Sp9 (trans-acting transcription factor 9) - Rat Genome Database

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Gene: Sp9 (trans-acting transcription factor 9) Mus musculus
Analyze
Symbol: Sp9
Name: trans-acting transcription factor 9
RGD ID: 1558322
MGI Page MGI
Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in embryonic limb morphogenesis. Predicted to be located in nucleus. Is expressed in several structures, including limb ectoderm; limb epithelium; and telencephalon. Orthologous to human SP9 (Sp9 transcription factor).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: buttonhead-like zinc finger transcription factor Sp9; transcription factor Sp9
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39273,094,809 - 73,106,115 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl273,102,269 - 73,115,050 (+)EnsemblGRCm39 Ensembl
GRCm38273,271,926 - 73,275,771 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl273,271,925 - 73,284,706 (+)EnsemblGRCm38mm10GRCm38
MGSCv37273,109,983 - 73,113,828 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36273,072,765 - 73,076,165 (+)NCBIMGSCv36mm8
MGSCv36274,106,229 - 74,109,373 (+)NCBIMGSCv36mm8
Celera274,958,305 - 74,962,121 (+)NCBICelera
Cytogenetic Map2C3NCBI
cM Map243.52NCBI
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
nucleus  (IEA)

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. MGDs mouse GO annotations MGD data from the GO Consortium
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:15358670   PMID:15820306   PMID:16141072   PMID:16141073   PMID:17376983   PMID:17470284  
PMID:17509151   PMID:19030180   PMID:19386638   PMID:19549840   PMID:21267068   PMID:21873635   PMID:23042297   PMID:27452460   PMID:27655933   PMID:28981617   PMID:29513653   PMID:29878134  
PMID:29967281   PMID:30635555   PMID:30699346   PMID:30796806   PMID:31001083   PMID:31070778   PMID:31491374   PMID:32234482   PMID:32868762   PMID:35156680   PMID:35377797   PMID:36081908  
PMID:36476860   PMID:37566909  


