Gene Dmel\scrt

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General Information

Symbol

Dmel\scrt

Species

D. melanogaster

Name

scratch

Annotation symbol

CG1130

Feature type

protein_coding_gene

FlyBase ID

FBgn0004880

Created / Updated

2004-08-09/2004-08-09

Genomic Location

Chromosome (arm)

Recombination map

Cytogenetic map

64A2-64A2

Sequence location

3L:3,983,916..3,988,589 [+]

Map ( GBrowse )

Summary Information

Automatically generated summary

See sections below for more information

The gene scratch is referred to in FlyBase by the symbol scrt (CG1130, FBgn0004880). It has the cytological map location 64A2. Its sequence location is 3L:3983916..3988589. Its molecular function is described as: transcription factor activity; zinc ion binding. It is involved in the biological processes: regulation of transcription; dendrite morphogenesis. 9 alleles are reported. The phenotypes of these alleles are annotated with: neuron; photoreceptor cell; macrochaeta; microchaeta; posterior crossvein; anterior crossvein; eye; wing; eye photoreceptor cell; pigment cell. It has one annotated transcript and one annotated polypeptide.

External Summaries

Detailed Mapping Data

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

64A2-64A2

Limits computationally determined from genome sequence between P{PZ}Sc2⁰⁵⁶³⁴ and P{PZ}l(3)rG166^rG166

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

64A-64A

(determined by in situ hybridisation)

(Roark et al., 1992)

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\scrt for information on other features

Comments on Gene Model

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Associated CDS (aa)

scrt-RA

FBtr0073165

NM_079187

3641

653

Additional Transcript Data & Comments

Reported size (kB)

6.5 (northern blot)

(Roark et al., 1995)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kD)

Length (aa)

Theoretical pI

RefSeq ID

GenBank protein

scrt-PA

FBpp0073022

70.8

653

8.00

NP_523911

AAF47819

Additional Polypeptide Data & Comments

Reported size (kD)

664 (aa)

(Roark et al., 1995)

Comments

External Data

Linkouts

PANTHER - Protein classification by function, families, and pathways

•

FBgn0004880

Crossreferences

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

•

Zinc finger, C2H2-type/integrase, DNA-binding (IPR013087)

Zinc finger, C2H2-like (IPR015880)

Zinc finger, C2H2-type (IPR007087)

Sequences Consistent with the Gene Model

DDBJ /
EMBL /
GenBank

DNA sequence

Protein sequence

Name

Maps to

Does NOT map to

Identified with

GH05150

(Rubin, 1999.4.23, BDGP Project Members, 2000-)

RH71479

(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

•

2251

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

ganglion mother cell

(Roark et al., 1995)

embryonic stage | 5.5 hr

stage 1 neuroblast | row 1..3

(Roark et al., 1995)

embryonic stage | 5-5.5 hr

ectoderm | restricted

(Roark et al., 1995)

embryonic stage | >6.5 hr

stage 1 neuroblast

(Roark et al., 1995)

embryonic stage | 4-12 hr

(Roark et al., 1995)

larval stage | third instar

eye-antennal disc | restricted

(Roark et al., 1995)

larval stage | third instar

ventral thoracic disc | restricted

(Roark et al., 1995)

embryonic stage

sensory organ mother cell

(Roark et al., 1995)

larval stage | third instar

dorsal mesothoracic disc | restricted

(Roark et al., 1995)

pupal stage

wing | restricted

(Roark et al., 1995)

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

AI107456

External Data & Images

Linkouts

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

•

FBgn0004880

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

•

FBgn0004880

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

•

FBgn0004880

FlyExpress - Embryonic expression images (BDGP data)

•

Show all FlyExpress processed images for scrt

Alleles & Phenotypes

Summary of Allele Phenotypes

Other Phenotypes

Allele

visible | recessive

behavior defective | recessive

uncoordinated | recessive

Phenotype manifest in

Allele

neuron

scrt^hs.PR

photoreceptor cell

scrt^hs.PR

macrochaeta

scrt^hs.PR

microchaeta

scrt^hs.PR

posterior crossvein

scrt^hs.PR

anterior crossvein

scrt^hs.PR

eye

wing

eye photoreceptor cell

scrt^jo11

pigment cell

scrt^jo11

Classical Alleles ( 7 )

For All Classical Alleles Show

Allele of scrt	Class	Mutagen	Known lesion
scrt^GAL4		P-element activity	Yes
scrt^KG02164			--
scrt^jo11	amorph	Δ2-3	Yes
scrt^jo14	loss of function	Δ2-3	Yes
scrt^jo16	loss of function	Δ2-3	Yes
scrt^jo17	loss of function	Δ2-3	Yes
scrt^jo6	loss of function	Δ2-3	Yes

Alleles Carried on Transgenic Constructs ( 2 )

For All Alleles Carried on Transgenic Constructs Show

Allele of scrt	Class	Mutagen	Stocks	Known lesion
scrt^GD4385		in vitro construct \| RNAi in vitro construct \| regulatory fusion	2	Yes
scrt^hs.PR		in vitro construct \| regulatory fusion	0	Yes

Aneuploid Aberrations

Useful deficiency

Df(3L)A466

Df(3L)GN34

Useful duplication

Dp(3;3)SMG38

Disrupted in

Df(3L)A466

(Roark et al., 1995)

Df(3L)Exel6099

(Ryder, 2004.4.26)

Df(3L)HR277

(Roark et al., 1995)

Transgenic Constructs & Insertions

Transgenic Constructs

Type of construct

Name

Expression data

reporter construct

UAS construct

heat-shock construct

Insertions

Type of insertions

Name

Expression data

miscellaneous insertions

P{GMroX1}l(3)64Ao^GMroX1

P{GawB}scrt^GAL4

P{SUPor-P}scrt^KG02164

insertion of enhancer trap

P{lacW}439

Yes

P{lacW}E7-3-44a

Yes

P{lacW}E7-3-44b

Yes

Related Comments

Please look at the allele reports for the complete phenotype data

scrt encodes a predicted transcription factor with five zinc fingers, related to the sna protein. scrt promotes neuronal cell fates by suppressing the expression of non-neuronal genes.

