Gene Dmel\trn

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General Information

Symbol

Dmel\trn

Species

D. melanogaster

Name

tartan

Annotation symbol

CG11280

Feature type

protein_coding_gene

FlyBase ID

FBgn0010452

Created / Updated

2003-12-01/2003-12-01

Genomic Location

Chromosome (arm)

Recombination map

Cytogenetic map

70A1-70A1

Sequence location

3L:13,107,373..13,111,188 [+]

Map ( GBrowse )

Summary Information

Automatically generated summary

See sections below for more information

The gene tartan is referred to in FlyBase by the symbol trn (CG11280, FBgn0010452). It has the cytological map location 70A1. Its sequence location is 3L:13107373..13111188. Its molecular function is described as protein binding. It is involved in the biological processes: cell adhesion; open tracheal system development; cell migration; branch fusion, open tracheal system. 9 alleles are reported. The phenotypes of these alleles are annotated with: abdominal lateral transverse muscle 1; abdominal lateral transverse muscle 2; abdominal lateral transverse muscle 3; abdominal lateral transverse muscle 4; abdominal dorsal transverse muscle 1; embryonic peripheral nervous system; embryonic/larval somatic muscle; embryonic dorsal trunk; embryonic lateral trunk; dorsal mesothoracic disc. It has one annotated transcript and one annotated polypeptide.

Detailed Mapping Data

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

70A1-70A1

Limits computationally determined from genome sequence between P{PZ}l(3)04220⁰⁴²²⁰&P{lacW}l(3)j10B6^j10B6 and P{PZ}stv⁰⁰⁵⁴³

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

70A1-70A2

(Laughon, 1993.9.24)

70A1-70A2

(determined by in situ hybridisation)

(Szeged Stock Center, 1998-)

70A-70A

(determined by in situ hybridisation)

(Salzberg et al., 1997)

70A-70A

(determined by in situ hybridisation)

(Deak et al., 1997)

Experimentally Determined Recombination Data

Location

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

Gene Model & Products

Please see the GBrowse view of Dmel\trn for information on other features

Comments on Gene Model

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Associated CDS (aa)

trn-RA

FBtr0075890

NM_079331

3374

737

Additional Transcript Data & Comments

Reported size (kB)

3.3 (northern blot)

(Chang et al., 1993)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kD)

Length (aa)

Theoretical pI

RefSeq ID

GenBank protein

trn-PA

FBpp0075624

81.9

737

7.61

NP_524055

AAF49839

Additional Polypeptide Data & Comments

Reported size (kD)

733 (aa)

(Chang et al., 1993)

Comments

External Data

Linkouts

PANTHER - Protein classification by function, families, and pathways

•

FBgn0010452

Crossreferences

InterPro domains - A database of protein families, domains, and functional sites

•

Cysteine-rich flanking region, C-terminal (IPR000483)

Leucine-rich repeat (IPR001611)

Leucine-rich repeat, typical subtype (IPR003591)

Leucine-rich repeat, cysteine-rich flanking region, N-terminal (IPR000372)

Sequences Consistent with the Gene Model

DDBJ /
EMBL /
GenBank

DNA sequence

Protein sequence

Name

Maps to

Does NOT map to

Identified with

GH10871

(BDGP Project Members, 2000-, Artero et al., 2003, Krause et al., 2006)

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

•

4250

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 | stage >=8

sense organ | precursor

(Chang et al., 1993)

embryonic stage | stage 15-16

embryonic/larval hindgut

(Chang et al., 1993)

larval stage | third instar

ventral thoracic disc

(Chang et al., 1993)

embryonic stage | stage 15,16

stomodeum

(Chang et al., 1993)

larval stage | third instar

morphogenetic furrow | anterior

(Chang et al., 1993)

embryonic stage | stage 15,16

proctodeum

(Chang et al., 1993)

embryonic stage | stage 16,17

central nervous system

(Chang et al., 1993)

larval stage | third instar

outer optic anlagen

(Chang et al., 1993)

