Scml4 (Scm polycomb group protein like 4) - Rat Genome Database

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Gene: Scml4 (Scm polycomb group protein like 4) Rattus norvegicus
Analyze
Symbol: Scml4
Name: Scm polycomb group protein like 4
RGD ID: 1310898
Description: Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in negative regulation of DNA-templated transcription. Predicted to be active in nucleus. Orthologous to human SCML4 (Scm polycomb group protein like 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC309859; sex comb on midleg-like 4; sex comb on midleg-like 4 (Drosophila); sex comb on midleg-like protein 4
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
mRatBN7.22046,347,242 - 46,440,103 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2046,347,413 - 46,440,103 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2048,064,892 - 48,157,484 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.02047,715,071 - 47,807,661 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02048,401,926 - 48,494,072 (+)NCBIRnor_WKY
Rnor_6.02047,596,531 - 47,689,245 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2047,596,575 - 47,689,245 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02049,258,704 - 49,350,697 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42046,771,530 - 46,864,100 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12046,798,632 - 46,889,789 (+)NCBI
Celera2053,538,104 - 53,629,929 (-)NCBICelera
Cytogenetic Map20q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleus  (IBA)

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. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Scml4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22046,347,242 - 46,440,103 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2046,347,413 - 46,440,103 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2048,064,892 - 48,157,484 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.02047,715,071 - 47,807,661 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02048,401,926 - 48,494,072 (+)NCBIRnor_WKY
Rnor_6.02047,596,531 - 47,689,245 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2047,596,575 - 47,689,245 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02049,258,704 - 49,350,697 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42046,771,530 - 46,864,100 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12046,798,632 - 46,889,789 (+)NCBI
Celera2053,538,104 - 53,629,929 (-)NCBICelera
Cytogenetic Map20q13NCBI
SCML4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386107,702,154 - 107,846,038 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl6107,702,154 - 107,824,317 (-)EnsemblGRCh38hg38GRCh38
GRCh376108,023,358 - 108,145,517 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366108,146,342 - 108,200,148 (-)NCBINCBI36Build 36hg18NCBI36
Celera6108,771,904 - 108,892,338 (-)NCBICelera
Cytogenetic Map6q21NCBI
HuRef6105,594,303 - 105,714,955 (-)NCBIHuRef
CHM1_16108,286,064 - 108,408,072 (-)NCBICHM1_1
T2T-CHM13v2.06108,881,077 - 109,002,036 (-)NCBIT2T-CHM13v2.0
Scml4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391042,736,314 - 42,836,778 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1042,736,366 - 42,836,776 (+)EnsemblGRCm39 Ensembl
GRCm381042,858,077 - 42,960,782 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1042,860,370 - 42,960,780 (+)EnsemblGRCm38mm10GRCm38
MGSCv371042,580,318 - 42,680,588 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361042,549,132 - 42,649,195 (+)NCBIMGSCv36mm8
Celera1043,727,280 - 43,828,323 (+)NCBICelera
Cytogenetic Map10B2NCBI
Scml4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541132,940,367 - 33,036,779 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541132,940,367 - 33,036,779 (-)NCBIChiLan1.0ChiLan1.0
SCML4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16109,379,532 - 109,498,016 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6109,379,532 - 109,498,016 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06105,517,185 - 105,633,576 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SCML4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11264,851,495 - 64,937,140 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1264,851,740 - 64,945,496 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1264,627,083 - 64,741,845 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01265,686,167 - 65,801,001 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1265,696,665 - 65,800,957 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11265,051,396 - 65,157,300 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01264,888,367 - 65,003,113 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01265,170,755 - 65,276,680 (-)NCBIUU_Cfam_GSD_1.0
Scml4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494699,765,133 - 99,827,226 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365644,043,248 - 4,144,950 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049365644,042,148 - 4,144,950 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCML4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl173,843,012 - 73,968,699 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1173,838,808 - 73,982,634 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2183,160,076 - 83,253,479 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SCML4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11366,034,219 - 66,165,842 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1366,034,792 - 66,156,205 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604038,363,175 - 38,491,300 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Scml4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462478014,502,821 - 14,578,402 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462478014,516,123 - 14,575,762 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Scml4
601 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:434
Count of miRNA genes:229
Interacting mature miRNAs:297
Transcripts:ENSRNOT00000064905
Prediction methods:Microtar, Miranda, 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
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201761783247606836Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202924438854435887Rat


