Gene Dmel\SF1

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General Information

Symbol

Dmel\SF1

Species

D. melanogaster

Name

Splicing factor 1

Annotation symbol

CG5836

Feature type

protein_coding_gene

FlyBase ID

FBgn0025571

Created / Updated

2003-12-01/2003-12-01

Genomic Location

Chromosome (arm)

Recombination map

Cytogenetic map

90B4-90B4

Sequence location

3R:13,366,145..13,370,873 [+]

Map ( GBrowse )

Summary Information

Automatically generated summary

See sections below for more information

The gene Splicing factor 1 is referred to in FlyBase by the symbol SF1 (CG5836, FBgn0025571). It has the cytological map location 90B4. Its sequence location is 3R:13366145..13370873. Its molecular function is described as: zinc ion binding; RNA binding. It is involved in the biological process nuclear mRNA splicing, via spliceosome. 3 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

90B4-90B4

Limits computationally determined from genome sequence between P{PZ}l(3)07882⁰⁷⁸⁸² and P{EP}cpo^EP3679

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

90B-90B

(Kramer, 1999.7.14)

90B-90B

(determined by in situ hybridisation)

(Mazroui et al., 1999)

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\SF1 for information on other features

Comments on Gene Model

DGC clone GM14833 appears problematic: incomplete CDS

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Associated CDS (aa)

SF1-RA

FBtr0083456

NM_079915

2785

787

Additional Transcript Data & Comments

Reported size (kB)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kD)

Length (aa)

Theoretical pI

RefSeq ID

GenBank protein

SF1-PA

FBpp0082897

87.4

787

10.20

NP_524654

AAF55430

Additional Polypeptide Data & Comments

Reported size (kD)

Comments

External Data

Linkouts

PANTHER - Protein classification by function, families, and pathways

•

FBgn0025571

Crossreferences

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

•

Zinc finger, CCHC-type (IPR001878)

K Homology (IPR004087)

K Homology, type 1 (IPR004088)

Sequences Consistent with the Gene Model

DDBJ /
EMBL /
GenBank

DNA sequence

Protein sequence

Name

Maps to

FBcl0298083

(Mazroui et al., 1999)

Does NOT map to

Identified with

GM08892

(Mazroui et al., 1999)

GM14833

(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

•

9790

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

Marker for

Subcellular Localization

CV Term

Summary of Polypeptide Expression

Stage

Tissue/Position

Reference

Marker for

Subcellular Localization

CV Term

External Data & Images

Linkouts

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

•

FBgn0025571

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

•

FBgn0025571

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

•

FBgn0025571

Alleles & Phenotypes

Summary of Allele Phenotypes

Lethality

Allele

viable

SF1^CB05052

Phenotype manifest in

Allele

Classical Alleles ( 2 )

For All Classical Alleles Show

Allele of SF1	Class	Mutagen	Stocks	Known lesion
SF1^CB05052		P-element activity	0	Yes
SF1^e01402		piggyBac transposase	1	--

Alleles Carried on Transgenic Constructs ( 1 )

For All Alleles Carried on Transgenic Constructs Show

Allele of SF1	Class	Mutagen	Stocks	Known lesion
SF1^GD5176		in vitro construct \| RNAi in vitro construct \| regulatory fusion	2	Yes

Aneuploid Aberrations

Useful deficiency

Df(3R)DG2

Useful duplication

Dp(3;3)C123.3

Transgenic Constructs & Insertions

Transgenic Constructs

Type of construct

Name

Expression data

UAS construct

P{GD5176}

Insertions

Type of insertions

Name

Expression data

miscellaneous insertions

PBac{RB}SF1^e01402

P{PTT-GB}SF1^CB05052

Related Comments

Please look at the allele reports for the complete phenotype data

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

Molecular Function

CV term

Evidence

References

RNA binding

inferred from electronic annotation with InterPro:IPR004087, InterPro:IPR004088

(FlyBase Curators et al., 2004-)

zinc ion binding

inferred from electronic annotation with InterPro:IPR001878

(FlyBase Curators et al., 2004-)

