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Gene Dmel\Vsx2

General Information
Symbol	Dmel\Vsx2	Species	D. melanogaster
Name	Visual system homeobox 2 ortholog	Annotation symbol	CG33980
Feature type	protein_coding_gene	FlyBase ID	FBgn0263512
Gene Model Status	Current	Stock availability	12 publicly available
Also Known As	CG15782, CG15783, CG15781, dVsx2, DChx2
Genomic Location
Chromosome (arm)	X	Recombination map
Cytogenetic map	5A3-5A6	Sequence location	X:5,422,960..5,454,216 [-]
Genomic Maps Select View:Gene Models/EvidenceExpression/RegulationMegaViewGene Disruptions, Stocks and Reagents modENCODE GBrowse	Decorated FastA GenBankGFF Gene region Extended Gene region CDSIntronsExonsTranslationsTranscripts3' UTR5' UTR
Summary Information
Automatically generated summary See sections below for more information	The gene Visual system homeobox 2 ortholog is referred to in FlyBase by the symbol Dmel\Vsx2 (CG33980, FBgn0263512). It is a protein_coding_gene from Drosophila melanogaster. Based on sequence similarity, it is predicted to have molecular function: sequence-specific DNA binding transcription factor activity; sequence-specific DNA binding. Based on sequence similarity, it is predicted to be involved in the biological process: regulation of transcription, DNA-dependent. 8 alleles are reported. The phenotype of these alleles is annotated with: mesothoracic tergum. It has one annotated transcript and one annotated polypeptide. Protein features are: CVC domain; Homeobox; Homeobox, conserved site; Homeodomain-like; Homeodomain-related; Paired-like homeodomain protein, OAR. Gene sequence location is X:5422960..5454216.
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.
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FB2012_01	Sequence features BKN32743 HFA18089 HFA17397 HFA18087 BKN29302 HFA18088 Unknown NewRecord NewRecord
FB2011_10	Controlled Vocabulary Terms P-stage cortex of medulla neuron third instar larval stage pupal stage restricted adult stage
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 5A3-5A6   Left limit from (method unavailable) (FBrf0106464) Right limit from (method unavailable) (FBrf0106464)
Experimentally Determined Cytological Location
Cytogenetic map Notes References 5A3-5A6     (Erclik et al., 1999)
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\Vsx2 for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
	Gene merge based on EST/cDNA data; GB:BT022190.
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) Vsx2-RA FBtr0100024  NM_001038743   2358   640
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 Vsx2-PA   FBpp0099911   68.7   640   8.00     NP_001033832   AAF46043
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • CVC domain (IPR023339) Homeobox (IPR001356) Paired-like homeodomain protein, OAR (IPR003654) Homeodomain-like (IPR009057) Homeodomain-related (IPR012287) Homeobox, conserved site (IPR017970)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE014298 AAF46043   BI637281   BT022190   BT029275   CO178260   CO274490   CO343640   EC220954   EC230212   EC254989   EL879941   EL879942
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	Q9W4B3
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
Notes
Polypeptide Expression
immunolocalization Stage Tissue/Position (including subcellular localization) Reference third instar larval stage   neuron of cortex of medulla   (Erclik et al., 2008) cortex of medulla | restricted   (Erclik et al., 2008) pupal stage   cortex of medulla | restricted   (Erclik et al., 2008) adult stage   cortex of medulla | restricted   (Erclik et al., 2008)
Additional Descriptive Data
	Vsx2 protein is first observed in third instar larvae in a subset of Vsx1-expressing cells in the medulla cortex and continues to be expressed in the medulla in pupae and adults. (Erclik et al., 2008)
Marker for
Subcellular Localization
CV Term
Notes
High-Throughput Expression Data
or
See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes. [an error occurred while processing this directive] modENCODE Temporal Expression Data (Graveley et al., 2011) FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
Expression Clusters
External Data & Images
Linkouts
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal, with Scer\GAL4pnr-MD237 Vsx2GD6417 lethal | pupal stage, with Scer\GAL4pnr-MD237 Vsx2GD6417 viable Vsx2f02921 viable, with Scer\GAL4pnr-MD237 Vsx2GD13371 Vsx2GD17376 Sterility Allele fertile Vsx2f02921 Other Phenotypes Allele visible, with Scer\GAL4pnr-MD237 Vsx2GD17376 Phenotype manifest in Allele mesothoracic tergum, with Scer\GAL4pnr-MD237 Vsx2GD17376
Classical Alleles ( 2 )
For All Classical Alleles Show
Allele of Vsx2 Class Mutagen Stocks Known lesion Vsx2f02921 piggyBac transposase 2 -- Vsx2f04494 1 --
Alleles Carried on Transgenic Constructs ( 6 )
For All Alleles Carried on Transgenic Constructs Show
Allele of Vsx2 Class Mutagen Stocks Known lesion Vsx2GD13371 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes Vsx2GD17376 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes Vsx2GD6417 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes Vsx2JF02121 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes Vsx2KK109302 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes Vsx2KK112743 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes
