Rspo4 (R-spondin 4) - Rat Genome Database

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Gene: Rspo4 (R-spondin 4) Rattus norvegicus
Analyze
Symbol: Rspo4
Name: R-spondin 4
RGD ID: 1563415
Description: Predicted to enable signaling receptor binding activity. Predicted to be involved in positive regulation of canonical Wnt signaling pathway. Predicted to act upstream of or within nail development. Predicted to be active in extracellular space. Human ortholog(s) of this gene implicated in nonsyndromic congenital nail disorder 4. Orthologous to human RSPO4 (R-spondin 4); PARTICIPATES IN Wnt signaling, canonical pathway; INTERACTS WITH 6-propyl-2-thiouracil; atrazine; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC499918; R-spondin family, member 4; R-spondin-4; RGD1563415; similar to OTTHUMP00000029946
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83160,817,611 - 160,852,071 (+)NCBIGRCr8
mRatBN7.23140,357,256 - 140,391,780 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3140,357,424 - 140,388,254 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.03147,358,690 - 147,391,719 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3147,358,858 - 147,389,698 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03153,710,530 - 153,741,899 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43142,185,028 - 142,216,015 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Cytogenetic Map3q41NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. The complex world of WNT receptor signalling. Niehrs C Nat Rev Mol Cell Biol. 2012 Dec;13(12):767-79. doi: 10.1038/nrm3470. Epub 2012 Nov 15.
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:17805348   PMID:29769720  


Genomics

Comparative Map Data
Rspo4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83160,817,611 - 160,852,071 (+)NCBIGRCr8
mRatBN7.23140,357,256 - 140,391,780 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3140,357,424 - 140,388,254 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.03147,358,690 - 147,391,719 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3147,358,858 - 147,389,698 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03153,710,530 - 153,741,899 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43142,185,028 - 142,216,015 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Cytogenetic Map3q41NCBI
RSPO4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3820958,452 - 1,002,311 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl20958,452 - 1,002,311 (-)EnsemblGRCh38hg38GRCh38
GRCh3720939,095 - 982,954 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3620887,095 - 930,904 (-)NCBINCBI36Build 36hg18NCBI36
Celera201,035,254 - 1,079,064 (-)NCBICelera
Cytogenetic Map20p13NCBI
HuRef20891,402 - 934,970 (-)NCBIHuRef
CHM1_120939,132 - 982,942 (-)NCBICHM1_1
T2T-CHM13v2.0201,005,419 - 1,049,278 (-)NCBIT2T-CHM13v2.0
Rspo4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392151,684,571 - 151,716,588 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2151,684,847 - 151,716,588 (+)EnsemblGRCm39 Ensembl
GRCm382151,842,647 - 151,874,668 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2151,842,927 - 151,874,668 (+)EnsemblGRCm38mm10GRCm38
MGSCv372151,668,663 - 151,700,404 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362151,534,368 - 151,564,918 (+)NCBIMGSCv36mm8
Celera2157,660,543 - 157,692,549 (+)NCBICelera
Cytogenetic Map2G3NCBI
cM Map274.83NCBI
Rspo4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955596265,466 - 295,116 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955596265,282 - 295,283 (-)NCBIChiLan1.0ChiLan1.0
RSPO4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2212,008,213 - 2,052,264 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1202,005,023 - 2,048,409 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0201,127,592 - 1,171,860 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.120897,774 - 907,772 (-)NCBIpanpan1.1PanPan1.1panPan2
RSPO4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12419,952,113 - 19,987,498 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2419,952,043 - 19,989,013 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2419,606,495 - 19,641,585 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02420,644,999 - 20,680,271 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2420,644,807 - 20,680,344 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12419,920,786 - 19,955,882 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02420,025,901 - 20,061,242 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02420,456,869 - 20,492,141 (+)NCBIUU_Cfam_GSD_1.0
Rspo4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640169,186,662 - 169,220,983 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648517,618,034 - 17,650,852 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648517,618,044 - 17,650,852 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RSPO4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1734,268,612 - 34,309,991 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11734,268,702 - 34,310,073 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21738,815,967 - 38,857,282 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RSPO4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1255,535,042 - 55,576,807 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl255,568,980 - 55,576,685 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660871,955,133 - 1,995,968 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rspo4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247412,252,489 - 2,255,603 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rspo4
118 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:129
Count of miRNA genes:93
Interacting mature miRNAs:97
Transcripts:ENSRNOT00000012951
Prediction methods:Microtar, Miranda, Rnahybrid
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
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3120538241165538241Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3137398739169034231Rat
1581568Rf53Renal function QTL 53urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3112681431157681431Rat
1300173Rf11Renal function QTL 113.38renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)3121056165145956249Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3122438700167438700Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)397084464142084464Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3127162703168026850Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3118839124163839124Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3107693393152693393Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3121056165157309487Rat
5686842Rf59Renal function QTL 59urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)3140069424146976080Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3130193298161695983Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
1581546Pur13Proteinuria QTL 132.930.0335urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)378196190146592722Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3138799500169034231Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)397551417147415807Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)395735366140735366Rat


