• Home
• Tools
  • BLAST
  • GBrowse
  • QueryBuilder
  • TermLink
  • ImageBrowse
  • Interactions Browser
  • Apollo
  • CytoSearch
  • QuickSearch
  • Batch Download
  • Coordinate Converter
  • Google™ FlyBase
  • Find A Person
  • Update An Address
  • Add A New Person
• Files
  • Downloads:
  • Precomputed files
  • Archived data
  • Releases FTP
  • Genomes FTP
  • Lists:
  • Transposons (Dmel)
  • Transposons (other)
  • Vectors & Constructs
  • Anatomical Terms
  • Map Conversion
• Species
  • Phylogeny
  • Synteny Table
  • Drosophilidae
  • Abbreviations
• Documents
  • About FlyBase
  • Reference Manual:
  • Sections
  • Contents
  • Nomenclature
  • Release Notes
• Resources
  • All resources
  • Interactive Fly
  • Textpresso for Fly
  • AAA site
  • BDGP
  • DHGP
  • DGRC
  • Model Organisms
  • Stock Collections:
  • Bloomington
  • DrosDel
  • Ehime
  • Exelixis (Harvard)
  • GDP (Baylor)
  • Kyoto
  • NIG-Fly
  • Szeged
  • Tucson
  • VDRC
• News
  • News
  • FlyBase Forum
  • FlyBase Positions
  • Meetings
  • Courses
  • Fly Board
  • White papers
  • Funding
  • bionet.dros
• Help
  • Google™ FlyBase
  • Site Map
  • FAQs
  • Report help
  • New to Flies
  • Pers. comm.
  • Author guidelines
  • Known Problems
  • Contact FlyBase
• Archives
  • Prior Home Page
  • R4.3 BLAST
  • R4.3 GBrowse
  • Older Archives

Gene Dmel\140up

General Information
Symbol	Dmel\140up	Species	D. melanogaster
Name	upstream of RpII140	Annotation symbol	CG9852
Feature type	protein_coding_gene	FlyBase ID	FBgn0010340
Created / Updated	2003-12-01/2003-12-01
Genomic Location
Chromosome (arm)	3R	Recombination map
Cytogenetic map	88A9-88A9	Sequence location	3R:9,949,940..9,951,252 [-]
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 upstream of RpII140 is referred to in FlyBase by the symbol 140up (CG9852, FBgn0010340). It has the cytological map location 88A9. Its sequence location is 3R:9949940..9951252. Its molecular function is described as protein transporter activity. It is involved in the biological processes: multicellular organismal development; protein transport. 7 alleles are reported. No phenotypic data is available. It has one annotated transcript and one annotated polypeptide.
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 88A9-88A9   Limits computationally determined from genome sequence between P{PZ}flfl01949 and P{lacW}trxj14A6&P{PZ}trx00347
Experimentally Determined Cytological Location
Cytogenetic map Notes References
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)	RpII140 (Hamilton et al., 1993)
Notes	140upZ6 maps 0.02cM from RpII140Z24, with 140up probably lying proximal to RpII140. (Hamilton et al., 1993)
Molecular Map Data
Gene Order (in direction of increasing cytology) References Gene Order (overall orientation not stated) References Overall orientation not stated: 140up- RpII140+ (Sitzler, 1999.8.31) Overall orientation not stated: Abi- twf+ 140up- (Wahlstrom et al., 2001)
Gene Model & Products
Please see the GBrowse view of Dmel\140up for information on other features
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) 140up-RA FBtr0082909  NM_057603   1127   261
Additional Transcript Data & Comments
Reported size (kB)	1.3 (northern blot) (Sitzler et al., 1991)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kD) Length (aa) Theoretical pI RefSeq ID GenBank protein 140up-PA   FBpp0082370   29.2   261   9.11     NP_476951   AAF55023
Additional Polypeptide Data & Comments
Reported size (kD)	261 (aa); 30 (kD predicted) (Sitzler et al., 1991)
Comments
External Data