Genomics

Comparative Map Data
Sp9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39273,094,809 - 73,106,115 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl273,102,269 - 73,115,050 (+)EnsemblGRCm39 Ensembl
GRCm38273,271,926 - 73,275,771 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl273,271,925 - 73,284,706 (+)EnsemblGRCm38mm10GRCm38
MGSCv37273,109,983 - 73,113,828 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36273,072,765 - 73,076,165 (+)NCBIMGSCv36mm8
MGSCv36274,106,229 - 74,109,373 (+)NCBIMGSCv36mm8
Celera274,958,305 - 74,962,121 (+)NCBICelera
Cytogenetic Map2C3NCBI
cM Map243.52NCBI
SP9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382174,334,954 - 174,338,500 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2174,334,954 - 174,338,500 (+)EnsemblGRCh38hg38GRCh38
GRCh372175,199,682 - 175,203,228 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362174,908,067 - 174,910,514 (+)NCBINCBI36Build 36hg18NCBI36
Celera2168,813,313 - 168,815,760 (+)NCBICelera
Cytogenetic Map2q31.1NCBI
HuRef2167,080,054 - 167,082,501 (+)NCBIHuRef
CHM1_12175,206,043 - 175,208,490 (+)NCBICHM1_1
T2T-CHM13v2.02174,823,644 - 174,827,190 (+)NCBIT2T-CHM13v2.0
Sp9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8378,554,345 - 78,556,875 (+)NCBIGRCr8
mRatBN7.2358,146,826 - 58,149,357 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl358,146,826 - 58,149,357 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx361,539,376 - 61,541,910 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0370,123,029 - 70,125,565 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0367,888,047 - 67,890,583 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0359,981,959 - 59,984,489 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl359,981,959 - 59,984,489 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0366,454,296 - 66,456,826 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4355,776,340 - 55,778,870 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera357,682,457 - 57,684,987 (+)NCBICelera
Cytogenetic Map3q23NCBI
Sp9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554491,003,517 - 1,006,012 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554491,003,462 - 1,006,023 (-)NCBIChiLan1.0ChiLan1.0
SP9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21376,999,456 - 77,002,954 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B77,004,631 - 77,017,929 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B61,612,140 - 61,615,694 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B179,067,759 - 179,069,855 (+)NCBIpanpan1.1PanPan1.1panPan2
SP9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13618,401,003 - 18,404,874 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3618,400,918 - 18,403,135 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3618,410,357 - 18,413,027 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03618,534,257 - 18,536,928 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3618,534,249 - 18,537,928 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13618,614,091 - 18,616,767 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03618,612,373 - 18,615,042 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03618,722,885 - 18,725,556 (+)NCBIUU_Cfam_GSD_1.0
SP9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1580,325,377 - 80,329,020 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11580,325,449 - 80,328,111 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21589,545,332 - 89,547,811 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SP9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11059,842,869 - 59,852,780 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1059,849,326 - 59,851,818 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666040139,740,519 - 139,752,964 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sp9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462478711,576,717 - 11,579,977 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462478711,576,707 - 11,579,871 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sp9
235 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:966
Count of miRNA genes:530
Interacting mature miRNAs:664
Transcripts:ENSMUST00000090813, ENSMUST00000147133
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1301769Orgwq2_morgan weight QTL 2 (mouse)Not determined2388712693421651Mouse
1357881Estoq1_membryo survival total QTL 1 (mouse)Not determined220897778118894840Mouse
1357454Kidq1_mkidney weight QTL 1 (mouse)Not determined220897778118894840Mouse
1357436Splq1_mspleen weight QTL 1 (mouse)Not determined220897778118894840Mouse
39128209Lwq14_mliver weight QTL 14 (mouse)220897778118894840Mouse
1558899Egq1_mearly growth QTL 1 (mouse)Not determined220897778118894840Mouse
1558966W10q9_mweight 10 weeks QTL 9 (mouse)Not determined220897778118894840Mouse
1558915W3q1_mweight 3 weeks QTL 1 (mouse)Not determined220897778118894840Mouse
1558738W6q1_mweight 6 weeks QTL 1 (mouse)Not determined220897778118894840Mouse
1357681Hrtq1_mheart weight QTL 1 (mouse)Not determined220897778118894840Mouse
1302174Dssc2_mdextran sodium sulfate induced colitis QTL2 (mouse)Not determined224224632148700377Mouse
1300577Capsq1_mcapsaicin sensitivity related QTL 1 (mouse)Not determined22760206084013384Mouse
4141854T2dm2sa_mtype 2 diabetes mellitus 2 in SMXA RI mice (mouse)Not determined229307947148374934Mouse
4141236Hbnr5_mHeligmosomoides bakeri nematode resistance 5 (mouse)Not determined31214567105143570Mouse
11038703Ltpr1_mLeishmania tropica response 1 (mouse)23997166573971811Mouse
1301109Dntcs2_mdental caries susceptibility 2 (mouse)Not determined240885493114910165Mouse
1301480Pbwg1_mpostnatal body weight growth 1 (mouse)Not determined24182071975820843Mouse
4141069Pbwg1.5_mpostnatal body weight growth 1.5 (mouse)Not determined4352061277520756Mouse
1300788Cia2_mcollagen induced arthritis QTL 2 (mouse)Not determined24352061277520756Mouse
1300671Cia4_mcollagen induced arthritis QTL 4 (mouse)Not determined24352061277520756Mouse
1301402Ap2q_malcohol preference 2 QTL (mouse)Not determined24352061277520756Mouse
1301411Pitm1_mprion incubation time 1 (mouse)Not determined24352061277520756Mouse
10755532Lymph5_mlymphocyte differential 5 (mouse)24419901778199017Mouse
1301344Lith1_mlithogenic gene 1 (mouse)Not determined245347635145312647Mouse
11532740Pbwg1.10_mpostnatal body weight growth 1.10 (mouse)24813241282132495Mouse
1558820Moo1_mmodifier of Odc1 (mouse)Not determined174826974682269934Mouse
1301747Eae21_mexperimental allergic encephalomyelitis 21 (mouse)Not determined24826974682269934Mouse
1301235Alcw4_malcohol withdrawal 4 (mouse)Not determined24826974682269934Mouse
1300568Hdl1_mhigh density lipoprotein (HDL) level 1 (mouse)Not determined24826974682269934Mouse
10755526Lymph1_mlymphocyte differential 1 (mouse)25081931484819314Mouse
1300875Taste1_mtaste-saccharin preference 1 (mouse)Not determined25092317584923278Mouse
1300761Lgth1_mbody length 1 (mouse)Not determined25170327685703425Mouse
13464141Hbbcq3_mhemoglobin concentration QTL 3 (mouse)25244801986448136Mouse
13463471Hctq6_mhematocrit QTL 6 (mouse)25244801986448136Mouse
4141406Alpq2_malcohol preference QTL 2 (mouse)Not determined25752411791524288Mouse
12738429Lfibq18_mliver fibrosis QTL 18 (mouse)25791999191919991Mouse
1357577Trmq3_mT cell ratio modifier QTL 3 (mouse)Not determined260520612119355518Mouse
13432178Actres2_mactivity response to ethanol/saline 2 (mouse)26069228774092287Mouse
13824983Vclq1_mcurvilinear velocity QTL 1 (mouse)261830344136841920Mouse
10044002Hdl7_mHDL level 7 (mouse)Not determined26300595497006113Mouse
10053681Lith24_mlithogenic gene 24 (mouse)Not determined26300595497006113Mouse
1301405Etohr_methanol response acute (mouse)Not determined26300595497006113Mouse
1301703Bomd3_mbone mineral density 3 (mouse)Not determined26300595497006113Mouse
1300662Etohila_methanol induced locomotor activity (mouse)Not determined26300595497006113Mouse
1301048Actre2_mactivity response to ethanol 2 (mouse)Not determined26300595497006113Mouse
1301873Hsl1_mhyperoxia susceptibility locus 1 (mouse)Not determined26357015497570301Mouse
5491197Mobq5_mmultigenic obesity QTL 5 (mouse)Not determined265269746162518926Mouse
1301059Hrtfm1_mheart failure modifier 1 (mouse)Not determined26759194074964933Mouse
1301660Iba1_minduction of brown adipocytes 1 (mouse)Not determined267647887101648142Mouse
13463482Mchq17_mmean corpuscular hemoglobin QTL 17 (mouse)267647887101648142Mouse
1301882Etohc2_methanol consumption 2 (mouse)Not determined268724269102724407Mouse
1301948Elsgp3_melevated serum gp70 3 (mouse)Not determined268724269102724407Mouse


