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Gene Dpse\Adh

General Information
Symbol	Dpse\Adh	Species	D. pseudoobscura pseudoobscura
Name		Annotation symbol	GA17214
Feature type	protein_coding_gene	FlyBase ID	FBgn0243561
Gene Model Status	Current	Stock availability	None publicly available
Also Known As	Adh
Genomic Location
Chromosome (arm)	4_group1	Recombination map	4-
Cytogenetic map		Sequence location	4_group1:3,221,867..3,222,754 [-]
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\Adh (GA17214, FBgn0243561). It is a protein_coding_gene from Drosophila pseudoobscura pseudoobscura. An electronic pipeline based on InterPro domains suggests that it has the molecular function: alcohol dehydrogenase (NAD) activity; nucleotide binding. An electronic pipeline based on InterPro domains suggests that it is involved in the biological process: oxidation-reduction process; alcohol metabolic process. 3 alleles are reported. No phenotypic data is available. It has one annotated transcript and one annotated polypeptide. Protein features are: Alcohol dehydrogenase, Drosophila-type; Alcohol dehydrogenase, insect-type; NAD(P)-binding domain; Short-chain dehydrogenase/reductase SDR; Short-chain dehydrogenase/reductase, conserved site. Gene sequence location is 4_group1:3221867..3222754.
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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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	4- (Richards et al., 2005.6.27)
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dpse\Adh 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\Adh-RA FBtr0280541  XM_001357339   765   254
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\Adh-PA   FBpp0278979   27.6   254   8.65     XP_001357375   EAL34444
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Alcohol dehydrogenase, Drosophila-type (IPR002425) Alcohol dehydrogenase, insect-type (IPR002424) Short-chain dehydrogenase/reductase SDR (IPR002198) NAD(P)-binding domain (IPR016040) Short-chain dehydrogenase/reductase, conserved site (IPR020904)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name M60979 AAA99022   M60980 AAA99023   M60981 AAA99025   M60982 AAA99016   M60983 AAA99017   M60984 AAA99018   M60985 AAA99020   M60986 AAA99019   M60987 AAA99021   M60988 AAA99024   U64521 AAB06136   U64522 AAB06137   U64523 AAB06138   U64524 AAB06139   U64525 AAB06140   U64526 AAB06141   U64527 AAB06142   U64528 AAB06143   U64529 AAB06144   U64530 AAB06145   U64531 AAB06146   U64532 AAB06147   U64533 AAB06148   U64534 AAB06149   U64535 AAB06150   U64536 AAB06151   U64537 AAB06152   U64538 AAB06153   U64539 AAB06154   U64540 AAB06155   U64541 AAB06156   U64542 AAB06157   U64543 AAB06158   U64544 AAB06159   U64545 AAB06160   U64546 AAB06161   U64547 AAB06162   U64548 AAB06163   U64549 AAB06164   U64550 AAB06165   U64551 AAB06166   U64552 AAB06167   U64553 AAB06168   U64554 AAB06169   U64555 AAB06170   U64556 AAB06171   U64557 AAB06172   U64558 AAB06173   U64559 AAB06174   U64560 AAB06175   X62181 CAA44102   X62182 CAA44103   X62183 CAA44104   X62184 CAA44105   X62185 CAA44106   X62186 CAA44107   X62187 CAA44108   X62188 CAA44109   X62189 CAA44110   X62190 CAA44111   X62191 CAA44112   X62192 CAA44113   X62193 CAA44114   X62194 CAA44115   X62195 CAA44116   X62196 CAA44117   X62197 CAA44118   X62198 CAA44119   X62199 CAA44120   X62200 CAA44121   X62201 CAA44122   X62202 