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Gene Dpse\run

General Information
Symbol	Dpse\run	Species	D. pseudoobscura pseudoobscura
Name		Annotation symbol	GA14956
Feature type	protein_coding_gene	FlyBase ID	FBgn0013862
Gene Model Status	Current	Stock availability	None publicly available
Genomic Location
Chromosome (arm)	XL_group1e	Recombination map
Cytogenetic map		Sequence location	XL_group1e:9,209,634..9,211,605 [+]
Genomic Maps	Decorated FastA GenBankGFF Gene region Extended Gene region CDSIntronsExonsTranslationsTranscripts3' UTR5' UTR
Summary Information
Automatically generated summary See sections below for more information	This gene is referred to in FlyBase by the symbol Dpse\run (GA14956, FBgn0013862). It is a protein_coding_gene from Drosophila pseudoobscura pseudoobscura. An electronic pipeline based on InterPro domains suggests that it has the molecular function: DNA binding; sequence-specific DNA binding transcription factor activity; ATP binding. An electronic pipeline based on InterPro domains suggests that it is involved in the biological process: regulation of transcription, DNA-dependent. No alleles are reported. It has one annotated transcript and one annotated polypeptide. Protein features are: Acute myeloid leukemia 1 (AML 1)/Runt; Acute myeloid leukemia 1 protein (AML 1)/Runt; p53-like transcription factor, DNA-binding; p53/RUNT-type transcription factor, DNA-binding domain. Gene sequence location is XL_group1e:9209634..9211605.
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
Update Feed	Click the icon below to subscribe to this FlyBase record and receive updates automatically through your feed reader.
FB2013_03
FB2013_02
All updates	Click here to see a list of all updates to this record from FB2010_08 and on.
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location
Experimentally Determined Cytological Location
Cytogenetic map Notes References
Experimentally Determined Recombination Data
Location	XL- (Richards et al., 2005.6.27) X-50.8 (Kovacevic and Schaeffer, 2000)
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dpse\run for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) Dpse\run-RA FBtr0275483  XM_001355007   1677   558
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein Dpse\run-PA   FBpp0273921   57.6   558   8.46     XP_001355043   EAL32099
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Acute myeloid leukemia 1 protein (AML1)/Runt (IPR000040) p53-like transcription factor, DNA-binding (IPR008967) Runt domain (IPR013524) p53/RUNT-type transcription factor, DNA-binding domain (IPR012346)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AF196134 AAF23906   AF196135 AAF23907   AF196136 AAF23908   AF196137 AAF23909   AF196138 AAF23910   AF196139 AAF23911   AF196140 AAF23912   AF196141 AAF23913   AF196142 AAF23914   AF196143 AAF23915   AF196144 AAF23916   AF196145 AAF23917   AF196146 AAF23918   AF196147 AAF23919   AF196148 AAF23920   AF196149 AAF23921   AF196150 AAF23922   AF196151 AAF23923   AF196152 AAF23924   AF196153 AAF23925   AF196154 AAF23926   AF196155 AAF23927   AF196156 AAF23928   AF196157 AAF23929   AF196158 AAF23930   AF196159 AAF23931   AF196160 AAF23932   AF196161 AAF23933   AF196162 AAF23934   AF196163 AAF23935   AF196164 AAF23936   AF196165 AAF23937   AF196166 AAF23938   AF196167 AAF23939   AF196168 AAF23940   AF196169 AAF23941   AF196170 AAF23942   AF196171 AAF23943   AF196172 AAF23944   AF196173 AAF23945   U22357 AAB52378
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	Q29GL0 Q9TW09 Q24612
Mapped Features
Mapped Features have been reorganized, please see this article for details. Additional mapped features and mutations can be found on GBrowse or related reports. Type Symbol & Location Additional Notes References
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
Subcellular Localization (GO Cellular Component)
CV term Evidence References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools
Reference	See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes.
