FlyBase Gene Report: Dmel\stc

General Information

Symbol

Dmel\stc

Species

D. melanogaster

Name

shuttle craft

Annotation Symbol

CG3647

Feature Type

protein_coding_gene

FlyBase ID

FBgn0001978

Gene Model Status

Current

Stock Availability

16 publicly available

Enzyme Name (EC)

Gene Summary

shuttle craft (stc) encodes a zinc finger transcription factor of the NFX1 family. Maternally contributed protein is essential for segmentation. During the late stages of embryonic neurogenesis, zygotically expressed stc product is involved in axon guidance, which is vital for proper muscle innervation. stc expression in the embryo is important for the adult life span and aging. [Date last reviewed: 2018-09-13] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
UniProtKB
Red Book
Interactive Fly

Also Known As

l(2)35Cb, l(2)br33, br33, BG:DS04929.4

Key Links

Genomic Location

Cytogenetic map

35C2-35C2

Sequence location

2L:15,113,480..15,118,069 [+]

Recombination map

2-51

RefSeq locus

NT_033779 REGION:15113480..15118069

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

Gene Ontology (GO) Annotations (9 terms)

Molecular Function (6 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (6 terms)

CV Term

Evidence

References

enables DNA-binding transcription factor activity, RNA polymerase II-specific

inferred from biological aspect of ancestor with PANTHER:PTN000270822

(GO Reference Genome Project, 2011-)

enables DNA-binding transcription factor activity

inferred from sequence or structural similarity with UniProtKB:Q12986

(Stroumbakis et al., 1996)

inferred from electronic annotation with InterPro:IPR034078

(InterPro Project Members, 2004-)

enables nucleic acid binding

inferred from electronic annotation with InterPro:IPR001374, InterPro:IPR034076, InterPro:IPR036867

(InterPro Project Members, 2004-)

enables RNA polymerase II transcription regulatory region sequence-specific DNA binding

inferred from biological aspect of ancestor with PANTHER:PTN000270822

(GO Reference Genome Project, 2011-)

enables ubiquitin protein ligase activity

inferred from sequence or structural similarity with UniProtKB:Q12986

(Gene Ontology Curators, 2002-)

enables zinc ion binding

inferred from electronic annotation with InterPro:IPR000967

(InterPro Project Members, 2004-)

inferred from sequence model

(Ying et al., 2011)

Biological Process (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in negative regulation of transcription by RNA polymerase II

inferred from biological aspect of ancestor with PANTHER:PTN000270871

(GO Reference Genome Project, 2011-)

involved_in protein autoubiquitination

inferred from sequence or structural similarity with UniProtKB:Q12986

(Gene Ontology Curators, 2002-)

Cellular Component (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

located_in nucleus

inferred from direct assay

(Stroumbakis et al., 1996)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000270822

(GO Reference Genome Project, 2011-)

located_in nucleus

inferred from electronic annotation with InterPro:IPR000967

(InterPro Project Members, 2004-)

Gene Group (FlyBase)

UNCLASSIFIED RING DOMAIN UBIQUITIN LIGASES

UNCLASSIFIED DNA BINDING DOMAIN TRANSCRIPTION FACTORS

Protein Family (UniProt)

Belongs to the NFX1 family. (P40798)

Protein Signatures (InterPro)

Catalytic Activity (EC/Rhea)

ubiquitin protein ligase activity

Summaries

Gene Snapshot

Gene Group (FlyBase)

UNCLASSIFIED RING DOMAIN UBIQUITIN LIGASES -: This group comprises RING domain ubiquitin ligases that do not classify under other groups in FlyBase.
UNCLASSIFIED DNA BINDING DOMAIN TRANSCRIPTION FACTORS -: This group comprises DNA-binding transcription factors that do not classify under other domain-based transcription factor groups in FlyBase.

Protein Function (UniProtKB)

Plays an essential role during the late stages of embryonic neurogenesis. May either fine-tune the guidance or the spatial maintenance of the migrating SNB and in nerve roots, which are composed of axons originating from distinct groups of motor neurons and may be required to either guide or maintain the position of these nerves along a direct and straight path to their ultimate targets in particular muscle fields. May play a role in egg chamber development and/or may confer essential maternal contributions to the early embryo.

