Spdef (SAM pointed domain containing ets transcription factor) - Rat Genome Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  FTP Download |  REST API |  Citing RGD |  Contact   
Gene: Spdef (SAM pointed domain containing ets transcription factor) Mus musculus
Analyze
Symbol: Spdef
Name: SAM pointed domain containing ets transcription factor
RGD ID: 1318474
MGI Page MGI
Description: Predicted to have DNA-binding transcription factor activity, RNA polymerase II-specific and sequence-specific double-stranded DNA binding activity. Involved in columnar/cuboidal epithelial cell differentiation; regulation of cell fate commitment; and regulation of transcription by RNA polymerase II. Localizes to nucleus. Is expressed in several structures, including alimentary system; brain; genitourinary system; integumental system; and sensory organ. Orthologous to human SPDEF (SAM pointed domain containing ETS transcription factor); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-sulfonyldiphenol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: P; PDE; PDEF; prostate epithelium-specific Ets transcription factor; prostate specific ets transcription factor; prostate-derived Ets factor; prostate-specific Ets; Pse; SAM pointed domain-containing Ets transcription factor
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391727,933,416 - 27,949,977 (-)NCBIGRCm39mm39
GRCm381727,714,446 - 27,731,003 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1727,714,352 - 27,728,955 (-)EnsemblGRCm38mm10GRCm38
MGSCv371727,851,392 - 27,865,896 (-)NCBIGRCm37mm9NCBIm37
MGSCv361727,442,039 - 27,456,509 (-)NCBImm8
Celera1728,266,225 - 28,280,705 (-)NCBICelera
Cytogenetic Map17A3.3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

Additional References at PubMed
PMID:10349636   PMID:10675039   PMID:10922068   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12477932   PMID:14681479   PMID:15489334   PMID:16141072   PMID:16141073   PMID:16230531  
PMID:16971476   PMID:17347682   PMID:17609113   PMID:17907201   PMID:18287559   PMID:18554416   PMID:19549527   PMID:19759516   PMID:19786015   PMID:20059953   PMID:20139077   PMID:20211142  
PMID:20412781   PMID:20610757   PMID:20801882   PMID:20932939   PMID:21126757   PMID:21267068   PMID:21383077   PMID:21398290   PMID:21677750   PMID:21791528   PMID:21873635   PMID:22056786  
PMID:22675208   PMID:23213461   PMID:23376423   PMID:23665202   PMID:24146773   PMID:24472151   PMID:24929016   PMID:24952961   PMID:25254494   PMID:25772331   PMID:25866971   PMID:28390865  
PMID:29415888   PMID:29477409   PMID:29579396   PMID:29848555   PMID:30010888   PMID:31524632   PMID:31776260  