Linkouts	PANTHER - Protein classification by function, families, and pathways • FBgn0010340
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Mitochondrial import inner membrane translocase, subunit Tim17/22 (IPR003397)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA941870   AC007441   AC007904   AE003703 AAF55023   AW942742   AY058577 AAL13806   BE975447   BE975448   BE978357   BP558096   BP558097   CK656983   EC052369   EC055831   M62973   M62975 AAD40352
UniProtKB/Swiss-Prot	P81928
UniProtKB/TrEMBL
Maps to	FBcl0298056 FBcl0298057 (FlyBase, 1992-)
Does NOT map to
Identified with	LD27182 (BDGP Project Members, 2000-)
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
External Data
Linkouts	DEDB - Drosophila exon database: splicing graphs • 9376
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  adult stage   (Sitzler et al., 1991)
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) AA941870
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0010340 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • FBgn0010340 GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies • FBgn0010340 FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for 140up Stage(s) 1-3 Stage(s) 13-16
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal | recessive 140upM13 140upZ29 140upZ30 140upZ6 Phenotype manifest in Allele
Classical Alleles ( 5 )
For All Classical Alleles Show
Allele of 140up Class Mutagen Stocks Known lesion 140upM13 ethyl methanesulfonate 0 -- 140upZ29 ethyl methanesulfonate 0 -- 140upZ30 ethyl methanesulfonate 0 -- 140upZ6 ethyl methanesulfonate 0 -- 140upf07279 piggyBac transposase 2 --
Alleles Carried on Transgenic Constructs ( 2 )
For All Alleles Carried on Transgenic Constructs Show
Allele of 140up Class Mutagen Stocks Known lesion 140upGD16421 in vitro construct | RNAi in vitro construct | regulatory fusion 1 Yes 140upGD1819 in vitro construct | RNAi in vitro construct | regulatory fusion 0 Yes
Aneuploid Aberrations
Useful deficiency	Df(3R)red-P52
Disrupted in	Df(3R)Exel7359 (Ryder, 2004.4.26) Df(3R)JY19 (Breen and Harte, 1991) Df(3R)red-P1 (Mortin et al., 1992) Df(3R)red-P52 (Breen and Harte, 1991, Mortin et al., 1992)
Not disrupted in	Df(3R)293γ5 (Mortin et al., 1992) Df(3R)JY28 (Breen and Harte, 1991) Df(3R)red-P6 (Breen and Harte, 1991, Mortin et al., 1992) Df(3R)red-P93 (Breen and Harte, 1991, Mortin et al., 1992) Df(3R)red2l (Breen and Harte, 1991) Df(3R)su(Hw)V (Breen and Harte, 1991, Mortin et al., 1992) Df(3R)trxE12 (Breen and Harte, 1991) T(Y;3)redP4 (Breen and Harte, 1991)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD16421} NA P{GD1819} NA
Insertions
	Type of insertions Name Expression data miscellaneous insertions PBac{WH}140upf07279 NA
Related Comments
	Please look at the allele reports for the complete phenotype data All known alleles are recessive lethals.   Sequences important for the transcription of RpII140 are located in the untranslated leader of the divergently transcribed 140up gene. (Wiedemann et al., 1997)
Gene Ontology: Function, Process & Cellular Component ( 4 )
Molecular Function
CV term Evidence References
protein transporter activity inferred from electronic annotation with InterPro:IPR003397 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
multicellular organismal development inferred from mutant phenotype (Sitzler et al., 1991)
protein transport inferred from electronic annotation with InterPro:IPR003397 (FlyBase Curators et al., 2004-)
Cellular Component
CV term Evidence References
mitochondrial inner membrane inferred from electronic annotation with InterPro:IPR003397 (FlyBase Curators et al., 2004-)