Biological Process

CV term

Evidence

References

nuclear mRNA splicing, via spliceosome

non-traceable author statement

(Kramer, 1999.7.14)

inferred from sequence or structural similarity with SGD_LOCUS:MSL5; SGD:S0004106 AND inferred from sequence or structural similarity with protein_id:CAA03883

(Mount and Salz, 2000)

Cellular Component

CV term

Evidence

References

nucleus

inferred from direct assay

(Mazroui et al., 1999)

spliceosome

non-traceable author statement

(Kramer, 1999.7.14)

inferred from sequence or structural similarity with SGD_LOCUS:MSL5; SGD:S0004106 AND inferred from sequence or structural similarity with protein_id:CAA03883

(Mount and Salz, 2000)

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

SF1 allele

Gene

References

External Data

Linkouts

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

•

68711

Orthologs

Genome-wide drosophilid orthologs

Curated drosophilid orthologs

Linkouts

InParanoid orthologs - Eukaryotic orthologs

•

ENSANGP00000017356
Anopheles gambiae (Ensembl)
ENSBTAP00000001376
Bos taurus (Ensembl)
ENSCAFP00000021003
Canis familiaris (Ensembl)
ENSCINP00000011534
Ciona intestinalis (Ensembl)
ENSP00000334414
Homo sapiens (Ensembl)
ENSMODP00000008209
Monodelphis domestica (Ensembl)
ENSPTRP00000006630
Pan troglodytes (Ensembl)
ENSRNOP00000028628
Rattus norvegicus (Ensembl)
GSTENP00037898001
Tetraodon nigroviridis (Ensembl)
ENSXETP00000018471
Xenopus tropicalis (Ensembl)
Q7XLQ4
Oryza sativa (Gramene)
AT5G51300.3
Arabidopsis thaliana (Arabidopsis)
WBGene00023811
Caenorhabditis briggsae (Wormbase)
WBGene00013808
Caenorhabditis elegans (Wormbase)
ZDB-GENE-030131-2492
Danio rerio (Zfin)
DDB0192004
Dictyostelium discoideum (Dictybase)
MGI:1095403
Mus musculus (Informatics)
YLR116W
Saccharomyces cerevisiae (Yeastgenome)
SPCC962.06c
Schizosaccharomyces pombe (Sanger)

Functional Complementation between Species

Inter-Species Misexpression Data

Produces phenotype in

Produces NO phenotype in

Stocks & Reagents

Stocks Listed in FlyBase ( 3 )

Harvard

PBac{RB}SF1^e01402

VDRC

v13426

w¹¹¹⁸; P{GD5176}v13426

v13425

w¹¹¹⁸; P{GD5176}v13425/TM3

Genomic Clones ( 2 )

cDNA Clones ( 33 )

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

•

FBgn0025571

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

•

FBgn0025571

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

Source for merge of: SF1 CG5836

(Bayraktaroglu, 2000.8.7)

Additional comments

Comments About Role

Comments About Molecular Function

Other Comments

External Crossreferences & Linkouts

Sequence Crossreferences

RefSeq (Transcripts)

•

NM_079915

RefSeq (Proteins)

•

NP_524654

DDBJ / EMBL / GenBank

•

UniProtKB/TrEMBL

•

Other Crossreferences

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

•

Zinc finger, CCHC-type (IPR001878)

K Homology (IPR004087)

K Homology, type 1 (IPR004088)

