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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88130,252,774 - 130,255,388 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl8130,252,782 - 130,257,367 (+)EnsemblGRCr8
mRatBN7.28121,375,263 - 121,377,877 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8121,375,308 - 121,377,877 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx8126,974,437 - 126,977,057 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08125,173,506 - 125,176,126 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08123,002,662 - 123,005,276 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.08130,350,504 - 130,353,126 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8130,350,510 - 130,353,140 (+)Ensemblrn6Rnor6.0
Rnor_5.08129,530,974 - 129,533,603 (+)NCBIRnor_5.0Rnor_5.0rn5
Celera8120,509,704 - 120,512,326 (+)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse:




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 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl8130,252,782 - 130,257,367 (+)EnsemblGRCr8
mRatBN7.28121,375,263 - 121,377,877 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8121,375,308 - 121,377,877 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx8126,974,437 - 126,977,057 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08125,173,506 - 125,176,126 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08123,002,662 - 123,005,276 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.08130,350,504 - 130,353,126 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8130,350,510 - 130,353,140 (+)Ensemblrn6Rnor6.0
Rnor_5.08129,530,974 - 129,533,603 (+)NCBIRnor_5.0Rnor_5.0rn5
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 (+)Ensemblhg38GRCh38
GRCh37342,623,332 - 42,638,426 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36342,607,302 - 42,611,494 (+)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm389121,710,389 - 121,712,921 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9121,710,329 - 121,713,388 (+)Ensemblmm10GRCm38
MGSCv379121,619,507 - 121,622,039 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
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 (-)Ensembl
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 (+)EnsemblpanPan2panpan1.1
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 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2311,688,171 - 11,691,409 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02312,003,260 - 12,006,499 (+)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 (-)EnsemblSpeTri2.0 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 (+)EnsemblsusScr11Sscrofa11.1
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462473077,095,297 - 77,097,711 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Ss18l2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v18112,871,388 - 112,875,985 (+)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)8102413464132782436Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)8105462581132782436Rat
634332Pia18Pristane induced arthritis QTL 184joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)884192326132782436Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)885348065130348065Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)879394435132782436Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)891340911131690273Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl 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
Ensembl Acc Id: ENSRNOT00000139677   ⟹   ENSRNOP00000104725
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl8130,252,782 - 130,257,367 (+)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 ENSRNOP00000104725
  ENSRNOP00000104725.1
Ensembl Acc Id: ENSRNOP00000064507   ⟸   ENSRNOT00000073376
RefSeq Acc Id: NP_001385628   ⟸   NM_001398699
- UniProtKB: M0R551 (UniProtKB/TrEMBL),   A6I451 (UniProtKB/TrEMBL),   A6I452 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000104725   ⟸   ENSRNOT00000139677
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
  ENSRNOG00000076482 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000139677 ENTREZGENE
  ENSRNOT00000139677.1 UniProtKB/TrEMBL
InterPro SSXT UniProtKB/TrEMBL
NCBI Gene 687029 ENTREZGENE
Pfam SSXT UniProtKB/TrEMBL
PhenoGen Ss18l2 PhenoGen
RatGTEx ENSRNOG00000047853 RatGTEx
  ENSRNOG00000076482 RatGTEx
UniProt A0ABK0LGS2_RAT UniProtKB/TrEMBL
  A6I451 ENTREZGENE, UniProtKB/TrEMBL
  A6I452 ENTREZGENE, UniProtKB/TrEMBL
  M0R551 ENTREZGENE


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