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000090813   ⟹   ENSMUSP00000088322
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl273,102,269 - 73,107,815 (+)Ensembl
GRCm38.p6 Ensembl273,271,925 - 73,277,471 (+)Ensembl
RefSeq Acc Id: ENSMUST00000147133
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl273,102,310 - 73,115,050 (+)Ensembl
GRCm38.p6 Ensembl273,271,966 - 73,284,706 (+)Ensembl
RefSeq Acc Id: NM_001005343   ⟹   NP_001005343
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39273,102,277 - 73,106,115 (+)NCBI
GRCm38273,271,926 - 73,275,771 (+)ENTREZGENE
MGSCv37273,109,983 - 73,113,828 (+)RGD
Celera274,958,305 - 74,962,121 (+)RGD
cM Map2 ENTREZGENE
Sequence:
RefSeq Acc Id: NM_001409583   ⟹   NP_001396512
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39273,094,809 - 73,106,115 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001005343   ⟸   NM_001005343
- UniProtKB: Q5QR89 (UniProtKB/Swiss-Prot),   Q64HY3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000088322   ⟸   ENSMUST00000090813
RefSeq Acc Id: NP_001396512   ⟸   NM_001409583
- UniProtKB: Q64HY3 (UniProtKB/Swiss-Prot),   Q5QR89 (UniProtKB/Swiss-Prot)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q64HY3-F1-model_v2 AlphaFold Q64HY3 1-484 view protein structure

Promoters
RGD ID:6832813
Promoter ID:MM_KWN:29697
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Kidney,   Lung
Transcripts:OTTMUST00000032085,   OTTMUST00000032086
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36273,109,771 - 73,110,271 (+)MPROMDB
RGD ID:6877618
Promoter ID:EPDNEW_M2257
Type:initiation region
Name:Sp9_1
Description:Mus musculus trans-acting transcription factor 9 , 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
GRCm38273,271,954 - 73,272,014EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:3574660 AgrOrtholog
Ensembl Genes ENSMUSG00000068859 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000090813 ENTREZGENE
  ENSMUST00000090813.6 UniProtKB/Swiss-Prot
Gene3D-CATH Classic Zinc Finger UniProtKB/Swiss-Prot
InterPro Znf_C2H2_sf UniProtKB/Swiss-Prot
  Znf_C2H2_type UniProtKB/Swiss-Prot
KEGG Report mmu:381373 UniProtKB/Swiss-Prot
MGD MGI:3574660 ENTREZGENE
NCBI Gene 381373 ENTREZGENE
PANTHER KRUEPPEL-LIKE TRANSCRIPTION FACTOR UniProtKB/Swiss-Prot
  TRANSCRIPTION FACTOR SP9 UniProtKB/Swiss-Prot
Pfam zf-C2H2 UniProtKB/Swiss-Prot
PhenoGen Sp9 PhenoGen
PROSITE ZINC_FINGER_C2H2_1 UniProtKB/Swiss-Prot
  ZINC_FINGER_C2H2_2 UniProtKB/Swiss-Prot
SMART ZnF_C2H2 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF57667 UniProtKB/Swiss-Prot
UniProt Q5QR89 ENTREZGENE
  Q64HY3 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q5QR89 UniProtKB/Swiss-Prot