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 2 5 8
Low 1 43 27 14 27 60 23 27 11
Below cutoff 31 14 14 14 7 8 6 12 14 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000064905   ⟹   ENSRNOP00000059803
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2046,347,511 - 46,440,103 (+)Ensembl
Rnor_6.0 Ensembl2047,596,675 - 47,689,245 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000087230   ⟹   ENSRNOP00000072278
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2046,347,511 - 46,413,893 (+)Ensembl
Rnor_6.0 Ensembl2047,596,575 - 47,686,862 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000096442   ⟹   ENSRNOP00000095139
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2046,347,511 - 46,440,103 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000110750   ⟹   ENSRNOP00000093018
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2046,347,413 - 46,440,103 (+)Ensembl
RefSeq Acc Id: NM_001107638   ⟹   NP_001101108
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22046,347,511 - 46,440,103 (+)NCBI
Rnor_6.02047,596,675 - 47,689,245 (+)NCBI
Rnor_5.02049,258,704 - 49,350,697 (+)NCBI
RGSC_v3.42046,771,530 - 46,864,100 (+)RGD
Celera2053,538,104 - 53,629,929 (-)RGD
Sequence:
RefSeq Acc Id: XM_006256572   ⟹   XP_006256634
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22046,347,242 - 46,437,322 (+)NCBI
Rnor_6.02047,596,531 - 47,686,465 (+)NCBI
Rnor_5.02049,258,704 - 49,350,697 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001101108 (Get FASTA)   NCBI Sequence Viewer  
  XP_006256634 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL99696 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001101108   ⟸   NM_001107638
- UniProtKB: D3ZRV1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256634   ⟸   XM_006256572
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K2K4 (UniProtKB/TrEMBL),   A0A8I6ASY0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072278   ⟸   ENSRNOT00000087230
RefSeq Acc Id: ENSRNOP00000059803   ⟸   ENSRNOT00000064905
RefSeq Acc Id: ENSRNOP00000093018   ⟸   ENSRNOT00000110750
RefSeq Acc Id: ENSRNOP00000095139   ⟸   ENSRNOT00000096442
Protein Domains
RBR   SAM   SLED

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K2K4-F1-model_v2 AlphaFold A0A0G2K2K4 1-414 view protein structure

Transcriptome

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

Promoters
RGD ID:13701676
Promoter ID:EPDNEW_R12196
Type:single initiation site
Name:Scml4_1
Description:Scm polycomb group protein like 4
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_6.02047,596,658 - 47,596,718EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310898 AgrOrtholog
BioCyc Gene G2FUF-3351 BioCyc
Ensembl Genes ENSRNOG00000026110 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000059803 ENTREZGENE
  ENSRNOP00000059803.1 UniProtKB/TrEMBL
  ENSRNOP00000072278.2 UniProtKB/TrEMBL
  ENSRNOP00000093018.1 UniProtKB/TrEMBL
  ENSRNOP00000095139 ENTREZGENE
  ENSRNOP00000095139.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000064905 ENTREZGENE
  ENSRNOT00000064905.2 UniProtKB/TrEMBL
  ENSRNOT00000087230.2 UniProtKB/TrEMBL
  ENSRNOT00000096442 ENTREZGENE
  ENSRNOT00000096442.1 UniProtKB/TrEMBL
  ENSRNOT00000110750.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.50 UniProtKB/TrEMBL
  3.90.1150.190 UniProtKB/TrEMBL
InterPro DUF3588 UniProtKB/TrEMBL
  SAM UniProtKB/TrEMBL
  SAM_type UniProtKB/TrEMBL
  SCML2_RBR UniProtKB/TrEMBL
  SLED_sf UniProtKB/TrEMBL
KEGG Report rno:309859 UniProtKB/TrEMBL
NCBI Gene 309859 ENTREZGENE
Pfam DUF3588 UniProtKB/TrEMBL
  RBR UniProtKB/TrEMBL
  SAM_1 UniProtKB/TrEMBL
PhenoGen Scml4 PhenoGen
SMART SAM UniProtKB/TrEMBL
Superfamily-SCOP SAM_homology UniProtKB/TrEMBL
UniProt A0A0G2K2K4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AHS8_RAT UniProtKB/TrEMBL
  A0A8I6ASY0 ENTREZGENE, UniProtKB/TrEMBL
  D3ZRV1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-07-31 Scml4  Scm polycomb group protein like 4  Scml4  sex comb on midleg-like 4 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Scml4  sex comb on midleg-like 4 (Drosophila)   Scml4_predicted  sex comb on midleg-like 4 (Drosophila) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Scml4_predicted  sex comb on midleg-like 4 (Drosophila) (predicted)      Symbol and Name status set to approved 70820 APPROVED