Pspn (persephin) - Rat Genome Database

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Gene: Pspn (persephin) Rattus norvegicus
Analyze
Symbol: Pspn
Name: persephin
RGD ID: 3432
Description: Predicted to enable growth factor activity. Predicted to be involved in glial cell-derived neurotrophic factor receptor signaling pathway and peripheral nervous system development. Predicted to act upstream of or within branching involved in ureteric bud morphogenesis. Predicted to be located in extracellular region. Predicted to be active in extracellular space. Orthologous to human PSPN (persephin); INTERACTS WITH ammonium chloride; bexarotene; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: PSP
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
GRCr891,927,911 - 1,930,785 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl91,927,911 - 1,928,752 (-)EnsemblGRCr8
mRatBN7.291,840,906 - 1,841,748 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl91,840,896 - 1,854,327 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx92,274,986 - 2,275,544 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.097,624,345 - 7,624,903 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.096,580,207 - 6,580,765 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0910,044,756 - 10,045,314 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl910,044,756 - 10,045,314 (+)Ensemblrn6Rnor6.0
Rnor_5.099,045,406 - 9,045,964 (+)NCBIRnor_5.0Rnor_5.0rn5
Celera96,675,626 - 6,676,184 (+)NCBICelera
Cytogenetic Map9q11NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
extracellular region  (IEA)
extracellular space  (IBA,IEA,ISO,ISS)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Persephin-overexpressing neural stem cells regulate the function of nigral dopaminergic neurons and prevent their degeneration in a model of Parkinson's disease. Akerud P, etal., Mol Cell Neurosci 2002 Oct;21(2):205-22.
2. 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.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. Persephin, a novel neurotrophic factor related to GDNF and neurturin. Milbrandt J, etal., Neuron 1998 Feb;20(2):245-53.
6. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
7. GOA pipeline RGD automated data pipeline
8. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9710270   PMID:10719212   PMID:16325003   PMID:20350599  


Genomics

Comparative Map Data
Pspn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr891,927,911 - 1,930,785 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl91,927,911 - 1,928,752 (-)EnsemblGRCr8
mRatBN7.291,840,906 - 1,841,748 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl91,840,896 - 1,854,327 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx92,274,986 - 2,275,544 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.097,624,345 - 7,624,903 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.096,580,207 - 6,580,765 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0910,044,756 - 10,045,314 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl910,044,756 - 10,045,314 (+)Ensemblrn6Rnor6.0
Rnor_5.099,045,406 - 9,045,964 (+)NCBIRnor_5.0Rnor_5.0rn5
Celera96,675,626 - 6,676,184 (+)NCBICelera
Cytogenetic Map9q11NCBI
PSPN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38196,375,148 - 6,375,933 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl196,375,148 - 6,379,058 (-)Ensemblhg38GRCh38
GRCh37196,375,159 - 6,375,944 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36196,326,305 - 6,326,860 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34196,326,304 - 6,326,860NCBI
Celera196,314,092 - 6,314,647 (-)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef196,135,450 - 6,136,005 (-)NCBIHuRef
CHM1_1196,374,930 - 6,375,485 (-)NCBICHM1_1
T2T-CHM13v2.0196,364,050 - 6,364,835 (-)NCBIT2T-CHM13v2.0
Pspn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391757,306,253 - 57,307,105 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1757,306,457 - 57,307,018 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381756,999,313 - 57,000,105 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1756,999,457 - 57,000,018 (-)Ensemblmm10GRCm38
MGSCv371757,138,880 - 57,139,441 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361756,684,581 - 56,685,139 (-)NCBIMGSCv36mm8
Celera1761,347,383 - 61,347,944 (-)NCBICelera
Cytogenetic Map17DNCBI
cM Map1729.62NCBI
Pspn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554953,220,239 - 3,220,800 (+)Ensembl
ChiLan1.0NW_0049554953,218,720 - 3,220,941 (+)NCBIChiLan1.0ChiLan1.0
PSPN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22010,775,852 - 10,776,664 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11910,001,783 - 10,002,611 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0195,396,022 - 5,398,108 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1196,318,428 - 6,320,344 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl196,318,428 - 6,320,344 (-)EnsemblpanPan2panpan1.1
PSPN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12053,780,895 - 53,783,876 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2053,783,171 - 53,783,696 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2053,529,886 - 53,530,605 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02054,437,246 - 54,437,964 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2054,437,440 - 54,437,964 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12053,503,708 - 53,504,427 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02053,952,047 - 53,952,766 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02054,181,799 - 54,182,517 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Pspn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118214,099,050 - 214,099,899 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365883,735,027 - 3,735,587 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365883,734,821 - 3,735,766 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PSPN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl272,701,099 - 72,701,958 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1272,698,413 - 72,701,974 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2273,213,561 - 73,215,664 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PSPN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.165,991,311 - 5,993,397 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660812,029,899 - 2,032,071 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pspn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248283,509,400 - 3,510,132 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Pspn
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1488,380,512 - 88,381,486 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Pspn
7 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:41
Count of miRNA genes:37
Interacting mature miRNAs:40
Transcripts:ENSRNOT00000071188
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631533Iresp3Immunoglobin response QTL316.2blood immunoglobulin E amount (VT:0002492)serum immunoglobulin E level (CMO:0002101)916094576Rat
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9121707400Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)949664545496645Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)949664545496645Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)9131250552Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)949664545496645Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9141763315Rat