FlyAtlas Anatomy Microarray
modENCODE Anatomy RNA-Seq
modENCODE Development RNA-Seq
modENCODE Cell Lines RNA-Seq
modENCODE Treatments RNA-Seq
Expression Clusters
External Data & Images
Linkouts
Alleles & Phenotypes
Summary of Allele Phenotypes
Phenotype manifest in Allele
Classical Alleles ( 0 )
For All Classical Alleles Show
Allele of Dpse\run Class Mutagen Stocks Known lesion
Alleles Carried on Transgenic Constructs ( 0 )
For All Alleles Carried on Transgenic Constructs Show
Allele of Dpse\run Class Mutagen Stocks Known lesion
Aneuploid Aberrations
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data
Insertions
	Type of insertions Name Expression data
Gene Ontology: Function, Process & Cellular Component ( 5 unique terms )
Terms Based on Experimental Evidence ( 0 terms )
Terms Based on Predictions or Assertions ( 5 terms )
Molecular Function
CV term Evidence References
ATP binding inferred from electronic annotation with InterPro:IPR000040 (FlyBase Curators et al., 2004-) DNA binding inferred from electronic annotation with InterPro:IPR000040, InterPro:IPR012346, InterPro:IPR013524 (FlyBase Curators et al., 2004-) sequence-specific DNA binding transcription factor activity inferred from electronic annotation with InterPro:IPR008967, InterPro:IPR012346, InterPro:IPR013524 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
regulation of transcription, DNA-dependent inferred from electronic annotation with InterPro:IPR000040, InterPro:IPR008967, InterPro:IPR012346, InterPro:IPR013524 (FlyBase Curators et al., 2004-)
Cellular Component
CV term Evidence References
nucleus inferred from electronic annotation with InterPro:IPR000040, InterPro:IPR012346 (FlyBase Curators et al., 2004-)
Sequence Ontology: Class of Gene
	nuclear_gene (Drosophila 12 Genomes Consortium, 2008, ) protein_coding_gene (Drosophila 12 Genomes Consortium, 2008, )
Interactions & Pathways
Summary of Physical Interactions
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions Dpse\run allele Gene References
External Data
Linkouts
Orthologs
OrthoDB Orthologs (1) - based on analysis using Dmel annotation version 5.41
OrthoDB Ortholog Groups
	OrthoDB orthology group searches (Waterhouse et al., 2011, Nucleic Acids Res. 39(Database issue): D283--D288) Drosophila inclusive ortholog search EOG6CVGT6 Dipteran inclusive ortholog search EOG6KPTKW Insect inclusive ortholog search EOG66Q5QF Arthropod inclusive ortholog search EOG6TTF1S Metazoa inclusive ortholog search EOG6F81FN
Ortholog(s) in Drosophila melanogaster (EOG6CVGT6)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\pros
Human Orthologs (0)
Gene OMIM HGNC
AAA Orthologs (1) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila melanogaster Dmel\run
Stocks & Reagents
Stocks Listed in FlyBase ( 0 )
Genomic Clones ( 0 )
cDNA Clones ( 0 )
	Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.
cDNA Clones, Fully Sequenced
BDGP DGC clones
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones
Other clones
RNAi & Array Information
Linkouts
Antibody Information
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of
Additional comments
Other Comments
	The frequency distribution of "silent" DNA polymorphisms has been studied in a number of D.simulans and D.pseudoobscura.pseudoobscura genes. (Akashi and Schaeffer, 1997)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • XM_001355007 RefSeq (Proteins) • XP_001355043 DDBJ / EMBL / GenBank • AAB52378 AAF23906 AAF23907 AAF23908 AAF23909 AAF23910 AAF23911 AAF23912 AAF23913 AAF23914 AAF23915 AAF23916 AAF23917 AAF23918 AAF23919 AAF23920 AAF23921 AAF23922 AAF23923 AAF23924 AAF23925 AAF23926 AAF23927 AAF23928 AAF23929 AAF23930 AAF23931 AAF23932 AAF23933 AAF23934 AAF23935 AAF23936 AAF23937 AAF23938 AAF23939 AAF23940 AAF23941 AAF23942 AAF23943 AAF23944 AAF23945 AF196134 AF196135 AF196136 AF196137 AF196138 AF196139 AF196140 AF196141 AF196142 AF196143 AF196144 AF196145 AF196146 AF196147 AF196148 AF196149 AF196150 AF196151 AF196152 AF196153 AF196154 AF196155 AF196156 AF196157 AF196158 AF196159 AF196160 AF196161 AF196162 AF196163 AF196164 AF196165 AF196166 AF196167 AF196168 AF196169 AF196170 AF196171 AF196172 AF196173 EAL32099 U22357 Entrez Gene - A searchable database of RefSeq genes. • 4815174 UniProtKB/TrEMBL • Q9TW09 Q29GL0 Q24612