Linkouts

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

•

68711

DEDB - Drosophila exon database: splicing graphs

•

9790

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

•

FBgn0025571

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

•

FBgn0025571

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

•

FBgn0025571

FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans

•

FBgn0025571

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

•

FBgn0025571

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

•

FBgn0025571

InParanoid orthologs - Eukaryotic orthologs

•

ENSANGP00000017356
Anopheles gambiae (Ensembl)
ENSBTAP00000001376
Bos taurus (Ensembl)
ENSCAFP00000021003
Canis familiaris (Ensembl)
ENSCINP00000011534
Ciona intestinalis (Ensembl)
ENSP00000334414
Homo sapiens (Ensembl)
ENSMODP00000008209
Monodelphis domestica (Ensembl)
ENSPTRP00000006630
Pan troglodytes (Ensembl)
ENSRNOP00000028628
Rattus norvegicus (Ensembl)
GSTENP00037898001
Tetraodon nigroviridis (Ensembl)
ENSXETP00000018471
Xenopus tropicalis (Ensembl)
Q7XLQ4
Oryza sativa (Gramene)
AT5G51300.3
Arabidopsis thaliana (Arabidopsis)
WBGene00023811
Caenorhabditis briggsae (Wormbase)
WBGene00013808
Caenorhabditis elegans (Wormbase)
ZDB-GENE-030131-2492
Danio rerio (Zfin)
DDB0192004
Dictyostelium discoideum (Dictybase)
MGI:1095403
Mus musculus (Informatics)
YLR116W
Saccharomyces cerevisiae (Yeastgenome)
SPCC962.06c
Schizosaccharomyces pombe (Sanger)

PANTHER - Protein classification by function, families, and pathways

•

FBgn0025571

Synonyms & Secondary IDs ( 6 )

Reported As

Symbol Synonym

CG5836

(Mount and Salz, 2000, )

cg5836

(Lasko, 2000)

dSF1

(Mazroui et al., 1999)

p70

(Kennedy et al., 1998)

SF1

(Akbari et al., 2006, Buszczak et al., 2007)

Name Synonym

Splicing factor 1

(Kennedy et al., 1998)

Secondary FlyBase IDs

FBgn0038518

References ( 18 )

Research paper

Buszczak et al., 2007, Genetics 175(3): 1505--1531: The Carnegie protein trap library: A versatile tool for Drosophila developmental studies. [FBrf0200345]
Orian et al., 2003, Genes Dev. 17(9): 1101--1114: Genomic binding by the Drosophila Myc, Max, Mad/Mnt transcription factor network. [FBrf0158942]
Lasko, 2000, J. Cell Biol. 150(2): F51--F56: The Drosophila melanogaster genome: translation factors and RNA binding proteins. [FBrf0129923]
Mount and Salz, 2000, J. Cell Biol. 150(2): F37--F43: Pre-messenger RNA processing factors in the Drosophila genome. [FBrf0129982]
Mazroui et al., 1999, RNA, N.Y. 5(12): 1615--1631: Splicing factor SF1 from Drosophila and Caenorhabditis: presence of an N-terminal RS domain and requirement for viability. [FBrf0123130]
Kennedy et al., 1998, Molec. Cell. Biol. 18(9): 5425--5434: A role for SRp54 during intron bridging of small introns with pyrimidine tracts upstream of the branch point. [FBrf0104552]

Supplementary material

Giot et al., 2003, Science 302(5651):: Tables S1 to S7. [FBrf0166452]

Review

Akbari et al., 2006, Dev. Biol. 293(2): 294--304: Unraveling cis-regulatory mechanisms at the abdominal-A and Abdominal-B genes in the Drosophila bithorax complex. [FBrf0199190]

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]
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]
Bayraktaroglu, 2000.8.7, Matches of the nc3 class to CGs.: Matches of the nc3 class to CGs. [FBrf0129568]

FlyBase analysis

FlyBase, 1992-, FlyBase curation: FlyBase curation. [FBrf0105495]

DNA/RNA sequence record

Kramer, 1999.7.14, GenBank/EMBL/DDBJ: AJ243904: Drosophila melanogaster mRNA for SF1 protein (SF1 gene). [FBrf0124758]

Computer file

Gene Disruption Project members and Exelixis, 2005, Genomic mapping of Exelixis insertion collection.: Genomic mapping of Exelixis insertion collection. [FBrf0184340]
Gene Disruption Project members, 2001-, [title not yet available]: [title not yet available] [FBrf0132177]
BDGP Project Members, 2000-, Berkeley Drosophila Genome Project.: Berkeley Drosophila Genome Project. [FBrf0125078]

Automatic genome annotation

FamiliarityBreedsContempt, 1999.11, [Annotations performed at the Celera Jamboreee.]: [Annotations performed at the Celera Jamboreee.] [FBrf0126705]

Curated genome annotation

Lasko, 1999.11, [Annotations performed at the Celera Jamboreee.]: [Annotations performed at the Celera Jamboreee.] [FBrf0126679]