Genomics

Comparative Map Data
Spdef
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391727,933,416 - 27,949,977 (-)NCBIGRCm39mm39
GRCm381727,714,446 - 27,731,003 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1727,714,352 - 27,728,955 (-)EnsemblGRCm38mm10GRCm38
MGSCv371727,851,392 - 27,865,896 (-)NCBIGRCm37mm9NCBIm37
MGSCv361727,442,039 - 27,456,509 (-)NCBImm8
Celera1728,266,225 - 28,280,705 (-)NCBICelera
Cytogenetic Map17A3.3NCBI
SPDEF
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl634,537,802 - 34,556,333 (-)EnsemblGRCh38hg38GRCh38
GRCh38634,537,800 - 34,556,329 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37634,505,579 - 34,524,106 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh37634,505,579 - 34,524,110 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36634,613,558 - 34,632,069 (-)NCBINCBI36hg18NCBI36
Build 34634,613,557 - 34,632,069NCBI
Celera636,059,916 - 36,078,425 (-)NCBI
Cytogenetic Map6p21.31NCBI
HuRef634,228,203 - 34,246,732 (-)NCBIHuRef
CHM1_1634,508,569 - 34,527,078 (-)NCBICHM1_1
Spdef
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2205,771,434 - 5,786,793 (-)NCBI
Rnor_6.0 Ensembl207,292,824 - 7,307,284 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0207,292,823 - 7,308,053 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0209,495,168 - 9,509,674 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4205,927,866 - 5,942,091 (-)NCBIRGSC3.4rn4RGSC3.4
Celera207,333,751 - 7,348,087 (-)NCBICelera
Cytogenetic Map20p12NCBI
Spdef
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554372,666,105 - 2,680,061 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554372,667,499 - 2,679,940 (-)NCBIChiLan1.0ChiLan1.0
SPDEF
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1635,202,983 - 35,209,639 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl635,202,983 - 35,209,639 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0634,102,610 - 34,140,800 (-)NCBIMhudiblu_PPA_v0panPan3
SPDEF
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl123,815,300 - 3,831,477 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1123,814,806 - 3,831,724 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Spdef
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493647624,563,591 - 24,571,739 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SPDEF
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl730,515,925 - 30,524,595 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1730,515,925 - 30,538,095 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2735,214,369 - 35,233,199 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SPDEF
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11737,555,797 - 37,562,522 (+)NCBI
ChlSab1.1 Ensembl1737,555,820 - 37,562,036 (+)Ensembl
Spdef
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475422,714,181 - 22,721,113 (+)NCBI