(UniProt, P40798)

Phenotypic Description (Red Book; Lindsley and Zimm 1992)

l(2)35Cb

l(2)35Cb1 escapes in heterozygous combination with Df(2L)Sco4, but not with other l(2)35Cb deficiencies.

Summary (Interactive Fly)

zinc finger, C4HC3 type (PHD finger), and RD-domain protein - maternal mutants exhibit defects in segmentation, while zygotic mutants show defects in axon guidance

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\stc for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)

Isoform displayed:

Pfam protein domains

InterPro name

classification

start

end

Protein Domains (via SMART)

Isoform displayed:

SMART protein domains

InterPro name

classification

start

end

Structure

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry P40798)

If you don't see a structure in the viewer, refresh your browser.

Model Confidence:

Very high (pLDDT > 90)
Confident (90 > pLDDT > 70)
Low (70 > pLDDT > 50)
Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

Low-frequency RNA-Seq exon junction(s) not annotated.

Gene model reviewed during 5.45

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

stc-RA

FBtr0080706

NM_057250

4124

1099

stc-RB

FBtr0080705

NM_057251

4145

1106

stc-RC

FBtr0332473

NM_001273531

4112

1095

stc-RD

FBtr0332474

NM_001273532

4133

1102

Additional Transcript Data and Comments

Reported size (kB)

4.0 (northern blot)

(Stroumbakis et al., 1996)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

stc-PA

FBpp0080266

122.4

1099

8.34

NP_476598

AAN10891

stc-PB

FBpp0080265

123.2

1106

8.34

FBpp0304749

121.9

1095

8.34

FBpp0304750

122.7

1102

8.34

M9PD57

NP_001260461

AGB92996

Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments

Reported size (kDa)

1106, 1099 (aa); 123 (kD predicted)

(Stroumbakis et al., 1996)

Comments

External Data

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\stc using the Feature Mapper tool.

External Data

Crossreferences

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

stc_1

Linkouts

Expression Data

Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

1.14

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism | ubiquitous

(Fisher et al., 2012)

primordial germ cell

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | ubiquitous

(Fisher et al., 2012)

primordial germ cell

(Fisher et al., 2012)

embryonic stage 9 -- 10

germline cell

(Fisher et al., 2012)

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 11 -- 12

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 13 -- 16

organism | ubiquitous

(Fisher et al., 2012)

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage -- adult stage

(Stroumbakis et al., 1996)

oogenesis & adult stage | female

ovary

(Stroumbakis et al., 1996)

Additional Descriptive Data

stc transcripts are detected throughout development on northern blots. They are most abundant in adult males and in ovaries.

(Stroumbakis et al., 1996)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 13 -- 17

larval brain | restricted

(Stroumbakis et al., 1996)

presumptive embryonic/larval central nervous system | restricted

(Stroumbakis et al., 1996)

Additional Descriptive Data

stc protein was detected in the central nervous system of stage 13-17 embryos. It is prominent in repeated clusters of cells in each neuromere along the length of the ventral nerve cord and in distinct groups of cells within the brain lobes.

(Stroumbakis et al., 1996)

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in nucleus

inferred from direct assay

(Stroumbakis et al., 1996)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\stc in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\stc

View exonic expression by tissue for Dmel\stc

Bulk Downloads

RNA-Seq RPKM values for all genes

Reference

See Gelbart and Emmert, 2013 for analysis details and data files for all genes.