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 140up allele Gene References
External Data
Linkouts	BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions • 66797
Orthologs
Genome-wide drosophilid orthologs	Dana\GF18787 Dere\GG21481 Dgri\GH19697 Dmoj\GI24553 Dper\GL23308 Dpse\GA22073 Dsec\GM25883 Dsim\GD20454 Dvir\140up Dwil\GK10906 Dyak\GE10058
Curated drosophilid orthologs	Dpse\GA22073   Dvir\140up
Linkouts	InParanoid orthologs - Eukaryotic orthologs • ENSANGP00000015214 Anopheles gambiae (Ensembl) ENSBTAP00000016702 Bos taurus (Ensembl) ENSCAFP00000016185 Canis familiaris (Ensembl) NEWSINFRUP00000139942 Takifugu rubripes (Ensembl) ENSGALP00000024914 Gallus gallus (Ensembl) ENSP00000264244 Homo sapiens (Ensembl) ENSMMUP00000015763 Macaca mulatta (Ensembl) ENSMODP00000022692 Monodelphis domestica (Ensembl) ENSPTRP00000026303 Pan troglodytes (Ensembl) ENSRNOP00000004023 Rattus norvegicus (Ensembl) WBGene00036650 Caenorhabditis briggsae (Wormbase) WBGene00021421 Caenorhabditis elegans (Wormbase) ZDB-CDNA-050417-370 Danio rerio (Zfin) ZDB-GENE-050417-369 Danio rerio (Zfin) MGI:1922139 Mus musculus (Informatics)
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}140upf07279
VDRC	v48717 w1118 P{GD16421}v48717
Bloomington	19065 w1118; PBac{WH}140upf07279/TM6B, Tb1
Genomic Clones ( 2 )
	BACR10E03 BACR01H04
cDNA Clones ( 6 )
	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	LD27182
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	LP22876
Other clones	EC052369 EC055831 bs43c11 bs77f04
RNAi & Array Information
Affy Oligo
Linkouts	DRSC - RNAi screening (Harvard): high-throughput cell culture data and design • FBgn0010340 GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data • FBgn0010340
Antibody Information
Other Information
Discoverer
Etymology
Identification
Position Effect Variegation Data
Relationship to Other Genes
Source for database identity of	Source for identity of: 140up CG9852 (Zheng, 1999.11)
Source for database merge of
Additional comments
Comments About Role
Comments About Molecular Function
Other Comments
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_057603 RefSeq (Proteins) • NP_476951 DDBJ / EMBL / GenBank • AA941870 AC007441 AC007904 AE003703 AAF55023 AW942742 AY058577 AAL13806 M62973 M62975 AAD40352 UniProtKB/Swiss-Prot • P81928
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Mitochondrial import inner membrane translocase, subunit Tim17/22 (IPR003397)
Linkouts
	BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions • 66797 DEDB - Drosophila exon database: splicing graphs • 9376 DRSC - RNAi screening (Harvard): high-throughput cell culture data and design • FBgn0010340 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0010340 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • FBgn0010340 FlyExpress - Embryonic expression images (BDGP data) • FBgn0010340 FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0010340 GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies • FBgn0010340 GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data • FBgn0010340 InParanoid orthologs - Eukaryotic orthologs • ENSANGP00000015214 Anopheles gambiae (Ensembl) ENSBTAP00000016702 Bos taurus (Ensembl) ENSCAFP00000016185 Canis familiaris (Ensembl) NEWSINFRUP00000139942 Takifugu rubripes (Ensembl) ENSGALP00000024914 Gallus gallus (Ensembl) ENSP00000264244 Homo sapiens (Ensembl) ENSMMUP00000015763 Macaca mulatta (Ensembl) ENSMODP00000022692 Monodelphis domestica (Ensembl) ENSPTRP00000026303 Pan troglodytes (Ensembl) ENSRNOP00000004023 Rattus norvegicus (Ensembl) WBGene00036650 Caenorhabditis briggsae (Wormbase) WBGene00021421 Caenorhabditis elegans (Wormbase) ZDB-CDNA-050417-370 Danio rerio (Zfin) ZDB-GENE-050417-369 Danio rerio (Zfin) MGI:1922139 Mus musculus (Informatics) PANTHER - Protein classification by function, families, and pathways • FBgn0010340 University of Chicago Dev. Expression • FBgn0010340
