SMKR1 (small lysine rich protein 1) - Rat Genome Database

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Gene: SMKR1 (small lysine rich protein 1) Homo sapiens
Analyze
Symbol: SMKR1
Name: small lysine rich protein 1
RGD ID: 7204969
HGNC Page HGNC:43561
Description: ASSOCIATED WITH genetic disease; Pleomorphic xanthoastrocytoma; pleomorphic xanthoastrocytoma; INTERACTS WITH 17beta-estradiol; all-trans-retinoic acid; cadmium dichloride
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: small lysine-rich protein 1
RGD Orthologs
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
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
GRCh387129,502,531 - 129,512,918 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl7129,502,531 - 129,512,918 (+)EnsemblGRCh38hg38GRCh38
GRCh377129,142,372 - 129,152,759 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map7q32.1NCBI
HuRef7123,503,646 - 123,514,099 (+)NCBIHuRef
CHM1_17129,075,865 - 129,086,318 (+)NCBICHM1_1
T2T-CHM13v2.07130,815,596 - 130,825,982 (+)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v27128,526,271 - 128,536,722 (+)NCBI
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
Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
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:30021884  


Genomics

Comparative Map Data
SMKR1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh387129,502,531 - 129,512,918 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl7129,502,531 - 129,512,918 (+)EnsemblGRCh38hg38GRCh38
GRCh377129,142,372 - 129,152,759 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map7q32.1NCBI
HuRef7123,503,646 - 123,514,099 (+)NCBIHuRef
CHM1_17129,075,865 - 129,086,318 (+)NCBICHM1_1
T2T-CHM13v2.07130,815,596 - 130,825,982 (+)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v27128,526,271 - 128,536,722 (+)NCBI
Smkr1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8459,562,818 - 59,576,401 (+)NCBIGRCr8
mRatBN7.2458,595,363 - 58,609,149 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl458,601,660 - 58,609,229 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0457,265,008 - 57,281,271 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Celera453,696,495 - 53,711,206 (+)NCBICelera
Cytogenetic Map4q22NCBI
Smkr1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495547910,288,231 - 10,288,701 (+)NCBIChiLan1.0ChiLan1.0
SMKR1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v26166,317,437 - 166,329,667 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1718,328,681 - 18,339,912 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v07121,464,310 - 121,474,543 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.17133,995,343 - 133,995,848 (+)NCBIpanpan1.1PanPan1.1panPan2
SMKR1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1147,274,867 - 7,284,067 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl147,274,868 - 7,283,955 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha146,962,037 - 6,970,829 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0147,039,932 - 7,048,931 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl147,037,786 - 7,049,492 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1147,245,316 - 7,254,132 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0146,987,436 - 6,996,251 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0147,131,832 - 7,140,844 (-)NCBIUU_Cfam_GSD_1.0