Position Markers
Spdef  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map17B1UniSTS
cM Map17 UniSTS
MARC_21610-21611:1033065458:1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381727,717,265 - 27,718,103UniSTSGRCm38
MGSCv371727,854,210 - 27,855,048UniSTSGRCm37
Celera1728,269,039 - 28,269,877UniSTS
Cytogenetic Map17B1UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1302100Circp2_mcircadian photosensitivity 2 (mouse)Not determined17128979566Mouse
12910527Nrq1a_mnoise-induced hearing loss resistant QTL 1a (mouse)17128979566Mouse
12910528Nrq1_mnoise-induced hearing loss resistant QTL 1 (mouse)17128979566Mouse
13524851Asrq8_macoustic startle response 8 (mouse)17130809908Mouse
10412276Leci2_mleukocyte endothelial cell interactions 2 (mouse)Not determined17312791337128037Mouse
1300890Bhr3_mbronchial hyperresponsiveness 3 (mouse)Not determined17392461548559063Mouse
4141215Mnic1_mmacronutrient intake, carbohydrate 1 (mouse)Not determined480447745359340Mouse
1300706Alan1_malloantigen response 1 (mouse)Not determined17480447746158776Mouse
1357789Kdnw3_mkidney weight 3 (mouse)Not determined17480447747574740Mouse
4141272Tfv1_mtotal food volume 1 (mouse)Not determined480447765330362Mouse
10043949Pbft7_mpercent body fat 7 (mouse)Not determined17667496240674962Mouse
4141608Phl1_mprogressive hearing loss 1 (mouse)Not determined17765701129268449Mouse
1301935Skull24_mskull morphology 24 (mouse)Not determined17836594042366175Mouse
1300787Cd8mts5_mCD8 memory T cell subset 5 (mouse)Not determined17836594042366175Mouse
1301338Lmr1_mleishmaniasis resistance 1 (mouse)Not determined17986241186688972Mouse
1302028Asbb3_mautoimmune susceptibility in C57BL/6J and BALB/c 3 (mouse)Not determined171065914544659245Mouse
4142342Lfnq4_mlung function QTL 4 (mouse)Not determined1098759739053168Mouse
4141067Hbnr2_mHeligmosomoides bakeri nematode resistance 2 (mouse)Not determined1166699745667145Mouse
14747010Mancz14_mmandible centroid size 14 (mouse)171177921045779210Mouse
4142150Stheal11_msoft tissue heal 11 (mouse)Not determined171206732483054339Mouse
12904946Tammq8_mtibialis anterior muscle mass QTL 8 (mouse)171223281346232813Mouse
13524847Asrq8a_macoustic startle response 8a (mouse)171242798746427987Mouse
11081168Tir7_mtrypanosome infection response 7 (mouse)171390439847904522Mouse
1300914Pcir4_mperiosteal circumference 4 (mouse)Not determined171484267848842786Mouse
1558886Lgth9_mbody length 9 (mouse)Not determined171484267848842786Mouse
1302070Tbbmd7_mtotal body bone mineral density 7 (mouse)Not determined171484267848842786Mouse
1300995Fembrs4_mfemur breaking strength 4 (mouse)Not determined171484267848842786Mouse
1302140Wta4_mweight adult 4 (mouse)Not determined171660074750600869Mouse
1302152Skull25_mskull morphology 25 (mouse)Not determined171660074750600869Mouse
1301505Tir1_mtrypanosome infection response 1 (mouse)Not determined171660074750600869Mouse
1302038Radpf1_mradiation pulmonary fibrosis 1 (mouse)Not determined171661519333600869Mouse
10412083Sm2_msusceptibility to Schistosoma mansoni infection 2 (mouse)Not determined171681096950811104Mouse
1302042Acsns3_mAngiostrongylus costaricensis nematode susceptibility 3 (mouse)Not determined171724323451243371Mouse
1300535Char3_mP. chabaudi malaria resistance QTL 3 (mouse)Not determined171724323451243371Mouse
10412214Sxbq3_mSGC/Knj cross B6 QTL 3 (mouse)Not determined171724323451243371Mouse
13452396Leusq3_mleucocytosis susceptibility QTL 3 (mouse)171724323451243371Mouse
13452399Leusq6_mleucocytosis susceptibility QTL 6 (mouse)171724323451243371Mouse
1301840Ssial4_msusceptibility to sialadenitiss 4 (mouse)Not determined171795643651959238Mouse
1301331Lbw1_mlupus NZB x NZW 1 (mouse)Not determined171819938152202007Mouse
1301056Pas2_mpulmonary adenoma susceptibility 2 (mouse)Not determined171820316552205351Mouse
15039354Nmrs36_mNAFLD-associated magnetic resonance shift 36 (mouse)171883413352834133Mouse
1301454Eae5_msusceptibility to experimental allergic encephalomyelitis 5 (mouse)Not determined172430185958301973Mouse
10412198Sst5_msusceptibility to tuberculosis 5 (mouse)Not determined172485760955405969Mouse
10412196Bbaa28_mB.burgdorferi-associated arthritis 28 (mouse)Not determined172536594043665344Mouse
12903990Opfaq5_mopen field activity QTL 5 (mouse)172573195128773124Mouse
10412204Bbaa29_mB.burgdorferi-associated arthritis 29 (mouse)Not determined172574029459740461Mouse
1558758Kcal2_mkilocalorie 2 (mouse)Not determined172618203852604676Mouse
1300602Eye2_meye weight 2 (mouse)Not determined172628636340794146Mouse
1302005Loco2_mlocomotor activity 2 (mouse)Not determined172657408160574223Mouse
12904013Cfq12_mconditioned fear QTL 12 (mouse)172660980730445981Mouse
11075105Modc1_mmodifier of Odc1 (mouse)172749681845311728Mouse
15039348Nmrs37_mNAFLD-associated magnetic resonance shift 37 (mouse)172750432261504322Mouse
10045977Tir9_mtrypanosome infection response 9 (mouse)Not determined172765914543574223Mouse

miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
Mir204mmu-miR-204-5pOncomiRDBexternal_infoNANA21446014

Predicted Target Of
Summary Value
Count of predictions:1171
Count of miRNA genes:432
Interacting mature miRNAs:513
Transcripts:ENSMUST00000025054, ENSMUST00000114870, ENSMUST00000127622, ENSMUST00000138970, ENSMUST00000167489
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.


