Ss18l2 (SS18 like 2) - Rat Genome Database

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Gene: Ss18l2 (SS18 like 2) Rattus norvegicus
Analyze
Symbol: Ss18l2
Name: SS18 like 2
RGD ID: 1590139
Description: Orthologous to human SS18L2 (SS18 like 2); INTERACTS WITH 4,4'-sulfonyldiphenol; bisphenol A; bisphenol F.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC687029; similar to differentially expressed in B16F10 1; SS18-like protein 2; synovial sarcoma translocation gene on chromosome 18-like 2
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
GRCr88130,252,774 - 130,255,388 (+)NCBIGRCr8
mRatBN7.28121,375,263 - 121,377,877 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8121,375,308 - 121,377,877 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8126,974,437 - 126,977,057 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08125,173,506 - 125,176,126 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08123,002,662 - 123,005,276 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08130,350,504 - 130,353,126 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8130,350,510 - 130,353,140 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08129,530,974 - 129,533,603 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera8120,509,704 - 120,512,326 (+)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Ss18l2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88130,252,774 - 130,255,388 (+)NCBIGRCr8
mRatBN7.28121,375,263 - 121,377,877 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8121,375,308 - 121,377,877 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8126,974,437 - 126,977,057 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08125,173,506 - 125,176,126 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08123,002,662 - 123,005,276 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08130,350,504 - 130,353,126 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8130,350,510 - 130,353,140 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08129,530,974 - 129,533,603 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera8120,509,704 - 120,512,326 (+)NCBICelera
Cytogenetic Map8q32NCBI
SS18L2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38342,581,840 - 42,596,934 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl342,581,840 - 42,596,934 (+)EnsemblGRCh38hg38GRCh38
GRCh37342,623,332 - 42,638,426 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36342,607,302 - 42,611,494 (+)NCBINCBI36Build 36hg18NCBI36
Build 34342,607,307 - 42,611,486NCBI
Celera342,572,703 - 42,576,900 (+)NCBICelera
Cytogenetic Map3p22.1NCBI
HuRef342,676,411 - 42,680,610 (+)NCBIHuRef
CHM1_1342,583,484 - 42,587,681 (+)NCBICHM1_1
T2T-CHM13v2.0342,599,834 - 42,614,928 (+)NCBIT2T-CHM13v2.0
Ss18l2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399121,539,455 - 121,541,987 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9121,539,395 - 121,542,454 (+)EnsemblGRCm39 Ensembl
GRCm389121,710,389 - 121,712,921 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9121,710,329 - 121,713,388 (+)EnsemblGRCm38mm10GRCm38
MGSCv379121,619,507 - 121,622,039 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv369121,559,087 - 121,561,619 (+)NCBIMGSCv36mm8
Celera9122,183,606 - 122,186,086 (+)NCBICelera
Cytogenetic Map9F4NCBI
cM Map972.56NCBI
Ss18l2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542028,203,226 - 28,205,284 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542028,203,226 - 28,205,284 (-)NCBIChiLan1.0ChiLan1.0
SS18L2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2242,544,464 - 42,558,008 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1342,549,244 - 42,562,770 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0342,487,389 - 42,500,908 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1343,552,858 - 43,565,687 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl343,552,858 - 43,565,681 (+)Ensemblpanpan1.1panPan2
SS18L2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12311,713,801 - 11,717,025 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2311,713,906 - 11,716,896 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2311,688,171 - 11,691,409 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02312,003,260 - 12,006,499 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2312,003,378 - 12,006,370 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12311,804,796 - 11,808,031 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02311,947,057 - 11,950,294 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02311,951,410 - 11,954,652 (+)NCBIUU_Cfam_GSD_1.0
Ss18l2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118200,165,497 - 200,169,181 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366952,517,698 - 2,521,467 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366952,517,840 - 2,521,504 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SS18L2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1326,108,434 - 26,112,759 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11326,108,287 - 26,112,625 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21328,775,531 - 28,779,380 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SS18L2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1224,038,276 - 4,046,447 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666041163,156,607 - 163,160,828 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ss18l2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473077,095,297 - 77,097,695 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473077,095,297 - 77,097,711 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ss18l2
4 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:106
Count of miRNA genes:84
Interacting mature miRNAs:94
Transcripts:ENSRNOT00000073376
Prediction methods:Microtar, 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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)876468691121468691Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat


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 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000073376   ⟹   ENSRNOP00000064507
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8121,375,308 - 121,377,877 (+)Ensembl
Rnor_6.0 Ensembl8130,350,510 - 130,353,140 (+)Ensembl
RefSeq Acc Id: NM_001398699   ⟹   NP_001385628
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88130,252,774 - 130,255,388 (+)NCBI
mRatBN7.28121,375,263 - 121,377,877 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001385628 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL76825 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000064507
  ENSRNOP00000064507.1
RefSeq Acc Id: ENSRNOP00000064507   ⟸   ENSRNOT00000073376
RefSeq Acc Id: NP_001385628   ⟸   NM_001398699
- UniProtKB: M0R551 (UniProtKB/TrEMBL),   A6I451 (UniProtKB/TrEMBL)
Protein Domains
SS18 N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R551-F1-model_v2 AlphaFold M0R551 1-77 view protein structure

Transcriptome

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

Promoters
RGD ID:13696390
Promoter ID:EPDNEW_R6914
Type:initiation region
Name:Ss18l2_1
Description:SS18 like 2
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_6.08130,350,536 - 130,350,596EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1590139 AgrOrtholog
BioCyc Gene G2FUF-28683 BioCyc
Ensembl Genes ENSRNOG00000047853 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000073376 ENTREZGENE
  ENSRNOT00000073376.3 UniProtKB/TrEMBL
InterPro SSXT UniProtKB/TrEMBL
KEGG Report rno:687029 UniProtKB/TrEMBL
NCBI Gene 687029 ENTREZGENE
Pfam SSXT UniProtKB/TrEMBL
PhenoGen Ss18l2 PhenoGen
RatGTEx ENSRNOG00000047853 RatGTEx
UniProt A6I451 ENTREZGENE, UniProtKB/TrEMBL
  A6I452_RAT UniProtKB/TrEMBL
  M0R551 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-05-04 Ss18l2  SS18 like 2  Ss18l2  synovial sarcoma translocation gene on chromosome 18-like 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-10-03 Ss18l2  synovial sarcoma translocation gene on chromosome 18-like 2  LOC687029  similar to differentially expressed in B16F10 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC687029  similar to differentially expressed in B16F10 1      Symbol and Name status set to provisional 70820 PROVISIONAL