Scml2 (Scm polycomb group protein like 2) - Rat Genome Database
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Gene: Scml2 (Scm polycomb group protein like 2) Rattus norvegicus
Analyze
Symbol: Scml2
Name: Scm polycomb group protein like 2
RGD ID: 1564289
Description: Predicted to be involved in several processes, including apoptotic process; cellular protein localization; and histone H2A-K119 monoubiquitination. Predicted to localize to PcG protein complex; XY body; and chromatin. Orthologous to human SCML2 (Scm polycomb group protein like 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; vinclozolin.
Type: protein-coding
RefSeq Status: MODEL
Also known as: LOC367793; RGD1564289; sex comb on midleg-like 2; sex comb on midleg-like 2 (Drosophila); sex comb on midleg-like protein 2; similar to transcriptional repressor Scml2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X33,523,179 - 33,677,672 (-)NCBI
Rnor_6.0 EnsemblX35,305,236 - 35,431,164 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X35,305,235 - 35,431,271 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X35,634,754 - 35,785,344 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X54,798,550 - 54,896,488 (-)NCBIRGSC3.4rn4RGSC3.4
CeleraX34,217,918 - 34,346,511 (-)NCBICelera
Cytogenetic MapXq14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
chromatin  (ISO)
nucleus  (IBA,ISO)
PcG protein complex  (ISO)
XY body  (ISO)

Molecular Function

References

Additional References at PubMed
PMID:10331946   PMID:21282530   PMID:25634095  


Genomics

Comparative Map Data
Scml2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X33,523,179 - 33,677,672 (-)NCBI
Rnor_6.0 EnsemblX35,305,236 - 35,431,164 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X35,305,235 - 35,431,271 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X35,634,754 - 35,785,344 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X54,798,550 - 54,896,488 (-)NCBIRGSC3.4rn4RGSC3.4
CeleraX34,217,918 - 34,346,511 (-)NCBICelera
Cytogenetic MapXq14NCBI
SCML2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX18,239,313 - 18,354,688 (-)EnsemblGRCh38hg38GRCh38
GRCh38X18,239,313 - 18,355,089 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X18,257,433 - 18,372,808 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X18,167,355 - 18,282,699 (-)NCBINCBI36hg18NCBI36
Build 34X18,017,090 - 18,132,435NCBI
CeleraX22,377,536 - 22,492,940 (-)NCBI
Cytogenetic MapXp22.13NCBI
HuRefX16,015,093 - 16,108,084 (-)NCBIHuRef
CHM1_1X18,287,820 - 18,403,223 (-)NCBICHM1_1
Scml2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X159,865,521 - 160,041,214 (+)NCBIGRCm39mm39
GRCm39 EnsemblX159,865,521 - 160,041,209 (+)Ensembl
GRCm38X161,082,525 - 161,258,218 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX161,082,525 - 161,258,213 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X157,600,704 - 157,696,145 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X156,507,165 - 156,599,764 (+)NCBImm8
CeleraX144,403,550 - 144,496,517 (+)NCBICelera
Cytogenetic MapXF4NCBI
Scml2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555193,696 - 84,237 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495551916,839 - 84,226 (+)NCBIChiLan1.0ChiLan1.0
SCML2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X18,228,712 - 18,344,155 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX18,226,256 - 18,344,155 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X10,862,608 - 10,977,851 (-)NCBIMhudiblu_PPA_v0panPan3
SCML2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 EnsemblX14,335,013 - 14,437,176 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1X14,334,769 - 14,436,614 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Scml2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364707,457,995 - 7,508,069 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCML2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX14,717,605 - 14,823,413 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X14,715,357 - 14,823,016 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X15,874,406 - 15,979,881 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SCML2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X16,680,560 - 16,803,443 (-)NCBI
ChlSab1.1 EnsemblX16,680,567 - 16,782,447 (-)Ensembl
Scml2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248293,095,925 - 3,175,062 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X144092703Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X428214049282140Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X595407850954078Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat
71116Niddm16Non-insulin dependent diabetes mellitus QTL 167.81blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X1815335263153352Rat
1598873Memor2Memory QTL 22.5exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)X2159262344320739Rat
2290375Gluco34Glucose level QTL 342.75blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X2159262344468300Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:141
Count of miRNA genes:125
Interacting mature miRNAs:128
Transcripts:ENSRNOT00000004968
Prediction methods:Microtar, Miranda, Pita, Rnahybrid
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.