Smkr1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511825,499,442 - 25,506,569 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365795,632,348 - 5,635,560 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SMKR1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1819,144,096 - 19,199,576 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11819,189,966 - 19,200,030 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21820,260,826 - 20,270,718 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SMKR1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl2198,111,164 - 98,122,915 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660425,281,553 - 5,293,413 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smkr1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247836,712,900 - 6,720,110 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in SMKR1
5 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 7q32.1-36.3(chr7:129310166-159282390)x3 copy number gain See cases [RCV000050876] Chr7:129310166..159282390 [GRCh38]
Chr7:128950007..159075079 [GRCh37]
Chr7:128737243..158767840 [NCBI36]
Chr7:7q32.1-36.3		 pathogenic
GRCh38/hg38 7q32.1-33(chr7:128747478-134018250)x3 copy number gain See cases [RCV000051072] Chr7:128747478..134018250 [GRCh38]
Chr7:128387532..133703003 [GRCh37]
Chr7:128174768..133353543 [NCBI36]
Chr7:7q32.1-33		 pathogenic
GRCh38/hg38 7p22.3-q36.3(chr7:53985-159282531)x1 copy number loss See cases [RCV000052250] Chr7:53985..159282531 [GRCh38]
Chr7:53985..159075220 [GRCh37]
Chr7:149068..158767981 [NCBI36]
Chr7:7p22.3-q36.3		 pathogenic
GRCh38/hg38 7q31.33-32.3(chr7:126859732-132750936)x1 copy number loss See cases [RCV000054171] Chr7:126859732..132750936 [GRCh38]
Chr7:126499786..132435696 [GRCh37]
Chr7:126287022..132086236 [NCBI36]
Chr7:7q31.33-32.3		 pathogenic
GRCh38/hg38 7p22.3-q36.3(chr7:54185-159282390)x1 copy number loss See cases [RCV000135401] Chr7:54185..159282390 [GRCh38]
Chr7:54185..159075079 [GRCh37]
Chr7:149268..158767840 [NCBI36]
Chr7:7p22.3-q36.3		 pathogenic
GRCh38/hg38 7q21.3-36.3(chr7:97419852-158923762)x3 copy number gain See cases [RCV000136717] Chr7:97419852..158923762 [GRCh38]
Chr7:97049164..158716453 [GRCh37]
Chr7:96887100..158409214 [NCBI36]
Chr7:7q21.3-36.3		 pathogenic
GRCh38/hg38 7q31.2-33(chr7:117326805-134790689)x1 copy number loss See cases [RCV000138226] Chr7:117326805..134790689 [GRCh38]
Chr7:116966859..134475440 [GRCh37]
Chr7:116754095..134125980 [NCBI36]
Chr7:7q31.2-33		 pathogenic
GRCh38/hg38 7q31.32-36.3(chr7:121863759-159335865)x3 copy number gain See cases [RCV000138847] Chr7:121863759..159335865 [GRCh38]
Chr7:121503813..159128555 [GRCh37]
Chr7:121291049..158821316 [NCBI36]
Chr7:7q31.32-36.3		 pathogenic
GRCh38/hg38 7q31.2-36.3(chr7:115459015-159325817)x3 copy number gain See cases [RCV000141413] Chr7:115459015..159325817 [GRCh38]
Chr7:115099069..159118507 [GRCh37]
Chr7:114886305..158811268 [NCBI36]
Chr7:7q31.2-36.3		 pathogenic
GRCh38/hg38 7q31.33-33(chr7:124170657-134163594)x1 copy number loss See cases [RCV000142552] Chr7:124170657..134163594 [GRCh38]
Chr7:123810711..133848346 [GRCh37]
Chr7:123597947..133498886 [NCBI36]
Chr7:7q31.33-33		 pathogenic
GRCh37/hg19 7q32.1-36.3(chr7:128312450-159119220) copy number gain not provided [RCV000767558] Chr7:128312450..159119220 [GRCh37]
Chr7:7q32.1-36.3		 pathogenic
TMEM106B-BRAF fusion deletion Pleomorphic xanthoastrocytoma [RCV000454357] Chr7:12258147..140494267 [GRCh37]
Chr7:7p21.3-q34		 pathogenic
GRCh37/hg19 7p22.3-q36.3(chr7:43360-159119707)x1 copy number loss See cases [RCV000446044] Chr7:43360..159119707 [GRCh37]
Chr7:7p22.3-q36.3		 pathogenic
GRCh37/hg19 7q22.1-36.3(chr7:98969247-159119707)x3 copy number gain See cases [RCV000447709] Chr7:98969247..159119707 [GRCh37]
Chr7:7q22.1-36.3		 pathogenic
GRCh37/hg19 7q32.1-34(chr7:127295698-139524358)x1 copy number loss See cases [RCV000447722] Chr7:127295698..139524358 [GRCh37]
Chr7:7q32.1-34		 pathogenic