larval stage,pupal stage

central nervous system

(Chang et al., 1993)

embryonic stage | stage 5

(Chang et al., 1993)

embryonic stage | stage >=8

embryonic peripheral nervous system | restricted

(Chang et al., 1993)

larval stage | third instar

eye-antennal disc

(Chang et al., 1993)

larval stage | third instar

inner optic anlagen

(Chang et al., 1993)

larval stage | third instar

dorsal mesothoracic disc

(Chang et al., 1993)

larval stage,pupal stage

peripheral nervous system

(Chang et al., 1993)

embryonic stage-adult stage

(Chang et al., 1993)

larval stage | third instar

morphogenetic furrow | posterior to

(Chang et al., 1993)

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)

Untitled Document detailed view

AI114170

External Data & Images

Linkouts

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

•

FBgn0010452

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

•

FBgn0010452

GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies

•

FBgn0010452

FlyExpress - Embryonic expression images (BDGP data)

•

Show all FlyExpress processed images for trn

Alleles & Phenotypes

Summary of Allele Phenotypes

Lethality

Allele

lethal | recessive

lethal | embryonic stage | recessive

lethal | adult stage | recessive

trn^S002405a

semi-lethal | recessive

trn^S002405a

Phenotype manifest in

Allele

abdominal lateral transverse muscle 1 (with In(3LR)C190)

trn^28.4

abdominal lateral transverse muscle 2 (with In(3LR)C190)

trn^28.4

abdominal lateral transverse muscle 3 (with In(3LR)C190)

trn^28.4

abdominal lateral transverse muscle 4 (with In(3LR)C190)

trn^28.4

abdominal dorsal transverse muscle 1 (with In(3LR)C190)

trn^28.4

embryonic peripheral nervous system

trn^28.4

embryonic/larval somatic muscle

trn^28.4

embryonic dorsal trunk

trn^28.4

embryonic lateral trunk

trn^28.4

lch5 neuron & embryo

dorsal mesothoracic disc, with Scer\GAL4^Act5C.PP

trn^Scer\UAS.cMa

dorsal mesothoracic disc | ventral compartment, with Scer\GAL4^Act5C.PP

trn^Scer\UAS.cMa

Classical Alleles ( 5 )

For All Classical Alleles Show

Allele of trn	Mutagen	Stocks	Known lesion
trn^28.4	Δ2-3	0	Yes
trn^S002405a	P-element activity	1	--
trn^S064117	Δ2-3 P-element activity	2	--
trn^f03162	piggyBac transposase	1	--
trn^Δ2.9	P-element activity	0	Yes

Alleles Carried on Transgenic Constructs ( 4 )

For All Alleles Carried on Transgenic Constructs Show

Allele of trn	Mutagen	Stocks	Known lesion
trn^GD2450	in vitro construct \| RNAi in vitro construct \| regulatory fusion	1	Yes
trn^Scer\UAS.cMa	in vitro construct \| regulatory fusion	0	Yes
trn^cMa	in vitro construct \| other	0	Yes
trn^{ΔC.Scer\UAS.T:Hsap\MYC}	in vitro construct \| deletion in vitro construct \| regulatory fusion in vitro construct \| coding region fusion	0	Yes

Aneuploid Aberrations

Useful deficiency

Df(3L)Ly

Useful duplication

Dp(3;3)M71

Disrupted in

Df(3L)BSC12

(Deal and Cook, 2002.1.22)

Df(3L)Exel6261

(Ryder, 2004.4.26)

Df(3L)Ly

(Szeged Stock Center, 1998-)

Transgenic Constructs & Insertions

Transgenic Constructs

Type of construct

Name

Expression data

UAS construct

P{GD2450}

P{UAS-trn.M}

P{UAS-trn.ΔC.MYC}

characterization construct

P{UAS-caps^Edtrn^Id}

P{UAS-trn^EdCcps^Id}

Insertions

Type of insertions

Name

Expression data

miscellaneous insertions

PBac{WH}trn^f03162

P{PTT-GB}CB05114

insertion of enhancer trap

P{lacW}trn^S002405a

Yes

P{lacW}trn^S064117

Yes

Related Comments

Please look at the allele reports for the complete phenotype data

trn is required for cell surface interactions important for normal organization of epidermal and subepidermal structures. Expression of the trn pair rule stripes requires ftz and ems.