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 4 4 4 2 12 26
Low 3 34 39 23 19 23 2 2 72 20 15 11 2
Below cutoff 8 12 12 12 6 8 3 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000004968   ⟹   ENSRNOP00000004968
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX35,305,236 - 35,431,164 (-)Ensembl
RefSeq Acc Id: XM_006227323   ⟹   XP_006227385
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX34,217,918 - 34,325,505 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006256906   ⟹   XP_006256968
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X35,305,235 - 35,410,266 (-)NCBI
Rnor_5.0X35,634,754 - 35,785,344 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008758409   ⟹   XP_008756631
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX34,217,918 - 34,338,107 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008758410   ⟹   XP_008756632
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX34,217,918 - 34,346,511 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008773216   ⟹   XP_008771438
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X35,305,235 - 35,422,873 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008773217   ⟹   XP_008771439
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X35,305,235 - 35,431,269 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017588215   ⟹   XP_017443704
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX34,217,918 - 34,331,554 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017588216   ⟹   XP_017443705
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX34,217,918 - 34,338,107 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017588217   ⟹   XP_017443706
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX34,217,918 - 34,338,107 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017588218   ⟹   XP_017443707
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX34,217,918 - 34,338,107 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017588219   ⟹   XP_017443708
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX34,217,918 - 34,338,107 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017588220   ⟹   XP_017443709
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX34,217,918 - 34,338,113 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017588221   ⟹   XP_017443710
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX34,217,918 - 34,338,105 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017602287   ⟹   XP_017457776
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X35,305,235 - 35,422,874 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017602288   ⟹   XP_017457777
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X35,305,235 - 35,422,866 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017602289   ⟹   XP_017457778
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X35,305,235 - 35,431,271 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039100194   ⟹   XP_038956122
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X33,523,179 - 33,677,672 (-)NCBI
RefSeq Acc Id: XM_039100195   ⟹   XP_038956123
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X33,523,179 - 33,677,663 (-)NCBI
Protein Sequences
Protein RefSeqs XP_038956122 (Get FASTA)   NCBI Sequence Viewer  
  XP_038956123 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_006227385   ⟸   XM_006227323
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_006256968   ⟸   XM_006256906
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008756632   ⟸   XM_008758410
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_008756631   ⟸   XM_008758409
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_008771439   ⟸   XM_008773217
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008771438   ⟸   XM_008773216
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017443709   ⟸   XM_017588220
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017443706   ⟸   XM_017588217
- Peptide Label: isoform X12
- Sequence:
RefSeq Acc Id: XP_017443708   ⟸   XM_017588219
- Peptide Label: isoform X14
- Sequence:
RefSeq Acc Id: XP_017443707   ⟸   XM_017588218
- Peptide Label: isoform X13
- Sequence:
RefSeq Acc Id: XP_017443705   ⟸   XM_017588216
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_017443710   ⟸   XM_017588221
- Peptide Label: isoform X15
- Sequence:
RefSeq Acc Id: XP_017443704   ⟸   XM_017588215
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_017457778   ⟸   XM_017602289
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017457776   ⟸   XM_017602287
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017457777   ⟸   XM_017602288
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000004968   ⟸   ENSRNOT00000004968
RefSeq Acc Id: XP_038956122   ⟸   XM_039100194
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038956123   ⟸   XM_039100195
- Peptide Label: isoform X2
Protein Domains
SAM