GRCh37/hg19 7q32.1-36.3(chr7:128276078-159119707)x3 copy number gain See cases [RCV000447956] Chr7:128276078..159119707 [GRCh37]
Chr7:7q32.1-36.3		 pathogenic
GRCh37/hg19 7p22.3-q36.3(chr7:43361-159119707) copy number gain See cases [RCV000510686] Chr7:43361..159119707 [GRCh37]
Chr7:7p22.3-q36.3		 pathogenic
GRCh37/hg19 7p22.3-q36.3(chr7:43361-159119707)x3 copy number gain See cases [RCV000511549] Chr7:43361..159119707 [GRCh37]
Chr7:7p22.3-q36.3		 pathogenic
GRCh37/hg19 7q22.1-36.3(chr7:98693388-159119707)x3 copy number gain not provided [RCV000682911] Chr7:98693388..159119707 [GRCh37]
Chr7:7q22.1-36.3		 pathogenic
GRCh37/hg19 7p22.3-q36.3(chr7:10704-159122532)x3 copy number gain not provided [RCV000746278] Chr7:10704..159122532 [GRCh37]
Chr7:7p22.3-q36.3		 pathogenic
GRCh37/hg19 7p22.3-q36.3(chr7:44935-159126310)x3 copy number gain not provided [RCV000746280] Chr7:44935..159126310 [GRCh37]
Chr7:7p22.3-q36.3		 pathogenic
GRCh37/hg19 7p22.3-q36.3(chr7:10365-159119707)x3 copy number gain not provided [RCV000848126] Chr7:10365..159119707 [GRCh37]
Chr7:7p22.3-q36.3		 pathogenic
GRCh37/hg19 7q31.32-32.2(chr7:121480906-129389003)x1 copy number loss not provided [RCV000847911] Chr7:121480906..129389003 [GRCh37]
Chr7:7q31.32-32.2		 pathogenic
GRCh37/hg19 7q31.1-36.3(chr7:109251060-159119707)x3 copy number gain not provided [RCV001005994] Chr7:109251060..159119707 [GRCh37]
Chr7:7q31.1-36.3		 pathogenic
GRCh37/hg19 7q32.1-33(chr7:129147455-132777678)x1 copy number loss not provided [RCV002473525] Chr7:129147455..132777678 [GRCh37]
Chr7:7q32.1-33		 uncertain significance
Single allele complex Ring chromosome 7 [RCV002280646] Chr7:43360..159119707 [GRCh37]
Chr7:7p22.3-q36.3		 pathogenic
GRCh37/hg19 7q32.1-34(chr7:127295698-139524358) copy number loss not specified [RCV002053727] Chr7:127295698..139524358 [GRCh37]
Chr7:7q32.1-34		 pathogenic
GRCh37/hg19 7q31.33-33(chr7:124103982-134693590) copy number loss not specified [RCV002053726] Chr7:124103982..134693590 [GRCh37]
Chr7:7q31.33-33		 pathogenic
GRCh37/hg19 7q31.33-33(chr7:123967475-132729981) copy number loss not specified [RCV002053723] Chr7:123967475..132729981 [GRCh37]
Chr7:7q31.33-33		 pathogenic
GRCh37/hg19 7p22.3-q36.3(chr7:56604613-96692931)x1 copy number loss See cases [RCV002287832] Chr7:56604613..96692931 [GRCh37]
Chr7:7p22.3-q36.3		 uncertain significance
NM_001195243.2(SMKR1):c.124G>A (p.Val42Ile) single nucleotide variant Inborn genetic diseases [RCV002968268] Chr7:129512367 [GRCh38]
Chr7:129152208 [GRCh37]
Chr7:7q32.1		 uncertain significance
NM_001195243.2(SMKR1):c.107A>G (p.Tyr36Cys) single nucleotide variant Inborn genetic diseases [RCV002945636] Chr7:129512350 [GRCh38]
Chr7:129152191 [GRCh37]
Chr7:7q32.1		 uncertain significance
NM_001195243.2(SMKR1):c.7G>C (p.Ala3Pro) single nucleotide variant Inborn genetic diseases [RCV002882605] Chr7:129512250 [GRCh38]
Chr7:129152091 [GRCh37]
Chr7:7q32.1		 uncertain significance
NM_001195243.2(SMKR1):c.127G>A (p.Ala43Thr) single nucleotide variant Inborn genetic diseases [RCV002719759] Chr7:129512370 [GRCh38]
Chr7:129152211 [GRCh37]
Chr7:7q32.1		 uncertain significance
NM_001195243.2(SMKR1):c.44A>T (p.His15Leu) single nucleotide variant Inborn genetic diseases [RCV003361472] Chr7:129512287 [GRCh38]
Chr7:129152128 [GRCh37]
Chr7:7q32.1		 uncertain significance
GRCh37/hg19 7q31.33-32.2(chr7:127076892-129405807)x1 copy number loss not provided [RCV003482986] Chr7:127076892..129405807 [GRCh37]
Chr7:7q31.33-32.2		 pathogenic
GRCh37/hg19 7q31.31-33(chr7:120582003-137699953)x1 copy number loss not specified [RCV003986721] Chr7:120582003..137699953 [GRCh37]
Chr7:7q31.31-33		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:345
Count of miRNA genes:249