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 65 158 90 89 58 84 58 6 341 182 10 137 77 92 31 15 15

Sequence


Ensembl Acc Id: ENSRNOT00000071188   ⟹   ENSRNOP00000065156
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl910,044,756 - 10,045,314 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000114711   ⟹   ENSRNOP00000077509
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,840,896 - 1,854,327 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000132641   ⟹   ENSRNOP00000104957
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl91,927,911 - 1,928,752 (-)Ensembl
RefSeq Acc Id: NM_013014   ⟹   NP_037146
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr891,927,911 - 1,928,752 (-)NCBI
mRatBN7.291,840,906 - 1,841,748 (-)NCBI
Rnor_6.0910,044,756 - 10,045,314 (+)NCBI
Rnor_5.099,045,406 - 9,045,964 (+)NCBI
Celera96,675,626 - 6,676,184 (+)RGD
Sequence:
RefSeq Acc Id: XM_063266696   ⟹   XP_063122766
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr891,927,911 - 1,930,785 (-)NCBI
Protein Sequences
Protein RefSeqs NP_037146 (Get FASTA)   NCBI Sequence Viewer  
  XP_063122766 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAC40058 (Get FASTA)   NCBI Sequence Viewer  
  CAA06410 (Get FASTA)   NCBI Sequence Viewer  
  EDL83593 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000077509.1
  ENSRNOP00000104957
GenBank Protein O70301 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_037146   ⟸   NM_013014
- Peptide Label: precursor
- UniProtKB: O70301 (UniProtKB/Swiss-Prot),   A6KQT5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000065156   ⟸   ENSRNOT00000071188
Ensembl Acc Id: ENSRNOP00000077509   ⟸   ENSRNOT00000114711
RefSeq Acc Id: XP_063122766   ⟸   XM_063266696
- Peptide Label: isoform X1
- UniProtKB: O70301 (UniProtKB/Swiss-Prot),   A6KQT5 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000104957   ⟸   ENSRNOT00000132641
Protein Domains
TGF-beta family profile

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O70301-F1-model_v2 AlphaFold O70301 1-156 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:3432 AgrOrtholog
BioCyc Gene G2FUF-28498 BioCyc
Ensembl Genes ENSRNOG00000049171 Ensembl
  ENSRNOG00000071190 Ensembl, UniProtKB/Swiss-Prot
  ENSRNOG00000081220 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000114711.1 UniProtKB/Swiss-Prot
  ENSRNOT00000132641 ENTREZGENE
Gene3D-CATH 2.10.90.10 UniProtKB/Swiss-Prot
InterPro Cystine-knot_cytokine UniProtKB/Swiss-Prot
  GDNF_fam UniProtKB/Swiss-Prot
  TGF-b_C UniProtKB/Swiss-Prot
KEGG Report rno:25525 UniProtKB/Swiss-Prot
NCBI Gene 25525 ENTREZGENE
PANTHER PERSEPHIN UniProtKB/Swiss-Prot
  PTHR12173 UniProtKB/Swiss-Prot
Pfam TGF_beta UniProtKB/Swiss-Prot
PhenoGen Pspn PhenoGen
PROSITE TGF_BETA_2 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000049171 RatGTEx
  ENSRNOG00000071190 RatGTEx
  ENSRNOG00000081220 RatGTEx
Superfamily-SCOP SSF57501 UniProtKB/Swiss-Prot
UniProt A6KQT5 ENTREZGENE, UniProtKB/TrEMBL
  O70301 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Pspn  Persephin      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_product member of the glial cell line-derived neurotrophic factor (GDNF) family 727462