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
X 35680004 35680005 C T snv LEC/Tj (KyushuU), DOB/Oda (KyushuU), HTX/Kyo (KyushuU), NIG-III/Hok (KyushuU), LE/Stm (KyushuU)
X 35680006 35680007 T G snv DOB/Oda (KyushuU), GH/OmrMcwi (MCW), BDIX/NemOda (KyushuU), F344/Jcl (KyushuU), NIG-III/Hok (KyushuU), SBN/Ygl (MCW), LEC/Tj (KyushuU), BUF/MNa (KyushuU), HWY/Slc (KyushuU), F344/Stm (KyushuU), FHL/EurMcwi (MCW), IS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU), RCS/Kyo (KyushuU), ACI/EurMcwi (MCW), BN/SsNSlc (KyushuU), COP/CrCrl (MCW & UW), SS/JrHsdMcwi (MCW), LE/Stm (KyushuU), FHH/EurMcwi (MCW), HTX/Kyo (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), F344/DuCrlCrlj (KyushuU), SR/JrHsd (MCW), F344/NSlc (KyushuU), ZF (KyushuU), KFRS3B/Kyo (KyushuU)
X 35680013 35680014 C T snv KFRS3B/Kyo (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), DOB/Oda (KyushuU), BDIX/NemOda (KyushuU), F344/Jcl (KyushuU), LEC/Tj (KyushuU), HWY/Slc (KyushuU), F344/Stm (KyushuU), IS-Tlk/Kyo (KyushuU), RCS/Kyo (KyushuU), BN/SsNSlc (KyushuU), F344/NSlc (KyushuU), HTX/Kyo (KyushuU), LE/Stm (KyushuU), F344/DuCrlCrlj (KyushuU), NIG-III/Hok (KyushuU), BUF/MNa (KyushuU), IS/Kyo (KyushuU), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), SBN/Ygl (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW), ZF (KyushuU), ACI/EurMcwi (MCW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
X 35350405 35350406 T G snv SR/JrHsd (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW), GH/OmrMcwi (MCW), SBN/Ygl (MCW), SS/JrHsdMcwi (MCW)
X 35350412 35350413 C T snv FHH/EurMcwi (MCW), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), SBN/Ygl (MCW), FHL/EurMcwi (MCW)
X 35350448 35350449 C T snv SR/JrHsd (MCW), COP/CrCrl (MCW & UW), CDR, CDS, SBH/Ygl (MCW), GH/OmrMcwi (MCW)
X 35352071 35352072 C T snv BN/SsN (MCW)
X 35352076 35352077 T G snv F344/NRrrc (MCW)
X 35387421 35387422 T C snv WN/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564289 AgrOrtholog
Ensembl Genes ENSRNOG00000003726 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000004968 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000004968 UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.50 UniProtKB/TrEMBL
  1.20.1380.20 UniProtKB/TrEMBL
InterPro DUF3588 UniProtKB/TrEMBL
  Mbt UniProtKB/TrEMBL
  SAM UniProtKB/TrEMBL
  SAM/pointed UniProtKB/TrEMBL
  SLED_sf UniProtKB/TrEMBL
NCBI Gene 367793 ENTREZGENE
Pfam DUF3588 UniProtKB/TrEMBL
  MBT UniProtKB/TrEMBL
  SAM_1 UniProtKB/TrEMBL
PhenoGen Scml2 PhenoGen
PROSITE MBT UniProtKB/TrEMBL
SMART MBT UniProtKB/TrEMBL
  SAM UniProtKB/TrEMBL
Superfamily-SCOP SSF47769 UniProtKB/TrEMBL
UniProt D3ZRL8_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-07-31 Scml2  Scm polycomb group protein like 2  Scml2  sex comb on midleg-like 2 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-07-28 Scml2  sex comb on midleg-like 2 (Drosophila)  RGD1564289  similar to transcriptional repressor Scml2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1564289  similar to transcriptional repressor Scml2   RGD1564289_predicted  similar to transcriptional repressor Scml2 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1564289_predicted  similar to transcriptional repressor Scml2 (predicted)  LOC367793  similar to transcriptional repressor Scml2  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC367793  similar to transcriptional repressor Scml2      Symbol and Name status set to provisional 70820 PROVISIONAL