Spryd4 (SPRY domain containing 4) - Rat Genome Database

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Gene: Spryd4 (SPRY domain containing 4) Rattus norvegicus
Analyze
Symbol: Spryd4
Name: SPRY domain containing 4
RGD ID: 1306649
Description: Predicted to be involved in regulation of microtubule cytoskeleton organization. Predicted to be located in nucleus. Predicted to be active in cytoplasm. Orthologous to human SPRYD4 (SPRY domain containing 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC288772; MGC116283; RGD1306649; similar to RIKEN cDNA 4633402N23 gene; SPRY domain-containing protein 4
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
mRatBN7.27633,400 - 637,564 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7633,394 - 637,557 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx73,391,989 - 3,393,809 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.075,268,005 - 5,269,825 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.075,569,826 - 5,571,646 (-)NCBIRnor_WKY
Rnor_6.072,621,960 - 2,625,982 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl72,621,961 - 2,623,781 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.072,600,836 - 2,604,858 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.471,495,475 - 1,497,060 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.171,495,959 - 1,497,054 (-)NCBI
Celera7512,078 - 513,899 (-)NCBICelera
Cytogenetic Map7q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Biological Process

Cellular Component
cytoplasm  (IBA)
membrane  (IEA)
nucleus  (ISO,ISS)

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
Additional References at PubMed
PMID:12477932   PMID:15489334   PMID:17852359   PMID:18614015  


Genomics

Comparative Map Data
Spryd4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27633,400 - 637,564 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7633,394 - 637,557 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx73,391,989 - 3,393,809 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.075,268,005 - 5,269,825 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.075,569,826 - 5,571,646 (-)NCBIRnor_WKY
Rnor_6.072,621,960 - 2,625,982 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl72,621,961 - 2,623,781 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.072,600,836 - 2,604,858 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.471,495,475 - 1,497,060 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.171,495,959 - 1,497,054 (-)NCBI
Celera7512,078 - 513,899 (-)NCBICelera
Cytogenetic Map7q11NCBI
SPRYD4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381256,468,578 - 56,479,708 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1256,468,578 - 56,479,708 (+)EnsemblGRCh38hg38GRCh38
GRCh371256,862,362 - 56,873,492 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361255,148,629 - 55,150,067 (+)NCBINCBI36Build 36hg18NCBI36
Celera1256,515,670 - 56,518,138 (+)NCBICelera
Cytogenetic Map12q13.3NCBI
HuRef1253,901,342 - 53,903,812 (+)NCBIHuRef
CHM1_11256,829,960 - 56,832,430 (+)NCBICHM1_1
T2T-CHM13v2.01256,436,289 - 56,447,410 (+)NCBIT2T-CHM13v2.0
Spryd4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910128,045,777 - 128,047,663 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl10128,045,777 - 128,047,676 (-)EnsemblGRCm39 Ensembl
GRCm3810128,209,908 - 128,211,794 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10128,209,908 - 128,211,807 (-)EnsemblGRCm38mm10GRCm38
MGSCv3710127,646,964 - 127,648,850 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3610127,612,857 - 127,614,743 (-)NCBIMGSCv36mm8
Celera10130,604,745 - 130,606,633 (-)NCBICelera
Cytogenetic Map10D3NCBI
Spryd4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554584,051,978 - 4,053,734 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554584,051,978 - 4,053,734 (+)NCBIChiLan1.0ChiLan1.0
SPRYD4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11232,696,661 - 32,699,160 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1232,696,670 - 32,699,160 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01232,443,657 - 32,446,127 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SPRYD4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.110720,099 - 722,139 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl10720,046 - 722,119 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha10783,303 - 785,354 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.010729,070 - 731,121 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl10729,026 - 732,353 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.110706,134 - 708,185 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.010949,239 - 951,290 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0101,072,964 - 1,075,015 (+)NCBIUU_Cfam_GSD_1.0
Spryd4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494558,044,244 - 58,046,508 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936646823,682 - 828,266 (+)EnsemblSpeTri2.0
SpeTri2.0NW_004936646823,724 - 825,659 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SPRYD4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl521,804,394 - 21,816,681 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1521,804,345 - 21,816,760 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2523,527,854 - 23,529,936 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SPRYD4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11152,427,903 - 52,429,407 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1152,427,919 - 52,428,958 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037193,552,056 - 193,554,563 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Spryd4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462480211,559,820 - 11,561,942 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462480211,559,817 - 11,561,852 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Spryd4
15 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:162
Count of miRNA genes:107
Interacting mature miRNAs:133
Transcripts:ENSRNOT00000004173
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
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat

