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 anatomical structure morphogenesis. Predicted to act upstream of or within apoptotic process and protein localization to chromosome. Predicted to be located in XY body and nucleus. Predicted to be part of PcG protein complex and chromatin. Orthologous to human SCML2 (Scm polycomb group protein like 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; gentamycin.
Type: protein-coding
RefSeq Status: MODEL
Previously 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: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X37,331,893 - 37,486,465 (-)NCBIGRCr8
mRatBN7.2X33,523,179 - 33,677,672 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX33,524,530 - 33,652,742 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0X35,305,235 - 35,431,271 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX35,305,236 - 35,431,164 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X35,634,754 - 35,785,344 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X54,798,550 - 54,896,488 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
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:10331946   PMID:21282530   PMID:25634095  


Genomics

Comparative Map Data
Scml2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X37,331,893 - 37,486,465 (-)NCBIGRCr8
mRatBN7.2X33,523,179 - 33,677,672 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX33,524,530 - 33,652,742 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0X35,305,235 - 35,431,271 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX35,305,236 - 35,431,164 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X35,634,754 - 35,785,344 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X54,798,550 - 54,896,488 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX34,217,918 - 34,346,511 (-)NCBICelera
Cytogenetic MapXq14NCBI
SCML2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X18,239,313 - 18,355,118 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX18,239,313 - 18,354,688 (-)EnsemblGRCh38hg38GRCh38
GRCh37X18,257,433 - 18,372,808 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X18,167,355 - 18,282,699 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X18,017,090 - 18,132,435NCBI
CeleraX22,377,536 - 22,492,940 (-)NCBICelera
Cytogenetic MapXp22.13NCBI
HuRefX16,015,093 - 16,108,084 (-)NCBIHuRef
CHM1_1X18,287,820 - 18,403,223 (-)NCBICHM1_1
T2T-CHM13v2.0X17,821,927 - 17,937,732 (-)NCBIT2T-CHM13v2.0
Scml2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X159,865,521 - 160,041,214 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX159,865,521 - 160,041,209 (+)EnsemblGRCm39 Ensembl
GRCm38X161,082,525 - 161,258,218 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX161,082,525 - 161,258,213 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X157,600,704 - 157,696,145 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X156,507,165 - 156,599,764 (+)NCBIMGSCv36mm8
CeleraX144,403,550 - 144,496,517 (+)NCBICelera
Cytogenetic MapXF4NCBI
cM MapX73.95NCBI
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
NHGRI_mPanPan1-v2X20,037,624 - 20,152,925 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X20,041,016 - 20,156,317 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X10,862,608 - 10,977,851 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X18,228,712 - 18,344,155 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX18,226,256 - 18,344,155 (-)Ensemblpanpan1.1panPan2
SCML2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X14,334,769 - 14,436,614 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX14,335,013 - 14,437,176 (-)EnsemblCanFam3.1canFam3CanFam3.1
ROS_Cfam_1.0X14,297,274 - 14,397,418 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX14,298,899 - 14,397,962 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X14,364,374 - 14,464,474 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X14,357,320 - 14,457,326 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X14,420,959 - 14,521,278 (-)NCBIUU_Cfam_GSD_1.0
Scml2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X7,457,990 - 7,558,030 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364707,458,007 - 7,508,069 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364707,457,995 - 7,508,069 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCML2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX14,717,606 - 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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X16,680,560 - 16,803,443 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX16,680,567 - 16,782,447 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605618,566,068 - 18,689,672 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Scml2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248293,095,925 - 3,175,062 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Scml2
593 total Variants
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.


QTLs in Region (mRatBN7.2)
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)X143491017Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X292789847927898Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7440600049406000Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X449454949494549Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
71116Niddm16Non-insulin dependent diabetes mellitus QTL 167.81blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X1529780260297802Rat
1598873Memor2Memory QTL 22.5exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)X2099094741052531Rat
2290375Gluco34Glucose level QTL 342.75blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X2099094741203591Rat


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

Nucleotide Sequences
RefSeq Transcripts XM_006227323 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256906 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008758409 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008758410 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008773216 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008773217 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588215 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588216 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588217 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588218 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588219 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588220 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588221 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602287 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602288 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602289 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100194 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100195 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063280419 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JAXUCZ010000021 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000004968   ⟹   ENSRNOP00000004968
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX33,524,530 - 33,652,742 (-)Ensembl
Rnor_6.0 EnsemblX35,305,236 - 35,431,164 (-)Ensembl
RefSeq Acc Id: XM_039100194   ⟹   XP_038956122
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X37,331,893 - 37,486,465 (-)NCBI
mRatBN7.2X33,523,179 - 33,677,672 (-)NCBI
RefSeq Acc Id: XM_039100195   ⟹   XP_038956123
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X37,331,893 - 37,486,461 (-)NCBI
mRatBN7.2X33,523,179 - 33,677,663 (-)NCBI
RefSeq Acc Id: XM_063280419   ⟹   XP_063136489
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X37,331,893 - 37,439,760 (-)NCBI
Protein Sequences
Protein RefSeqs XP_038956122 (Get FASTA)   NCBI Sequence Viewer  
  XP_038956123 (Get FASTA)   NCBI Sequence Viewer  
  XP_063136489 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000004968
  ENSRNOP00000004968.8
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000004968   ⟸   ENSRNOT00000004968
RefSeq Acc Id: XP_038956122   ⟸   XM_039100194
- Peptide Label: isoform X1
- UniProtKB: D3ZRL8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038956123   ⟸   XM_039100195
- Peptide Label: isoform X3
- UniProtKB: D3ZRL8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063136489   ⟸   XM_063280419
- Peptide Label: isoform X2
Protein Domains
SLED

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZRL8-F1-model_v2 AlphaFold D3ZRL8 1-925 view protein structure

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:1564289 AgrOrtholog
BioCyc Gene G2FUF-2512 BioCyc
Ensembl Genes ENSRNOG00000003726 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000004968.8 UniProtKB/TrEMBL
Gene3D-CATH 2.30.30.140 UniProtKB/TrEMBL
  3.90.1150.190 UniProtKB/TrEMBL
InterPro DUF3588 UniProtKB/TrEMBL
  Mbt UniProtKB/TrEMBL
  SLED_sf UniProtKB/TrEMBL
NCBI Gene 367793 ENTREZGENE
PANTHER POLYCOMB GROUP PROTEIN UniProtKB/TrEMBL
  SCM POLYCOMB GROUP PROTEIN-LIKE 2 UniProtKB/TrEMBL
Pfam DUF3588 UniProtKB/TrEMBL
  MBT UniProtKB/TrEMBL
PhenoGen Scml2 PhenoGen
PROSITE MBT UniProtKB/TrEMBL
RatGTEx ENSRNOG00000003726 RatGTEx
SMART MBT UniProtKB/TrEMBL
Superfamily-SCOP Tudor/PWWP/MBT UniProtKB/TrEMBL
UniProt D3ZRL8 ENTREZGENE, 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