CAA44123   X62203 CAA44124   X62204 CAA44125   X62205 CAA44126   X62206 CAA44127   X62207 CAA44128   X62208 CAA44129   X62209 CAA44130   X62210 CAA44131   X62211 CAA44132   X62212 CAA44133   X62213 CAA44134   X62214 CAA44135   X62215 CAA44136   X62216 CAA44137   X62217 CAA44138   X62218 CAA44139   X62219 CAA44140   X62220 CAA44141   X62221 CAA44142   X62222 CAA44143   X62223 CAA44144   X62224 CAA44145   X62225 CAA44146   X62226 CAA44147   X62227 CAA44148   X62228 CAA44149   X62229 CAA44150   X62230 CAA44151   X62231 CAA44152   X62232 CAA44153   X62233 CAA44154   X62234 CAA44155   X62235 CAA44156   X62236 CAA44157   X62237 CAA44158   X62238 CAA44159   X64468 CAA45797   X64469 CAA45798   X64470 CAA45799   X64471 CAA45800   X64472 CAA45801   X64473 CAA45802   X64474 CAA45803   X64475 CAA45804   X64476 CAA45805   X64477 CAA45806   X64478 CAA45807   X64479 CAA45808   X64480 CAA45809   X64481 CAA45810   X64482 CAA45811   X64483 CAA45812   X64484 CAA45813   X64485 CAA45814   X64486 CAA45815   X64487 CAA45816   X64488 CAA45817   X64489 CAA45818
UniProtKB/Swiss-Prot	Q6LCE4
UniProtKB/TrEMBL
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
Other Phenotypes Allele electrophoretic variant Dpse\Adh94 Dpse\Adh100 Dpse\Adh106 Phenotype manifest in Allele
Classical Alleles ( 3 )
For All Classical Alleles Show
Allele of Dpse\Adh Class Mutagen Stocks Known lesion Dpse\Adh100 natural population 0 -- Dpse\Adh106 natural population 0 -- Dpse\Adh94 natural population 0 --
Alleles Carried on Transgenic Constructs ( 0 )
For All Alleles Carried on Transgenic Constructs Show
Allele of Dpse\Adh 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 ( 3 unique terms )
Terms Based on Experimental Evidence ( 0 terms )
Terms Based on Predictions or Assertions ( 3 terms )
Molecular Function
CV term Evidence References
alcohol dehydrogenase (NAD) activity inferred from electronic annotation with InterPro:IPR002424, InterPro:IPR002425 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
alcohol metabolic process inferred from electronic annotation with InterPro:IPR002425 (FlyBase Curators et al., 2004-) oxidation-reduction process inferred from electronic annotation with InterPro:IPR002424, InterPro:IPR002425 (FlyBase Curators et al., 2004-)
Cellular Component ( 0 terms)
Sequence Ontology: Class of Gene
	nuclear_gene (Drosophila 12 Genomes Consortium, 2008) protein_coding_gene (FlyBase, 1992-, 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\Adh 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 EOG6M39VS Dipteran inclusive ortholog search No orthologs identified Insect inclusive ortholog search EOG6K3JS8 Arthropod inclusive ortholog search No orthologs identified Metazoa inclusive ortholog search EOG68DCPM
Ortholog(s) in Drosophila melanogaster (EOG6M39VS)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\Adh Y
Human Orthologs (0)
Gene OMIM HGNC
AAA Orthologs (1) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila melanogaster Dmel\Adh
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	Source for merge of: Dpse\Adh+Dpse\Adhr Dpse\Adh (FlyBase, 1992-)