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
nervous system
renal system
reproductive system
respiratory system
5 11 26 80 29 29 3 7 3 6 83 50 64 17 55 26

Sequence


Ensembl Acc Id: ENSRNOT00000012951   ⟹   ENSRNOP00000012951
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3140,357,424 - 140,388,254 (+)Ensembl
Rnor_6.0 Ensembl3147,358,858 - 147,389,698 (+)Ensembl
RefSeq Acc Id: XM_006235262   ⟹   XP_006235324
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83160,817,611 - 160,852,071 (+)NCBI
mRatBN7.23140,357,256 - 140,391,780 (+)NCBI
Rnor_6.03147,358,690 - 147,391,719 (+)NCBI
Rnor_5.03153,710,530 - 153,741,899 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063285081   ⟹   XP_063141151
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83160,817,611 - 160,852,071 (+)NCBI
Protein Sequences
Protein RefSeqs XP_006235324 (Get FASTA)   NCBI Sequence Viewer  
  XP_063141151 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000012951
  ENSRNOP00000012951.5
RefSeq Acc Id: XP_006235324   ⟸   XM_006235262
- Peptide Label: isoform X1
- UniProtKB: D4ACX0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000012951   ⟸   ENSRNOT00000012951
RefSeq Acc Id: XP_063141151   ⟸   XM_063285081
- Peptide Label: isoform X2
Protein Domains
R-spondin Fu-CRD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4ACX0-F1-model_v2 AlphaFold D4ACX0 1-228 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:1563415 AgrOrtholog
BioCyc Gene G2FUF-47299 BioCyc
Ensembl Genes ENSRNOG00000009662 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012951 ENTREZGENE
  ENSRNOT00000012951.7 UniProtKB/TrEMBL
Gene3D-CATH Hormone Receptor, Insulin-like Growth Factor Receptor 1, Chain A, domain 2 UniProtKB/TrEMBL
InterPro Furin_repeat UniProtKB/TrEMBL
  Growth_fac_rcpt UniProtKB/TrEMBL
  R-spondin UniProtKB/TrEMBL
  Rspo_Fu-CRD_dom UniProtKB/TrEMBL
  Thrombospondin_1_rpt UniProtKB/TrEMBL
KEGG Report rno:499918 UniProtKB/TrEMBL
NCBI Gene 499918 ENTREZGENE
PANTHER NEUROHYPOPHYSIAL HORMONES, N-TERMINAL DOMAIN CONTAINING PROTEIN UniProtKB/TrEMBL
  R-SPONDIN-4 UniProtKB/TrEMBL
Pfam Furin-like_2 UniProtKB/TrEMBL
PhenoGen Rspo4 PhenoGen
PROSITE TSP1 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000009662 RatGTEx
SMART SM00261 UniProtKB/TrEMBL
  TSP1 UniProtKB/TrEMBL
Superfamily-SCOP Grow_fac_recept UniProtKB/TrEMBL
UniProt D4ACX0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-01 Rspo4  R-spondin 4  Rspo4  R-spondin family, member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Rspo4  R-spondin family, member 4  RGD1563415_predicted  similar to OTTHUMP00000029946 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1563415_predicted  similar to OTTHUMP00000029946 (predicted)  LOC499918  similar to OTTHUMP00000029946  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC499918  similar to OTTHUMP00000029946      Symbol and Name status set to provisional 70820 PROVISIONAL