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Acute myeloid leukemia 1 protein (AML1)/Runt (IPR000040) p53-like transcription factor, DNA-binding (IPR008967) Runt domain (IPR013524) p53/RUNT-type transcription factor, DNA-binding domain (IPR012346)
Linkouts
	FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0013862 modMine - Data generated by the modENCODE project. • FBgn0013862
Synonyms & Secondary IDs ( 5 )
Reported As
Symbol Synonym	dpse_GLEANR_1195 (Drosophila 12 Genomes Consortium, 2008) Dpse\GA14956   Dpse\run (Drosophila 12 Genomes Consortium, 2008, ) run (Drosophila 12 Genomes Consortium, 2008)
Name Synonym	runt (Pepling, 1995.3.7, Bartolome and Charlesworth, 2006, Walrad et al., 2010)
Secondary FlyBase IDs
References ( 19 )
Research paper	Walrad et al., 2010, Mol. Biol. Cell 21(13): 2315--2326 Distinct contributions of conserved modules to runt transcription factor activity. [FBrf0211193] Drosophila 12 Genomes Consortium et al., 2007, Nature 450(7167): 203--218 Evolution of genes and genomes on the Drosophila phylogeny. [FBrf0200326] Bartolome and Charlesworth, 2006, Genetics 173(2): 779--791 Rates and patterns of chromosomal evolution in Drosophila pseudoobscura and D. miranda. [FBrf0193909] Yi et al., 2003, Genetics 164(4): 1369--1381 A survey of chromosomal and nucleotide sequence variation in Drosophila miranda. [FBrf0162140] Dunn et al., 2001, Genetics 157(1): 295--305 Substitution rates in Drosophila nuclear genes. Implications for translational selection. [FBrf0132336] Noor et al., 2001, Mol. Biol. Evol. 18(4): 551--556 Evolutionary history of microsatellites in the Obscura Group of Drosophila. [FBrf0134759] Kovacevic and Schaeffer, 2000, Genetics 156(1): 155--172 Molecular population genetics of X-linked genes in Drosophila pseudoobscura. [FBrf0129909] Noor et al., 2000, Genet. Res. (Camb.) 75(1): 25--35 Microsatellite variation in populations of Drosophila pseudoobscura and Drosophila persimilis. [FBrf0126788] Civetta and Singh, 1998, Mol. Biol. Evol. 15(7): 901--909 Sex-related genes, directional sexual selection, and speciation. [FBrf0102904] Akashi and Schaeffer, 1997, Genetics 146(1): 295--307 Natural selection and the frequency distributions of 'silent' DNA polymorphism in Drosophila. [FBrf0093333] Moriyama and Powell, 1997, J. Mol. Evol. 45(5): 514--523 Codon usage bias and tRNA abundance in Drosophila. [FBrf0098854] Pepling and Gergen, 1995, Proc. Natl. Acad. Sci. U.S.A. 92(20): 9087--9091 Conservation and function of the transcriptional regulatory protein runt. [FBrf0084259]
Personal communication to FlyBase	Drosophila 12 Genomes Consortium, 2008, personal communication to FlyBase Symbols and class of gene information for the GLEANR consensus sequences of the 11 sequenced non-melanogaster Drosophila species (Drosophila ananassae, erecta, grimshawi, mojavensis, persimilis, pseudoobscura, sechellia, simulans, willistoni, virilis and yakuba). [FBrf0202436] FlyBase Curators et al., 2004-, Gene Ontology annotation in FlyBase through association of InterPro records with GO terms. Gene Ontology annotation in FlyBase through association of InterPro records with GO terms. [FBrf0174215]
Abstract	Walrad et al., 2004, A. Dros. Res. Conf. 45: 376A Runts conserved regions outside the runt domain: evidence of functional significance. [FBrf0174160] Walrad et al., 2003, A. Dros. Res. Conf. 44: 354C Runts conserved regions outside the runt domain: evidence of functional significance. [FBrf0154981]
FlyBase analysis	FlyBase, 2008, Associations of D. pseudoobscura GLEANR gene predictions (Release 2.1) with previously known genes in FlyBase. Associations of D. pseudoobscura GLEANR gene predictions (Release 2.1) with previously known genes in FlyBase. [FBrf0202438]
DNA/RNA sequence record	Richards et al., 2005.6.27, GenBank/EMBL/DDBJ: CH379064 Drosophila pseudoobscura strain MV2-25 ChXL_group1e genomic scaffold, whole genome shotgun sequence. [FBrf0197235] Pepling, 1995.3.7, GenBank/EMBL/DDBJ: U22357 Drosophila pseudoobscura runt gene, complete cds. [FBrf0118844]