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) The phylogenetic relationships and divergence times of 39 drosophilid species have been studied by using the coding region of the Adh gene. (Russo et al., 1995) The homologous genomic region containing Adh and Adhr is analysed. Ka and Ks values are determined (Ks values for Adh are significantly lower than values for Adhr) and amino acid comparisons reveal conserved regions shared by Adh and Adhr which have been assigned to known functional domains. (Albalat et al., 1994) Dpse\Adh has been compared with the Adh sequences of the melanogaster species subgroup. (Jeffs et al., 1994) An analysis of linkage disequilibrium for all segregating sites in the Dpse\Adh region has been performed to determine how much association exists among polymorphic sites in a genomic sequence that has not been influenced by selection or population subdivision. (Schaeffer and Miller, 1993) Phylogenetic DNA sequence comparison of ten Drosophila species has been used to elucidate the secondary structure of Adh mRNA. One possible pairing region in the 5' leader sequence and 22 in the coding and noncoding regions have been identified by seeking an equivalent pairing region in homologous RNA. Most are short range pairings such as hairpins. The rate of coevolution in noncoding pairing region is higher than in coding regions in accordance with selective constraints on substitution rates in coding region. (Stephan and Kirby, 1993) Phylogenetic relationships in Drosophila are studied using the Alcohol dehydrogenase locus in several species. (Thomas and Hunt, 1993) Nucleotide sequence data from the Dpse\Adh region of 18 isochromosomal strains of D.pseudoobscura.pseudoobscura were used to demonstrate that the lack of amino acid polymorphisms in Dpse\Adh gene product is because the neutral rate of nonsynonymous sites is low. (Schaeffer and Miller, 1992) A 3.4kb region of Dpse\Adh was sequenced for 99 isochromosomal strains from 13 North and South American populations: tests for genetic differentiation between populations fail to show substructure among North American populations. Nucleotide diversity is consistant with direct and indirect measures of gene flow that show extensive dispersal between populations of D.pseudoobscura.pseudoobscura. (Schaeffer and Miller, 1992) ADH in the obscura group lacks amino acids 3 and 4 when compared to the melanogaster group and has accumulated most of its amino acid replacements in the third exon. (Marfany and Gonzalez-Duarte, 1991) The degree of genetic differentiation and the time of divergence were estimated for the population of D.pseudoobscura.pseudoobscura at Bogota by comparison of 3388 nucleotides in the Dpsb\Adh and Dpsb\Adhr region. The Bogota and North American populations separated at least 155000 years ago. (Schaeffer and Miller, 1991)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • XM_001357339 RefSeq (Proteins) • XP_001357375 DDBJ / EMBL / GenBank • AAA99016 AAA99017 AAA99018 AAA99019 AAA99020 AAA99021 AAA99022 AAA99023 AAA99024 AAA99025 AAB06136 AAB06137 AAB06138 AAB06139 AAB06140 AAB06141 AAB06142 AAB06143 AAB06144 AAB06145 AAB06146 AAB06147 AAB06148 AAB06149 AAB06150 AAB06151 AAB06152 AAB06153 AAB06154 AAB06155 AAB06156 AAB06157 AAB06158 AAB06159 AAB06160 AAB06161 AAB06162 AAB06163 AAB06164 AAB06165 AAB06166 AAB06167 AAB06168 AAB06169 AAB06170 AAB06171 AAB06172 AAB06173 AAB06174 AAB06175 CAA44102 CAA44103 CAA44104 CAA44105 CAA44106 CAA44107 CAA44108 CAA44109 CAA44110 CAA44111 CAA44112 CAA44113 CAA44114 CAA44115 CAA44116 CAA44117 CAA44118 CAA44119 CAA44120 CAA44121 CAA44122 CAA44123 CAA44124 CAA44125 CAA44126 CAA44127 CAA44128 CAA44129 CAA44130 CAA44131 CAA44132 CAA44133 CAA44134 CAA44135 CAA44136 CAA44137 