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Gene Dmel\mud

General Information
Symbol	Dmel\mud	Species	D. melanogaster
Name	mushroom body defect	Annotation symbol	CG12047
Feature type	protein_coding_gene	FlyBase ID	FBgn0002873
Created / Updated	2005-01-10/2005-01-10
Genomic Location
Chromosome (arm)	X	Recombination map	1-50
Cytogenetic map	12E5-12E6	Sequence location	X:14,141,876..14,152,633 [+]
Map ( 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 mushroom body defect is referred to in FlyBase by the symbol mud (CG12047, FBgn0002873). It has the cytological map location 12E5-12E6. Its sequence location is X:14141876..14152633. Its molecular function is described as: steroid hormone receptor activity; superoxide dismutase activity; transcription factor activity; metal ion binding. It is involved in the biological processes: spindle assembly involved in female meiosis II; mushroom body development; superoxide metabolic process; regulation of transcription, DNA-dependent. 11 alleles are reported. The phenotypes of these alleles are annotated with 25 unique terms, many of which group under: adult segment; nervous system; adult brain; dorso-lateral dopamine neuron; organ system; abdominal segment 7; egg; abdominal 5 neuroblast ventro-medial cluster; antennal segment; peripheral nervous system. It has 3 annotated transcripts and 3 annotated polypeptides.
External Summaries
Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage	mud: mushroom body defect (J.C. Hall) Neuropile of mushroom bodies (usually in dorsal brain) is missing (Heisenberg, 1980); penetrance for this anatomical phenotype (on which criterion the mutant was isolated) ca. 90%. Calyces that should innervate pedunculi and lobes of mushroom bodies are enlarged, as are antennal lobes in anterior brain. At sites of calyces, large numbers of thin axons form distinct lobes outside main neuropile of brain. Viability of mutant females poor, and they are sterile as well. Development of mushroom bodies apparently normal until pupation, when "reconstruction" of this bilaterally paired brain entity (this process being a normal feature of wild-type metamorphosis) is aberrant (Technau and Heisenberg, 1982). Supernumerary neuroblasts observed in the larval brain, owing to anomalous proliferation of such cells postembryonically.
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 12E5-12E6   Limits computationally determined from genome sequence between P{EP}l(1)G0007EP764 and P{EP}EP1599
Experimentally Determined Cytological Location
Cytogenetic map Notes References 12E-12E   (Guan, 1999.7.31)
Experimentally Determined Recombination Data
Location	1-50 (Heisenberg, 1980)
Left of (cM)
Right of (cM)
Notes
Molecular Map Data
Gene Order (in direction of increasing cytology) References Gene Order (overall orientation not stated) References Overall orientation not stated: mRNA-capping-enzyme- CG32599+ mud+ (Guan, 1999.7.31)
Gene Model & Products
Please see the GBrowse view of Dmel\mud for information on other features
Comments on Gene Model
	DGC clone LD29039 appears problematic: incomplete CDS
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) mud-RA FBtr0073905  NM_167400   7634   2328 mud-RB FBtr0073906  NM_167399   8210   2520 mud-RC FBtr0073907  NM_080495   5991   1871
Additional Transcript Data & Comments
Reported size (kB)	6.003 (longest cDNA) (Guan et al., 2000)
Comments	This transcript is based on EST clone LD24364, which has a nonconsensus splice site following exon 6. (Guan et al., 2000)
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kD) Length (aa) Theoretical pI RefSeq ID GenBank protein mud-PA   FBpp0073722   266.9   2328   5.51     NP_727770   AAF48362 mud-PB   FBpp0073723   288.8   2520   5.55     NP_727769   AAN09583 mud-PC   FBpp0073724   216.1   1871   5.03     NP_536743   AAN09584
Additional Polypeptide Data & Comments
Reported size (kD)	2501, 1871 (aa) (Guan et al., 2000)
Comments	Each mud protein isoform is predicted to have a long coiled-coil in the central region, and a carboxy-terminal transmembrane domain. The region predicted to form a coiled-coil includes a segment of 42 amino acids that is repeated 10 times. The 1871 amino acid isoform is predicted to have a single transmembrane segment, whereas the two longer isoforms are predicted to have two transmembrane segments each. (Guan et al., 2000, Guan et al., 2000, Guan et al., 2000)
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Manganese and iron superoxide dismutase (IPR001189) Prefoldin (IPR009053) RuvA domain 2-like (IPR010994) Nuclear hormone receptor, ligand-binding (IPR008946)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA392172   AA820568   AA949597   AA951447   AA952024   AE003495 AAF48362   AE003495 AAN09583   AE003495 AAN09584   AF174134 AAF88146   AF209068 AAF89163   AI455461   AI512725   AW942926   AY058595 AAL13824   BF503886   BI228050   BI230863   BI355966   BP542150   BT024978   CO273644   CO279851   CO315085   CO328916   CZ483683   DQ465527 ABF00987   EC065548   EC070875   EC070876   EC073022   EC207312   EC217166   EC219387   EC221174   EC232491   EC242466   EC251218   EL874863   EL874864   EL874992   EL874993   LD24364
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	Q1KN24 Q8IR54 Q8IR55 Q95TR6 Q9NCL3 Q9NCW7 Q9VY43
Maps to	80G4 DS05471 (Guan, 1999.7.31)
Does NOT map to
Identified with	LD11076 LD29552 LD44694 (Guan, 1999.7.31) LD24364 LD31911 (Guan et al., 2000, Guan, 1999.7.31) LD29039 (BDGP Project Members, 2000-, Guan, 1999.7.31)
Mapped Features & Mutations
Please see GBrowse or insertion reports for information on insertions of transgenic constructs and features not listed here Type Symbol & Location Additional Notes References rescue fragment mud[+t18] X:14,137,826..14,156,035 comment=Position of restriction fragment on reference sequence inferred by FlyBase curator. evidence=experimental linked_to=SnaBI-SnaBI_rfrag (Guan et al., 2000)
External Data
Linkouts	DEDB - Drosophila exon database: splicing graphs • 2807
Crossreferences
Expression Data
FlyBase-Curated Data
Transcript and Protein data	Please see the FlyBase Gene Expression Report for details of gene expression from the literature.