(Roark et al., 1995)

Ecol\lacZ reporter gene construct demonstrates scrt pan-neural enhancer is composed of CNS and PNS specific subelements.

(Emery and Bier, 1995)

Molecular and phenotypic analysis suggests that scrt functions as a transcription factor and promotes neuronal cell fates by suppressing expression of genes promoting non-neuronal fates.

(Roark et al., 1995)

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)

dsRNA has been made from templates generated with primers directed against this gene. RNAi of scrt results in reduced arborization of ddaD and ddaE neurons, defects in dendrite morphogenesis and reproducible defects in da dendrite development.

(Parrish et al., 2006)

Gene Ontology: Function, Process & Cellular Component ( 5 )

Molecular Function

CV term

Evidence

References

transcription factor activity

inferred from sequence or structural similarity with UniProtKB:P18747

(FlyBase, 1992-)

zinc ion binding

inferred from electronic annotation with InterPro:IPR007087, InterPro:IPR015880

(FlyBase Curators et al., 2004-)

Biological Process

CV term

Evidence

References

dendrite morphogenesis

inferred from mutant phenotype

(Parrish et al., 2006)

regulation of transcription

inferred from sequence or structural similarity with UniProtKB:P18747

(FlyBase, 1992-)

Cellular Component

CV term

Evidence

References

nucleus

inferred from sequence or structural similarity with UniProtKB:P18747

(FlyBase, 1992-)

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

scrt allele

Gene

References

External Data

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

•

63955

Orthologs

Genome-wide drosophilid orthologs

Dana\GF25020

Dere\GG15174

Dgri\GH15771

Dmoj\GI12551

Dpse\GA28473

Dsec\GM14603

Dsim\GD13794

Dvir\GJ16103

Dwil\GK17507

Dyak\GE21392

Curated drosophilid orthologs

Dpse\GA10900

Linkouts

InParanoid orthologs - Eukaryotic orthologs

•

ENSANGP00000005793
Anopheles gambiae (Ensembl)
NEWSINFRUP00000154443
Takifugu rubripes (Ensembl)
NEWSINFRUP00000164333
Takifugu rubripes (Ensembl)
ENSGALP00000009415
Gallus gallus (Ensembl)
ENSP00000246104
Homo sapiens (Ensembl)
ENSMMUP00000022838
Macaca mulatta (Ensembl)
ENSMODP00000024360
Monodelphis domestica (Ensembl)
ENSRNOP00000006833
Rattus norvegicus (Ensembl)
GSTENP00023463001
Tetraodon nigroviridis (Ensembl)
WBGene00033442
Caenorhabditis briggsae (Wormbase)
WBGene00000468
Caenorhabditis elegans (Wormbase)
ZDB-CDNA-050327-72
Danio rerio (Zfin)
ZDB-GENE-050327-72
Danio rerio (Zfin)
MGI:2139287
Mus musculus (Informatics)
MGI:2176606
Mus musculus (Informatics)

Functional Complementation between Species

Inter-Species Misexpression Data

Produces phenotype in

Produces NO phenotype in

Stocks & Reagents

Stocks Listed in FlyBase ( 4 )

Bloomington

4358

P{lacW}439

13930

y¹ w^67c23; P{SUPor-P}KG02164 ry⁵⁰⁶/TM3, Sb¹ Ser¹

VDRC

v41071

w¹¹¹⁸; P{GD4385}v41071

v41070

w¹¹¹⁸; P{GD4385}v41070/TM3

Genomic Clones ( 1 )

BACR09C02

cDNA Clones ( 14 )

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

Affy Oligo

Linkouts

DRSC - RNAi screening (Harvard): high-throughput cell culture data and design

•

FBgn0004880

GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data

•

FBgn0004880

Antibody Information

Other Information

Discoverer

Etymology

Etymology: gene named after the scratched mutant phenotype in the eye and the five zinc fingers of the encoded product.

(Roark et al., 1995)

Identification

Position Effect Variegation Data

Relationship to Other Genes

Source for database identity of

Source for identity of: scrt CG1130

(Shue, 1999.11)

Source for database merge of

Source for merge of: scrt BcDNA:RH71479 Source for merge of scrt BcDNA:RH71479 was a shared cDNA (date:030728). Source for merge of: scrt anon-WO02059370.57 Source for merge of scrt anon-WO02059370.57 was sequence comparison (date:051113).

(FlyBase, 1996-)

Additional comments

Comments About Role

Comments About Molecular Function

Other Comments

Area matching Drosophila EST AI107456.

(Davies, 2001.3.15)

Candidate gene for quantitative trait (QTL) locus determining bristle number.

(Nuzhdin et al., 1999)

External Crossreferences & Linkouts

Sequence Crossreferences

RefSeq (Transcripts)