Aneuploid Aberrations
Disrupted in	Df(1)Exel6235 (Erclik et al., 2008, Ryder, 2004.4.26) Df(1)Vsx2B1 (Erclik et al., 2008)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{KK109302} NA P{KK112743} NA P{TRiP.JF02121} NA
Insertions
	Type of insertions Name Expression data miscellaneous insertions PBac{WH}Vsx2f02921 NA PBac{WH}Vsx2f04494 NA insertion of enhancer trap binary system P{GawB}MzVum No
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
sequence-specific DNA binding inferred from sequence or structural similarity with InterPro:IPR001356 (FlyBase, 1992-) sequence-specific DNA binding transcription factor activity inferred from sequence or structural similarity with InterPro:IPR001356 (FlyBase, 1992-)
Biological Process
CV term Evidence References
multicellular organismal development inferred from electronic annotation with InterPro:IPR003654 (FlyBase Curators et al., 2004-) regulation of transcription, DNA-dependent inferred from sequence or structural similarity with InterPro:IPR001356 (FlyBase, 1992-)
Cellular Component
CV term Evidence References
nucleus inferred from sequence or structural similarity with InterPro:IPR001356 (FlyBase, 1992-)
Sequence Ontology: Class of Gene
	gene   nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
Protein-protein
Interacting group Assay References
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions Vsx2 allele Gene References
External Data
Linkouts
Orthologs
Genome-wide drosophilid orthologs	Dana\GF21193 Dere\GG18493 Dper\GL16530 Dpse\GA13956 Dsec\GM12642 Dsim\GD16257 Dwil\GK24958 Dyak\GE16810
Curated drosophilid orthologs	Dpse\GA13954   Dpse\GA13955   Dpse\GA13956
Linkouts
Stocks & Reagents
Stocks Listed in FlyBase ( 12 )
Bloomington	18598 w1118 PBac{WH}Vsx2f02921 26223 y1 v1; P{TRiP.JF02121}attP2
Harvard	- PBac{WH}Vsx2f02921 - PBac{WH}Vsx2f04494
VDRC	v104792 P{KK109302}VIE-260B v104981 P{KK112743}VIE-260B v14960 w1118 P{GD6417}v14960 v14577 w1118; P{GD6417}v14577 v23300 w1118; P{GD13371}v23300 v23302 w1118; P{GD13371}v23302 v49191 w1118; P{GD17376}v49191 v49192 w1118; P{GD17376}v49192
Genomic Clones ( 2 )
	BACR07P13 BACR27J18 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 11 )
	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	IP01192 IP09721
Other clones	DPiM_IP01192
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	SD19248
Other clones	12966 214575.31 CK01.70C.D4 EK056246 EK114252 EP17643 IP09821
RNAi & Array Information
Linkouts
Antibody Information
	polyclonal (Erclik et al., 2008, Erclik et al., 2008)
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of	Source for identity of: Vsx2 CG33980 (Erclik et al., 2008)
Source for database merge of	Source for merge of: CG15781 CG15782 CG15783 (FlyBase Genome Annotators, 2005) Source for merge of: Vsx2 Chx2 (Erclik, 2011.8.24)
Additional comments	Annotations CG15781, CG15782 and CG15783 merged as CG33980 in release 4.3 of the genome annotation. (FlyBase Genome Annotators, 2005)
Other Comments
	RNAi generated by PCR using primers directed to this gene causes a cell growth and viability phenotype when assayed in Kc167 and S2R+ cells. (Boutros et al., 2004) Identification: Identified on the basis of sequence similarity to murine Chx10. (Erclik et al., 1999)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_001038743 RefSeq (Proteins) • NP_001033832 DDBJ / EMBL / GenBank • AAF46042.1 AAF46043 AAF46043.1 Entrez Gene - A searchable database of RefSeq genes. • 31469 UniProtKB/TrEMBL • Q9W4B3
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • CVC domain (IPR023339) Homeobox (IPR001356) Paired-like homeodomain protein, OAR (IPR003654) Homeodomain-like (IPR009057) Homeodomain-related (IPR012287) Homeobox, conserved site (IPR017970)
Linkouts
Synonyms & Secondary IDs ( 10 )
Reported As
Symbol Synonym	CG15781 (Giot et al., 2003, Hoskins et al., 2005) CG15782 (Giot et al., 2003, Popovici et al., 2001, Hoskins et al., 2005, Davis et al., 2005) CG15783 (Boutros et al., 2004, Hoskins et al., 2005, Li et al., 2009) CG33980 (Erclik et al., 2008, Perkins et al., 2009.3.31, Keleman et al., 2009.8.5) Chx2 (Erclik, 2011.8.24, ) DChx2 (Erclik et al., 1999) dChx2 (Erclik et al., 2006) dVsx2 (Erclik et al., 2008, Erclik et al., 2008) Vsx2 (Erclik, 2011.8.24, )
Name Synonym	CG33980   Chx2   Visual system homeobox 2 ortholog
Secondary FlyBase IDs
	FBgn0026558 FBgn0029772 FBgn0029773 FBgn0029774 FBgn0053980 FBpp0070754 FBpp0070755 FBtr0070788 FBtr0070789
References ( 26 )
Generate a list of	All references relating to this gene ( 26 )
List References by type	Research paper  ( 6 ) Supplementary material  ( 4 ) Personal communication to FlyBase  ( 7 ) Abstract  ( 3 ) FlyBase analysis  ( 3 ) Computer file  ( 1 ) Automatic genome annotation  ( 1 ) Curated genome annotation  ( 1 )
Recent research papers (0)
	All research papers listed in FlyBase were published before 2010 Show research papers ...