CAA44138 CAA44139 CAA44140 CAA44141 CAA44142 CAA44143 CAA44144 CAA44145 CAA44146 CAA44147 CAA44148 CAA44149 CAA44150 CAA44151 CAA44152 CAA44153 CAA44154 CAA44155 CAA44156 CAA44157 CAA44158 CAA44159 CAA45797 CAA45798 CAA45799 CAA45800 CAA45801 CAA45802 CAA45803 CAA45804 CAA45805 CAA45806 CAA45807 CAA45808 CAA45809 CAA45810 CAA45811 CAA45812 CAA45813 CAA45814 CAA45815 CAA45816 CAA45817 CAA45818 EAL34444 M60979 M60980 M60981 M60982 M60983 M60984 M60985 M60986 M60987 M60988 U64521 U64522 U64523 U64524 U64525 U64526 U64527 U64528 U64529 U64530 U64531 U64532 U64533 U64534 U64535 U64536 U64537 U64538 U64539 U64540 U64541 U64542 U64543 U64544 U64545 U64546 U64547 U64548 U64549 U64550 U64551 U64552 U64553 U64554 U64555 U64556 U64557 U64558 U64559 U64560 X62181 X62182 X62183 X62184 X62185 X62186 X62187 X62188 X62189 X62190 X62191 X62192 X62193 X62194 X62195 X62196 X62197 X62198 X62199 X62200 X62201 X62202 X62203 X62204 X62205 X62206 X62207 X62208 X62209 X62210 X62211 X62212 X62213 X62214 X62215 X62216 X62217 X62218 X62219 X62220 X62221 X62222 X62223 X62224 X62225 X62226 X62227 X62228 X62229 X62230 X62231 X62232 X62233 X62234 X62235 X62236 X62237 X62238 X64468 X64469 X64470 X64471 X64472 X64473 X64474 X64475 X64476 X64477 X64478 X64479 X64480 X64481 X64482 X64483 X64484 X64485 X64486 X64487 X64488 X64489 Entrez Gene - A searchable database of RefSeq genes. • 4818070 UniProtKB/Swiss-Prot • Q6LCE4
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Alcohol dehydrogenase, Drosophila-type (IPR002425) Alcohol dehydrogenase, insect-type (IPR002424) Short-chain dehydrogenase/reductase SDR (IPR002198) NAD(P)-binding domain (IPR016040) Short-chain dehydrogenase/reductase, conserved site (IPR020904)
Linkouts
	FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0243561 modMine - Data generated by the modENCODE project. • FBgn0243561
Synonyms & Secondary IDs ( 10 )
Reported As
Symbol Synonym	Adh (Morrell et al., 2006, Parsch, 2003, Drosophila 12 Genomes Consortium, 2008, Katoh et al., 2000, Malaspinas et al., 2011, de Setta et al., 2007, Schaeffer, 2002, Charlesworth et al., 2005) ADH (Clark and Wang, 1994, Dorit and Ayala, 1995, Meghlaoui and Veuille, 1997) adh (Schaeffer, 1991.9.3, Schaeffer, 1991.9.3, Schaeffer, 1991.9.3, Schaeffer, 1991.9.3, Schaeffer, 1991.9.3, Schaeffer, 1991.9.3, Schaeffer, 1991.9.3, Schaeffer, 1991.9.3, Schaeffer, 1991.9.3, Schaeffer, 1991.9.3) DpADH (Henikoff and Wallace, 1988) dpse_GLEANR_16615 (Drosophila 12 Genomes Consortium, 2008) Dpse\Adh (Drosophila 12 Genomes Consortium, 2008, ) Dpse\Adh+Dpse\Adhr   Dpse\GA17214
Name Synonym	Alcohol dehydrogenase (Moriyama and Hartl, 1993) alcohol dehydrogenase (Katoh et al., 2000, Schaeffer, 2002)
Secondary FlyBase IDs
	FBgn0012688 FBgn0082493
References ( 93 )
Generate a list of	All references relating to this gene ( 93 )
List References by type	Research paper  ( 70 ) Review  ( 3 ) Personal communication to FlyBase  ( 2 ) Abstract  ( 4 ) FlyBase analysis  ( 2 ) DNA/RNA sequence record  ( 11 ) Conference report  ( 1 )
Recent research papers ( 2 )
	Palmieri et al., 2012, PLoS ONE 7(10): e46415 Evaluation of Different Reference Based Annotation Strategies Using RNA-Seq - A Case Study in Drososphila pseudoobscura. [FBrf0219653] Malaspinas et al., 2011, Bull. Math. Biol. 73(4): 795--810 Parametric analysis of alignment and phylogenetic uncertainty. [FBrf0214321] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...