Markers in Region
RH130821  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27633,186 - 633,377 (+)MAPPERmRatBN7.2
Rnor_6.072,621,616 - 2,621,806NCBIRnor6.0
Rnor_5.072,600,492 - 2,600,682UniSTSRnor5.0
RGSC_v3.471,495,050 - 1,495,240UniSTSRGSC3.4
Celera7511,734 - 511,924UniSTS
Cytogenetic Map7q11UniSTS
RH141440  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27633,754 - 633,944 (+)MAPPERmRatBN7.2
Rnor_6.072,622,184 - 2,622,373NCBIRnor6.0
Rnor_5.072,601,060 - 2,601,249UniSTSRnor5.0
Celera7512,302 - 512,491UniSTS
Cytogenetic Map7q11UniSTS


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 56 41 18 41 8 11 70 35 41 11 8
Low 1 1 4
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000004173   ⟹   ENSRNOP00000004173
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7633,394 - 635,379 (-)Ensembl
Rnor_6.0 Ensembl72,621,961 - 2,623,781 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000106511   ⟹   ENSRNOP00000090225
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7633,419 - 637,557 (-)Ensembl
RefSeq Acc Id: NM_001037765   ⟹   NP_001032854
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27633,531 - 635,352 (-)NCBI
Rnor_6.072,621,960 - 2,623,781 (-)NCBI
Rnor_5.072,600,836 - 2,604,858 (-)NCBI
RGSC_v3.471,495,475 - 1,497,060 (-)RGD
Celera7512,078 - 513,899 (-)RGD
Sequence:
RefSeq Acc Id: XM_006240746   ⟹   XP_006240808
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27633,400 - 637,564 (-)NCBI
Rnor_6.072,621,960 - 2,625,982 (-)NCBI
Rnor_5.072,600,836 - 2,604,858 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001032854 (Get FASTA)   NCBI Sequence Viewer  
  XP_006240808 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH99138 (Get FASTA)   NCBI Sequence Viewer  
  EDL84883 (Get FASTA)   NCBI Sequence Viewer  
  Q4FZT8 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001032854   ⟸   NM_001037765
- UniProtKB: Q4FZT8 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006240808   ⟸   XM_006240746
- Peptide Label: isoform X1
- UniProtKB: Q4FZT8 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000004173   ⟸   ENSRNOT00000004173
RefSeq Acc Id: ENSRNOP00000090225   ⟸   ENSRNOT00000106511
Protein Domains
B30.2/SPRY

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q4FZT8-F1-model_v2 AlphaFold Q4FZT8 1-207 view protein structure

Transcriptome

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

Promoters
RGD ID:13694927
Promoter ID:EPDNEW_R5452
Type:multiple initiation site
Name:Spryd4_1
Description:SPRY domain containing 4
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_6.072,623,780 - 2,623,840EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306649 AgrOrtholog
BioCyc Gene G2FUF-35389 BioCyc
Ensembl Genes ENSRNOG00000003127 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000004173 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000090225.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000004173 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000106511.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.920 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7456187 IMAGE-MGC_LOAD
InterPro B30.2/SPRY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  B30.2/SPRY_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Butyrophylin_SPRY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ConA-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SPRY_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:288772 UniProtKB/Swiss-Prot
MGC_CLONE MGC:116283 IMAGE-MGC_LOAD
NCBI Gene 288772 ENTREZGENE
Pfam SPRY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Spryd4 PhenoGen
PRINTS BUTYPHLNCDUF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE B302_SPRY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SPRY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49899 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6AD59_RAT UniProtKB/TrEMBL
  Q4FZT8 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Spryd4  SPRY domain containing 4  RGD1306649  similar to RIKEN cDNA 4633402N23 gene  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1306649  similar to RIKEN cDNA 4633402N23 gene  RGD1306649_predicted  similar to RIKEN cDNA 4633402N23 gene (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1306649_predicted  similar to RIKEN cDNA 4633402N23 gene (predicted)  LOC288772_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC288772_predicted  similar to RIKEN cDNA 4633402N23 gene (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL