Synpo2l (synaptopodin 2-like) - Rat Genome Database

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Gene: Synpo2l (synaptopodin 2-like) Rattus norvegicus
Analyze
Symbol: Synpo2l
Name: synaptopodin 2-like
RGD ID: 1565434
Description: Predicted to enable actin binding activity. Predicted to be involved in several processes, including positive regulation of Rho protein signal transduction; positive regulation of stress fiber assembly; and sarcomere organization. Predicted to be active in Z disc; actin cytoskeleton; and nucleus. Orthologous to human SYNPO2L (synaptopodin 2 like); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; alpha-Zearalanol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC305675; RGD1565434; similar to synaptopodin 2-like; synaptopodin 2-like protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8153,681,224 - 3,690,673 (+)NCBIGRCr8
mRatBN7.2153,631,974 - 3,641,429 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl153,631,834 - 3,641,429 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx153,642,161 - 3,651,606 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0155,028,637 - 5,038,079 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0153,640,972 - 3,650,415 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0154,064,706 - 4,074,151 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl154,064,706 - 4,072,635 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0158,165,795 - 8,175,373 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4153,857,420 - 3,865,349 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera15952,778 - 962,215 (-)NCBICelera
Cytogenetic Map15p16NCBI
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

Cellular Component
actin cytoskeleton  (IBA)
nucleus  (IBA,ISO)
Z disc  (IBA,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. 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
Additional References at PubMed
PMID:20215401   PMID:29206857   PMID:35352799  


Genomics

Comparative Map Data
Synpo2l
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8153,681,224 - 3,690,673 (+)NCBIGRCr8
mRatBN7.2153,631,974 - 3,641,429 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl153,631,834 - 3,641,429 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx153,642,161 - 3,651,606 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0155,028,637 - 5,038,079 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0153,640,972 - 3,650,415 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0154,064,706 - 4,074,151 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl154,064,706 - 4,072,635 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0158,165,795 - 8,175,373 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4153,857,420 - 3,865,349 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera15952,778 - 962,215 (-)NCBICelera
Cytogenetic Map15p16NCBI
SYNPO2L
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381073,644,886 - 73,656,029 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1073,644,881 - 73,663,803 (-)EnsemblGRCh38hg38GRCh38
GRCh371075,404,644 - 75,415,787 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361075,075,296 - 75,080,793 (-)NCBINCBI36Build 36hg18NCBI36
Build 341075,075,295 - 75,080,793NCBI
Celera1068,690,238 - 68,701,428 (-)NCBICelera
Cytogenetic Map10q22.2NCBI
HuRef1069,398,153 - 69,409,343 (-)NCBIHuRef
CHM1_11075,686,395 - 75,697,582 (-)NCBICHM1_1
T2T-CHM13v2.01074,516,308 - 74,527,453 (-)NCBIT2T-CHM13v2.0
Synpo2l
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391420,709,013 - 20,718,422 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1420,709,014 - 20,718,422 (-)EnsemblGRCm39 Ensembl
GRCm381420,658,945 - 20,668,354 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1420,658,946 - 20,668,354 (-)EnsemblGRCm38mm10GRCm38
MGSCv371421,478,640 - 21,487,528 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361419,447,970 - 19,456,858 (-)NCBIMGSCv36mm8
Celera1417,042,162 - 17,051,061 (-)NCBICelera
Cytogenetic Map14A3NCBI
cM Map1411.53NCBI
Synpo2l
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543718,177,867 - 18,188,983 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543718,177,867 - 18,186,772 (+)NCBIChiLan1.0ChiLan1.0
SYNPO2L
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2885,820,535 - 85,831,913 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11085,825,857 - 85,840,508 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01070,192,289 - 70,204,008 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11072,648,952 - 72,660,184 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1072,648,952 - 72,660,184 (-)Ensemblpanpan1.1panPan2
SYNPO2L
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1424,168,030 - 24,177,710 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl424,169,707 - 24,177,813 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha424,305,570 - 24,315,236 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0424,448,146 - 24,457,808 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl424,448,151 - 24,464,766 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1424,345,386 - 24,355,030 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0424,545,915 - 24,555,569 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0424,900,946 - 24,910,606 (-)NCBIUU_Cfam_GSD_1.0
Synpo2l
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721356,913,572 - 56,925,652 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365215,407,754 - 5,418,368 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365215,407,767 - 5,418,368 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYNPO2L
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1476,456,168 - 76,466,641 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11476,456,170 - 76,466,661 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21482,583,031 - 82,593,284 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SYNPO2L
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1957,629,836 - 57,650,458 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl957,631,111 - 57,646,400 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604818,212,812 - 18,223,759 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Synpo2l
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247547,247,838 - 7,255,815 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247547,245,825 - 7,255,926 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Synpo2l
21 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:44
Count of miRNA genes:40
Interacting mature miRNAs:43
Transcripts:ENSRNOT00000011956
Prediction methods: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
1354657Despr13Despair related QTL 130.0022locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)15129912054Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15134723002Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15134723002Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15134723002Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
5684946Bss98Bone structure and strength QTL 983.90.0026tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)15105825014481294Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)colorectal tumor number (CMO:0001794)15226636822711984Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)15226636822711984Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat

Markers in Region
Synpo2l  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2153,635,694 - 3,635,844 (+)MAPPERmRatBN7.2
Rnor_6.0154,068,427 - 4,068,576NCBIRnor6.0
Rnor_5.0158,169,645 - 8,169,794UniSTSRnor5.0
RGSC_v3.4153,861,141 - 3,861,290UniSTSRGSC3.4
Celera15958,345 - 958,494UniSTS
Cytogenetic Map15p16UniSTS


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 43 8 11 8
Low 8 8 8 36 34 29 8
Below cutoff 2 32 16 18 16 38 1 12 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000011956   ⟹   ENSRNOP00000011956
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl153,631,834 - 3,641,429 (+)Ensembl
Rnor_6.0 Ensembl154,064,706 - 4,072,635 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000118985   ⟹   ENSRNOP00000081435
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl153,635,667 - 3,641,429 (+)Ensembl
RefSeq Acc Id: NM_001305138   ⟹   NP_001292067
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8153,681,224 - 3,690,673 (+)NCBI
mRatBN7.2153,631,974 - 3,641,429 (+)NCBI
Rnor_6.0154,064,706 - 4,074,151 (+)NCBI
Celera15952,778 - 962,215 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001305139   ⟹   NP_001292068
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8153,685,010 - 3,690,673 (+)NCBI
mRatBN7.2153,635,760 - 3,641,429 (+)NCBI
Rnor_6.0154,068,492 - 4,074,151 (+)NCBI
Celera15952,778 - 958,429 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039093229   ⟹   XP_038949157
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8153,685,123 - 3,690,672 (+)NCBI
mRatBN7.2153,635,873 - 3,641,428 (+)NCBI
RefSeq Acc Id: XM_039093230   ⟹   XP_038949158
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8153,685,123 - 3,690,672 (+)NCBI
mRatBN7.2153,635,873 - 3,641,428 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001292067   ⟸   NM_001305138
- Peptide Label: isoform 1
- UniProtKB: D3ZZ68 (UniProtKB/TrEMBL),   A6KKP4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001292068   ⟸   NM_001305139
- Peptide Label: isoform 2
- UniProtKB: A0A8I5ZSY9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000011956   ⟸   ENSRNOT00000011956
RefSeq Acc Id: XP_038949158   ⟸   XM_039093230
- Peptide Label: isoform X1
- UniProtKB: A6KKP5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038949157   ⟸   XM_039093229
- Peptide Label: isoform X1
- UniProtKB: A6KKP5 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000081435   ⟸   ENSRNOT00000118985
Protein Domains
PDZ

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZZ68-F1-model_v2 AlphaFold D3ZZ68 1-978 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:1565434 AgrOrtholog
BioCyc Gene G2FUF-14551 BioCyc
Ensembl Genes ENSRNOG00000008949 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000011956 ENTREZGENE
  ENSRNOT00000011956.5 UniProtKB/TrEMBL
  ENSRNOT00000118985 ENTREZGENE
  ENSRNOT00000118985.1 UniProtKB/TrEMBL
Gene3D-CATH 2.30.42.10 UniProtKB/TrEMBL
InterPro PDZ/DHR/GLGF UniProtKB/TrEMBL
  PDZ_sf UniProtKB/TrEMBL
KEGG Report rno:305675 UniProtKB/TrEMBL
NCBI Gene 305675 ENTREZGENE
PANTHER PUTATIVE-RELATED UniProtKB/TrEMBL
  SYNAPTOPODIN 2-LIKE PROTEIN UniProtKB/TrEMBL
Pfam PDZ UniProtKB/TrEMBL
PhenoGen Synpo2l PhenoGen
PROSITE PDZ UniProtKB/TrEMBL
RatGTEx ENSRNOG00000008949 RatGTEx
SMART PDZ UniProtKB/TrEMBL
Superfamily-SCOP PDZ UniProtKB/TrEMBL
UniProt A0A8I5ZSY9 ENTREZGENE, UniProtKB/TrEMBL
  A6KKP4 ENTREZGENE, UniProtKB/TrEMBL
  A6KKP5 ENTREZGENE, UniProtKB/TrEMBL
  D3ZZ68 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-06 Synpo2l  synaptopodin 2-like  RGD1565434_predicted  similar to synaptopodin 2-like (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1565434_predicted  similar to synaptopodin 2-like (predicted)  LOC305675  similar to synaptopodin 2-like  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC305675  similar to synaptopodin 2-like      Symbol and Name status set to provisional 70820 PROVISIONAL