmGKB
UniProt H3BR10 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-14 SMLR1  small leucine rich protein 1    small leucine-rich protein 1  Symbol and/or name change 5135510 APPROVED