Developmental Proteome: Life Cycle

Developmental Proteome: Embryogenesis

External Data and Images

Linkouts

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0001978

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

34888/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0001978

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0001978

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0001978

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

Flygut - An atlas of the Drosophila adult midgut

FBgn0001978

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 16 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 7 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of stc

Transgenic constructs containing regulatory region of stc

Aberrations (Deficiencies and Duplications) ( 166 )

Inferred from experimentation ( 166 )

Gene disrupted in

Df(2L)A48

(Cai et al., 2001, Spradling et al., 1999, Fossett et al., 1994, Grau et al., 1984, Ashburner et al., 1982, Ashburner et al., 1982)

Df(2L)A72

(Roote et al., 1996, Fossett et al., 1994, Ashburner et al., 1990, Ashburner et al., 1982, Ashburner et al., 1982)

Df(2L)A215

(Fossett et al., 1994, Ashburner et al., 1982)

Df(2L)A220

(Roote et al., 1996, Fossett et al., 1994, Ashburner et al., 1982)

Df(2L)A246

(Fossett et al., 1994, Ashburner et al., 1982)

Df(2L)A263

(Furukawa et al., 1992, Ashburner et al., 1982)

Df(2L)A264

(Fossett et al., 1994, Ashburner et al., 1982)

Df(2L)A337

(Fossett et al., 1994)

Df(2L)A376

(Fossett et al., 1994, Ashburner, 1982, Ashburner et al., 1982)

Df(2L)A377

(Ashburner, 1982, Ashburner et al., 1982)

Df(2L)A400

(Roote et al., 1996, Fossett et al., 1994, Ashburner, 1982, Ashburner et al., 1982)

Df(2L)Adh-nBR55

(Roote, 1995.3.24)

Df(2L)Adh-nBR101

(Fossett et al., 1994)

Df(2L)Adh-nBR102

(Fossett et al., 1994)

Df(2L)Adh-nBR103

(Fossett et al., 1994)

Df(2L)Adh-nBR105

(Roote, 1996.1.11, Roote, 1996.8, Roote et al., 1996, Fossett et al., 1994)

Df(2L)Adh-nBR118

(Fossett et al., 1994)

Df(2L)Adh-nBR120

(Fossett et al., 1994)

Df(2L)Adh-nBR122

(Roote, 1996.1.11, Roote, 1996.8, Roote et al., 1996, Fossett et al., 1994)

Df(2L)Adh-nBR125

(Fossett et al., 1994)

Df(2L)Adh-nBR126

(Fossett et al., 1994)

Df(2L)Adh-nBR128

(Roote, 1996.1.11, Roote, 1996.8, Roote et al., 1996, Fossett et al., 1994)

Df(2L)Adh-nBR129

(Fossett et al., 1994)

Df(2L)Adh-nBR130

(Fossett et al., 1994)

Df(2L)Adh-nBR131

(Roote, 1996.1.11, Roote, 1996.8, Fossett et al., 1994)

Df(2L)b80e4

(Ashburner et al., 1990)

Df(2L)b84h50

(Roote, 1996.8, Furukawa et al., 1992)

Df(2L)b88c58

(Roote, 1996.8, Alexandrov and Alexandrova, 1991)

Df(2L)do1

(Ashburner, 1982)

Df(2L)ED1050

(Roote, 2004.6.24)

Df(2L)el20

(Ashburner et al., 1990)

Df(2L)el28

(Furukawa et al., 1992, Ashburner et al., 1990)

Df(2L)el80f1

(Ashburner et al., 1983)

Df(2L)Exel7062

(Ryder, 2004.4.26)

Df(2L)fn1

(Grau et al., 1984, Ashburner et al., 1982, Ashburner et al., 1982)

Df(2L)fn5

(Furukawa et al., 1992, Ashburner et al., 1982)

Df(2L)fn26

(Ashburner et al., 1990, Ashburner et al., 1982)

Df(2L)fn27

(Ashburner et al., 1990, Ashburner, 1982, Ashburner et al., 1982, Ashburner et al., 1982)

Df(2L)k05007-mr19

(Roote, 2000.6.13)

Df(2L)k09033-mr19

(Roote, 2000.6.13)

Df(2L)n78l3

(Ashburner et al., 1990, Ashburner et al., 1982)

Df(2L)nNxF1

(Roote, 1996.8, Roote et al., 1996)

Df(2L)nNxF2

(Roote et al., 1996)

Df(2L)noc11

(Ashburner et al., 1990)

Df(2L)osp29

(Cai et al., 2001, Furukawa et al., 1992, Grau et al., 1984, Ashburner et al., 1982)