Synonyms & Secondary IDs ( 8 )
Reported As
Symbol Synonym	140up   CG9852   DmRP140up (Wiedemann et al., 1997) DmRP140-upstream (Sitzler, 1999.8.31, Sitzler et al., 1991) l(3)88Ba   l(3)Z6 (Breen and Harte, 1991, ) unnamed (Sitzler, 1999.8.31)
Name Synonym	upstream of RpII140
Secondary FlyBase IDs
	FBgn0004843
References ( 19 )
Research paper	Ceriani et al., 2002, J. Neurosci. 22(21): 9305--9319 Genome-wide expression analysis in Drosophila reveals genes controlling circadian behavior. [FBrf0152147] Wahlstrom et al., 2001, J. Cell Biol. 155(5): 787--795 Twinfilin is required for actin-dependent developmental processes in Drosophila. [FBrf0141598] Wiedemann et al., 1997, Biochim. biophys. Acta 1350(3): 282--286 Transcription of DmRP140, the gene coding for the second-largest subunit of RNA polymerase II. [FBrf0092726] Hamilton et al., 1993, Genetics 134(2): 517--529 Reverse genetics of Drosophila RNA polymerase II: identification and characterization of RpII140, the genomic locus for the second-largest subunit. [FBrf0058600] Mortin et al., 1992, Genetics 131: 895--903 Mutations in the second-largest subunit of Drosophila RNA polymerase II interact with Ubx. [FBrf0056267] Breen and Harte, 1991, Mech. Dev. 35: 113--127 Molecular characterization of the trithorax gene, a positive regulator of homeotic gene expression in Drosophila. [FBrf0054607] Sitzler et al., 1991, Gene 100: 155--162 Analysis of the promoter region of the housekeeping gene DmRP140 by sequence comparison of Drosophila melanogaster and Drosophila virilis. [FBrf0054010]
Supplementary material	Dietzl et al., 2007, Nature 448(7150): Supplementary Table 1. [FBrf0202579]
Personal communication to FlyBase	Dickson et al., 2007.7.18, RNAi construct and insertion data submitted by the Vienna Drosophila RNAi Center RNAi construct and insertion data submitted by the Vienna Drosophila RNAi Center [FBrf0200327] Bloomington Drosophila Stock Center, 2004.11.6, Exelixis insertion alleles that are not in FlyBase. Exelixis insertion alleles that are not in FlyBase. [FBrf0179797] 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] Ryder, 2004.4.26, Exelixis CG deletion data. Exelixis CG deletion data. [FBrf0184335]
Abstract	Oldenburg et al., 1993, Europ. Dros. Res. Conf. 13: Poster G4 Analysis of the promoter region of the housekeeping gene Dmrp140. [FBrf0058349]
FlyBase analysis	FlyBase, 1996-, FlyBase inference based on genome sequence analysis. FlyBase inference based on genome sequence analysis. [FBrf0104946] FlyBase, 1992-, FlyBase curation FlyBase curation. [FBrf0105495]
DNA/RNA sequence record	Sitzler, 1999.8.31, GenBank/EMBL/DDBJ: M62975 Drosophila melanogaster RNA polymerase II second largest subunit upstream (DmRP140-upstream) gene, exons 1-4 and complete cds. [FBrf0120782] Sitzler, 1999.8.31, GenBank/EMBL/DDBJ: M62973 Drosophila melanogaster RNA polymerase II second largest subunit (DmRP 140) gene, upstream bidirectional promoter region. [FBrf0120781]
Curated genome annotation	Zheng, 1999.11, [Annotations performed at the Celera Jamboreee.] [Annotations performed at the Celera Jamboreee.] [FBrf0126702]
Computer file	BDGP Project Members, 2000-, Berkeley Drosophila Genome Project. Berkeley Drosophila Genome Project. [FBrf0125078]