Summary of Transcript Expression
Stage Tissue/Position Reference  embryonic stage   (Guan et al., 2000)  larval stage   (Guan et al., 2000)  embryonic stage   (Guan et al., 2000)  adult stage   (Guan et al., 2000)  embryonic stage   (Guan et al., 2000)  larval stage | male   (Guan et al., 2000)
Marker for
Subcellular Localization
CV Term
Summary of Polypeptide Expression
Stage Tissue/Position Reference
Marker for
Subcellular Localization
CV Term
Microarray Data
	Developmental timecourse, Costello et al., 2008 (Original data from Arbeitman et al., 2002) AA952024
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0002873 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • FBgn0002873 GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies • FBgn0002873
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal | female mud1 mud3 lethal | embryonic stage | non-rescuable maternal effect | recessive mud4 semi-lethal mud1 mud2 mud3 mud4 Other Phenotypes Allele wild-type mud+t18 mud+tcos24 chemical sensitive mud4 chemical sensitive (with mud1) mud4 chemical sensitive (with mud4) mud1 chemical sensitive | codominant mud4 Sterility Allele sterile (with Df(1)KA9) mud1 female sterile mud1 mud2 mud3 mud4 male fertile mud1 mud2 mud3 mud4 Phenotype manifest in Allele calyx of mushroom body mud1 mud2 mud4 Kenyon cell mud1 mud4 mushroom body mud1 mud2 mud4 neuropil mud1 antennal lobe mud1 lobe of mushroom body mud1 mud4 central body complex mud1 mud4 abdominal 2 neuroblast ventro-medial cluster mud2 abdominal 3 neuroblast ventro-medial cluster mud2 abdominal 4 neuroblast ventro-medial cluster mud2 abdominal 5 neuroblast ventro-medial cluster mud2 abdominal 6 neuroblast ventro-medial cluster mud2 abdominal 7 neuroblast ventro-medial cluster mud2 abdominal 2 neuroblast dorso-lateral cluster mud2 abdominal 3 neuroblast dorso-lateral cluster mud2 abdominal 4 neuroblast dorso-lateral cluster mud2 abdominal 5 neuroblast dorso-lateral cluster mud2 abdominal 6 neuroblast dorso-lateral cluster mud2 abdominal 7 neuroblast dorso-lateral cluster mud2 stalk of mushroom body mud2 adult mushroom body mud4 medial lobe mud4 vertical branch of mushroom body mud4 egg | maternal effect mud4 egg & chromatin | maternal effect mud4 egg & spindle | maternal effect mud4 macrochaeta mudBG02499
Classical Alleles ( 7 )
For All Classical Alleles Show
Allele of mud Class Mutagen Stocks Known lesion mud1 ethyl methanesulfonate 1 Yes mud2 PM hybrid dysgenesis 0 Yes mud3 ethyl methanesulfonate 0 Yes mud4 ethyl methanesulfonate 1 -- mudBG02499 P-element activity 0 Yes mudf01205 piggyBac transposase 1 -- mudunspecified 0 --
Alleles Carried on Transgenic Constructs ( 4 )
For All Alleles Carried on Transgenic Constructs Show
Allele of mud Class Mutagen Stocks Known lesion mud+t18 in vitro construct | genomic fragment 0 Yes mud+tcos24 in vitro construct | genomic fragment 0 Yes mudGD3353 in vitro construct | RNAi in vitro construct | regulatory fusion 0 Yes mudpJMD1 in vitro construct | genomic fragment 0 Yes
Aneuploid Aberrations
Useful deficiency	Df(1)KA9
Disrupted in	Df(1)KA9 (Guan et al., 2000) Df(1)RK3 (Guan et al., 2000) Df(1)benCO1 (Guan et al., 2000) Df(1)benCO2 (Guan et al., 2000)
Not disrupted in	Df(1)NP5 (Guan et al., 2000, Mitchell, 1997.2.17) Df(1)RK5 (Guan et al., 2000) Df(1)g (Guan et al., 2000) T(1;Y)B146 (Scott, 2008.5.20)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD3353} NA characterization construct P{mud.cos24} NA P{mud.pJMD1} NA P{mud.pZHRC} NA
Insertions
	Type of insertions Name Expression data miscellaneous insertions PBac{WH}mudf01205 NA P{GT1}mudBG02499 NA insertion of mobile activating element P{GSV1}EP-689EP-689 NA
Related Comments
	Please look at the allele reports for the complete phenotype data Mutation of mud interferes with the regulation of central nervous system development by affecting the proliferation pattern. (Prokop and Technau, 1994) Neuropil of mushroom bodies (usually in dorsal brain) is missing (Heisenberg, 1980); penetrance for this anatomical phenotype (on which criterion the mutant was isolated) ca. 90%. Calyces that should innervate pedunculi and lobes of mushroom bodies are enlarged, as are antennal lobes in anterior brain. At sites of calyces, large numbers of thin axons form distinct lobes outside main neuropil of brain. Viability of mutant females poor and they are sterile as well. Development of mushroom bodies apparently normal until pupation, when 'reconstruction' of this bilaterally paired brain entity (this process being a normal feature of wild-type metamorphosis) is aberrant (Technau and Heisenberg, 1982). Supernumerary neuroblasts observed in the larval brain, owing to anomalous proliferation of such cells postembryonically.