(Chang et al., 1993)

The primary target genes of Egfr are pnt, vnd and Fas3, these are induced in different ectodermal domains. Secondary target genes oc, argos and trn are activated by pnt in response to Egfr signalling. The proper induction of these genes requires the concomitant inactivation of aop, mediated by Egfr signalling.

(Gabay et al., 1996)

Gene Ontology: Function, Process & Cellular Component ( 6 )

Molecular Function

CV term

Evidence

References

protein binding

inferred from electronic annotation with InterPro:IPR001611

(FlyBase Curators et al., 2004-)

Biological Process

CV term

Evidence

References

branch fusion, open tracheal system

inferred from mutant phenotype

(Krause et al., 2006)

cell adhesion

non-traceable author statement

(Krause et al., 2003)

non-traceable author statement

(de Celis, 2003)

cell migration

traceable author statement

(Tyler and Baker, 2003)

open tracheal system development

inferred from mutant phenotype

(Krause et al., 2003)

Cellular Component

CV term

Evidence

References

plasma membrane

non-traceable author statement

(Laughon, 1993.9.24)

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

trn allele

Gene

References

unspecified

(Krause et al., 2006, Milan et al., 2002)

External Data

Linkouts

BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions

•

64836

Orthologs

Genome-wide drosophilid orthologs

Dana\GF24031

Dere\GG15627

Dgri\GH17150

Dmoj\GI11760

Dpse\GA10887

Dsec\GM25399

Dsim\GD14431

Dvir\GJ13467

Dwil\GK17431

Dyak\Trn

Curated drosophilid orthologs

Dpse\GA10887

Dsim\CG11280

(Metta et al., 2006)

Linkouts

InParanoid orthologs - Eukaryotic orthologs

•

ENSANGP00000024845
Anopheles gambiae (Ensembl)
ENSBTAP00000005771
Bos taurus (Ensembl)
ENSBTAP00000012009
Bos taurus (Ensembl)
ENSCAFP00000004886
Canis familiaris (Ensembl)
ENSCAFP00000008934
Canis familiaris (Ensembl)
NEWSINFRUP00000178959
Takifugu rubripes (Ensembl)
ENSMODP00000019945
Monodelphis domestica (Ensembl)
ENSPTRP00000002213
Pan troglodytes (Ensembl)
ENSRNOP00000008655
Rattus norvegicus (Ensembl)
ENSRNOP00000012844
Rattus norvegicus (Ensembl)
GSTENP00027213001
Tetraodon nigroviridis (Ensembl)
ENSXETP00000034272
Xenopus tropicalis (Ensembl)
WBGene00026853
Caenorhabditis briggsae (Wormbase)
ZDB-CDNA-040912-138
Danio rerio (Zfin)
ZDB-GENE-040912-136
Danio rerio (Zfin)
MGI:106036
Mus musculus (Informatics)
MGI:106037
Mus musculus (Informatics)

Functional Complementation between Species

Inter-Species Misexpression Data

Produces phenotype in

Produces NO phenotype in

Stocks & Reagents

Stocks Listed in FlyBase ( 5 )

Harvard

PBac{WH}trn^f03162

VDRC

v5242

w¹¹¹⁸; P{GD2450}v5242

Szeged

1114

y¹ w¹; P{lacW}trn^S064117/TM3, Sb¹ Ser¹

y¹ w¹; P{lacW}trn^S002405a P{lacW}S002405b/TM3, Sb¹ Ser¹

Bloomington

4550

y¹ w^67c23; P{lacW}trn^S064117/TM3, Sb¹ Ser¹

Genomic Clones ( 1 )

BACR13C22

cDNA Clones ( 29 )

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