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000025054   ⟹   ENSMUSP00000025054
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl1727,714,352 - 27,728,953 (-)Ensembl
RefSeq Acc Id: ENSMUST00000114870   ⟹   ENSMUSP00000110520
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl1727,714,659 - 27,728,955 (-)Ensembl
RefSeq Acc Id: ENSMUST00000127622
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl1727,714,451 - 27,717,719 (-)Ensembl
RefSeq Acc Id: ENSMUST00000138970   ⟹   ENSMUSP00000117743
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl1727,719,992 - 27,728,924 (-)Ensembl
RefSeq Acc Id: ENSMUST00000167489   ⟹   ENSMUSP00000127056
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl1727,714,449 - 27,728,889 (-)Ensembl
RefSeq Acc Id: ENSMUST00000233880
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl1727,714,442 - 27,718,349 (-)Ensembl
RefSeq Acc Id: NM_001357728   ⟹   NP_001344657
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391727,933,420 - 27,949,977 (-)NCBI
GRCm381727,714,446 - 27,731,003 (-)NCBI
Sequence:
RefSeq Acc Id: NM_013891   ⟹   NP_038919
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391727,933,421 - 27,947,925 (-)NCBI
GRCm381727,714,447 - 27,728,951 (-)NCBI
MGSCv371727,851,392 - 27,865,896 (-)RGD
Celera1728,266,225 - 28,280,705 (-)RGD
cM Map17 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006524379   ⟹   XP_006524442
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391727,933,416 - 27,947,959 (-)NCBI
GRCm381727,714,446 - 27,728,985 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006524380   ⟹   XP_006524443
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391727,933,416 - 27,948,553 (-)NCBI
GRCm381727,714,446 - 27,729,017 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006524381   ⟹   XP_006524444
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391727,933,416 - 27,945,604 (-)NCBI
GRCm381727,714,446 - 27,726,630 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_038919   ⟸   NM_013891
- UniProtKB: Q9WTP3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006524443   ⟸   XM_006524380
- Peptide Label: isoform X1
- UniProtKB: Q9WTP3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006524442   ⟸   XM_006524379
- Peptide Label: isoform X1
- UniProtKB: Q9WTP3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006524444   ⟸   XM_006524381
- Peptide Label: isoform X1
- UniProtKB: Q9WTP3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001344657   ⟸   NM_001357728
RefSeq Acc Id: ENSMUSP00000117743   ⟸   ENSMUST00000138970
RefSeq Acc Id: ENSMUSP00000110520   ⟸   ENSMUST00000114870
RefSeq Acc Id: ENSMUSP00000127056   ⟸   ENSMUST00000167489
RefSeq Acc Id: ENSMUSP00000025054   ⟸   ENSMUST00000025054
Protein Domains
ETS   PNT

Promoters
RGD ID:13675306
Promoter ID:EPDNEW_M21802
Type:multiple initiation site
Name:Spdef_1
Description:Mus musculus SAM pointed domain containing ets transcriptionfactor , transcript variant 1, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381727,728,949 - 27,729,009EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1353422 AgrOrtholog
Ensembl Genes ENSMUSG00000024215 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000025054 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000110520 UniProtKB/TrEMBL
  ENSMUSP00000117743 UniProtKB/TrEMBL
  ENSMUSP00000127056 UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000025054 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000114870 UniProtKB/TrEMBL
  ENSMUST00000138970 UniProtKB/TrEMBL
  ENSMUST00000167489 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  1.10.150.50 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Ets_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pointed_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAM/pointed_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:30051 UniProtKB/Swiss-Prot
MGD MGI:1353422 ENTREZGENE
NCBI Gene 30051 ENTREZGENE
Pfam Ets UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAM_PNT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Spdef PhenoGen
PRINTS ETSDOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE ETS_DOMAIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ETS_DOMAIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ETS_DOMAIN_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PNT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART ETS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAM_PNT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46785 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF47769 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A3F2YNL9_MOUSE UniProtKB/TrEMBL
  B2KF87_MOUSE UniProtKB/TrEMBL
  Q9WTP3 ENTREZGENE, UniProtKB/Swiss-Prot