Gene Ontology: Function, Process & Cellular Component ( 10 )
Molecular Function
CV term Evidence References
metal ion binding inferred from electronic annotation with InterPro:IPR001189 (FlyBase Curators et al., 2004-)
steroid hormone receptor activity inferred from electronic annotation with InterPro:IPR008946 (FlyBase Curators et al., 2004-)
superoxide dismutase activity inferred from electronic annotation with InterPro:IPR001189 (FlyBase Curators et al., 2004-)
transcription factor activity inferred from electronic annotation with InterPro:IPR008946 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
mushroom body development traceable author statement (Guan et al., 2000) inferred from mutant phenotype (de Belle and Heisenberg, 1996)
regulation of transcription, DNA-dependent inferred from electronic annotation with InterPro:IPR008946 (FlyBase Curators et al., 2004-)
spindle assembly involved in female meiosis II inferred from mutant phenotype (Yu et al., 2006)
superoxide metabolic process inferred from electronic annotation with InterPro:IPR001189 (FlyBase Curators et al., 2004-)
Cellular Component
CV term Evidence References
nucleus inferred from electronic annotation with InterPro:IPR008946 (FlyBase Curators et al., 2004-)
spindle midzone inferred from direct assay (Yu et al., 2006)
Sequence Ontology: Class of Gene
	protein_coding_gene   nuclear_gene
Interactions & Pathways
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions mud allele Gene References mud4 w (Campbell and Nash, 2001)
External Data
Linkouts	BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions • 69318 Drosophila PIMRider - The Drosophila Protein Interaction map • 521244
Orthologs
Genome-wide drosophilid orthologs	Dana\GF22554 Dere\GG17839 Dgri\GH12928 Dper\GL14926 Dsim\GD17165 Dvir\GJ19063 Dwil\GK20155
Curated drosophilid orthologs	Dpse\GA11358
Linkouts
Functional Complementation between Species
Inter-Species Misexpression Data
Produces phenotype in
Produces NO phenotype in
Stocks & Reagents
Stocks Listed in FlyBase ( 3 )
Harvard	- PBac{WH}mudf01205
Bloomington	9562 mud1/FM7i, P{ActGFP}JMR3 9563 mud4/FM7i, P{ActGFP}JMR3
Genomic Clones ( 1 )
	BACR12J05
cDNA Clones ( 16 )
	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	IP14842
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	AT05112 LD29552 RE16121 LD11076 RE25468 LD31911 RE37037 LD44694
Other clones	LD24364 IP14942 EK111723 EK238963 EK291648 IP15042 EK136160
RNAi & Array Information
Affy Oligo
Linkouts	DRSC - RNAi screening (Harvard): high-throughput cell culture data and design • FBgn0002873 GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data • FBgn0002873
Antibody Information
Other Information
Discoverer
Etymology
Identification
Position Effect Variegation Data
Relationship to Other Genes
Source for database identity of
Source for database merge of
Additional comments	Source for split of: CG12047 Annotation CG12047 split into CG12047 (which corresponds to mud) and CG32599 in release 3 of the genome annotation. (FlyBase Genome Annotators, 2002-2003)
Comments About Role
Comments About Molecular Function
Other Comments
	Expression is enriched in embryonic gonads. (Shigenobu et al., 2006)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_167400 NM_167399 NM_080495 RefSeq (Proteins) • NP_727770 NP_727769 NP_536743 DDBJ / EMBL / GenBank • AAN09584.1 AAN09583.1 AAF48362.2 AAN09583.2 AA392172 AA820568