Interacting mature miRNAs:267
Transcripts:ENST00000462322, ENST00000488846
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
RH94383  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh377129,152,253 - 129,152,395UniSTSGRCh37
Build 367128,939,489 - 128,939,631RGDNCBI36
Celera7123,948,976 - 123,949,118RGD
Cytogenetic Map7q32.1UniSTS
HuRef7123,513,579 - 123,513,721UniSTS
CRA_TCAGchr7v27128,536,202 - 128,536,344UniSTS
GeneMap99-GB4 RH Map7588.38UniSTS


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 entire extraembryonic component
High
Medium 51 205 3 32 3 8 18 794 15 525 118 2 3
Low 747 398 996 143 1209 77 1358 380 2526 303 542 1075 77 346 696 4
Below cutoff 1499 1731 396 355 617 264 2350 1532 386 89 327 381 91 699 1577 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000462322   ⟹   ENSP00000454370
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7129,502,531 - 129,512,918 (+)Ensembl
RefSeq Acc Id: ENST00000488846
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7129,502,792 - 129,512,638 (+)Ensembl
RefSeq Acc Id: NM_001195243   ⟹   NP_001182172
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh387129,502,531 - 129,512,918 (+)NCBI
GRCh377129,142,320 - 129,152,773 (+)NCBI
HuRef7123,503,646 - 123,514,099 (+)NCBI
CHM1_17129,075,865 - 129,086,318 (+)NCBI
T2T-CHM13v2.07130,815,596 - 130,825,982 (+)NCBI
CRA_TCAGchr7v27128,526,271 - 128,536,722 (+)NCBI
Sequence:
RefSeq Acc Id: XM_024446620   ⟹   XP_024302388
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh387129,502,531 - 129,512,918 (+)NCBI
Sequence:
RefSeq Acc Id: XM_054356951   ⟹   XP_054212926
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.07130,815,596 - 130,825,982 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001182172 (Get FASTA)   NCBI Sequence Viewer  
  XP_024302388 (Get FASTA)   NCBI Sequence Viewer  
  XP_054212926 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000454370
  ENSP00000454370.1
GenBank Protein H3BMG3 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001182172   ⟸   NM_001195243
- UniProtKB: H3BMG3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_024302388   ⟸   XM_024446620
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSP00000454370   ⟸   ENST00000462322
RefSeq Acc Id: XP_054212926   ⟸   XM_054356951
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-H3BMG3-F1-model_v2 AlphaFold H3BMG3 1-65 view protein structure

Promoters
RGD ID:7211903
Promoter ID:EPDNEW_H11697
Type:initiation region
Name:SMKR1_2
Description:small lysine rich protein 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H11698  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh387129,502,227 - 129,502,287EPDNEW
RGD ID:7211905
Promoter ID:EPDNEW_H11698
Type:initiation region
Name:SMKR1_1
Description:small lysine rich protein 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H11697  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh387129,502,531 - 129,502,591EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:43561 AgrOrtholog
COSMIC SMKR1 COSMIC
Ensembl Genes ENSG00000240204 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000462322 ENTREZGENE
  ENST00000462322.3 UniProtKB/Swiss-Prot
GTEx ENSG00000240204 GTEx
HGNC ID HGNC:43561 ENTREZGENE
Human Proteome Map SMKR1 Human Proteome Map
InterPro SMKR1 UniProtKB/Swiss-Prot
KEGG Report hsa:100287482 UniProtKB/Swiss-Prot
NCBI Gene SMKR1 ENTREZGENE
PANTHER PTHR37932 UniProtKB/Swiss-Prot
  SMALL LYSINE-RICH PROTEIN 1 UniProtKB/Swiss-Prot
PharmGKB PA166049099 PharmGKB
UniProt H3BMG3 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-14 SMKR1  small lysine rich protein 1    small lysine-rich protein 1  Symbol and/or name change 5135510 APPROVED