Df(2L)osp38

(Ashburner et al., 1990)

Df(2L)Sco7

(Ashburner et al., 1990, Ashburner et al., 1983)

Df(2L)Sco^rv4

(Roote et al., 1996, Ashburner et al., 1990, Ashburner et al., 1983)

Df(2L)Sco^rv23

(Grau et al., 1984, Ashburner et al., 1983, Ashburner, 1982)

Df(2L)TE35B-1

(Gubb et al., 1985)

Df(2L)TE35B-2

(Gubb et al., 1985)

Df(2L)TE35B-5

(Roote, 1996.8, Gubb et al., 1985)

Df(2L)TE35B-6

(Roote et al., 1996, Gubb et al., 1985)

Df(2L)TE35BC-3

(Cai et al., 2001, Ashburner et al., 1990, Grau et al., 1984, Gubb et al., 1984, Ashburner, 1982, Ashburner et al., 1982)

Df(2L)TE35BC-4

(Ashburner et al., 1990, Gubb et al., 1984, Ashburner, 1982, Ashburner et al., 1982)

Df(2L)TE35BC-6

(Gubb et al., 1984)

Df(2L)TE35BC-8

(Gubb et al., 1984)

Df(2L)TE35BC-24

(Zhu et al., 2005, Gubb et al., 1984)

Df(2L)TE35BC-34

(Ashburner et al., 1990, Gubb et al., 1984)

Df(2L)TE35BC-35

(Gubb et al., 1984)

Df(2L)TE35D-4

(Roote, 1997.6.6, Stroumbakis et al., 1996, Ashburner et al., 1990)

Df(2L)TE35D-16

(Ashburner et al., 1990)

Df(2L)TE35D-18

(Furukawa et al., 1992)

Df(2L)TE35D-20

(Ashburner et al., 1990)

Df(2L)TE35D-23

(Ashburner et al., 1990)

In(2L)75c

(Grau et al., 1984, Ashburner, 1982)

In(2L)C158^LSco^rv11R

(Ashburner and Harrington, 1984, Ashburner et al., 1983)

In(2L)C158^LSco^rv17R

(Ashburner and Harrington, 1984, Ashburner et al., 1983)

In(2L)dpp^s22Ldpp^d36R

(Ashburner et al., 1990)

In(2L)el18

(Ashburner et al., 1990)

In(2L)TE35B-13

(Gubb et al., 1985)

In(2LR)noc^4LSco^rv9R

(Cai et al., 2001, Ashburner and Harrington, 1984)

In(2LR)pkD1-rv8

(Roote, 1997.6.6)

In(2LR)TE35B-6^LSco^rv9R

(Ashburner and Harrington, 1984)

Tp(2;2)A446

(Fossett et al., 1994, Ashburner et al., 1982, Ashburner et al., 1982)

Ts(2Lt;3Lt)TE35B-4+Ts(2Rt;3Rt)Sco^rv13

(Ashburner and Harrington, 1984)

Ts(2Lt;3Lt)TE35BC-3+Ts(2Rt;3Rt)Sco^rv13

(Ashburner and Harrington, 1984, Ashburner et al., 1983)

Gene partially disrupted in

Df(2L)Sco^rv4

(Ashburner et al., 1999.10.12)

Gene not disrupted in

Df(2L)64j

(Furukawa et al., 1992, Ashburner et al., 1990, Ashburner, 1982)

Df(2L)A47

(Fossett et al., 1994, Ashburner et al., 1982)

Df(2L)A63

(Fossett et al., 1994, Ashburner et al., 1982, Ashburner et al., 1982)

Df(2L)A178

(Fossett et al., 1994, Ashburner et al., 1982, Ashburner et al., 1982)

Df(2L)A217

(Fossett et al., 1994, Ashburner et al., 1982)

Df(2L)A245

(Fossett et al., 1994, Ashburner et al., 1982)

Df(2L)A260

(Ashburner et al., 1982)

Df(2L)A266

(Fossett et al., 1994, Ashburner et al., 1982, Ashburner et al., 1982)

Df(2L)A267

(Fossett et al., 1994, Ashburner et al., 1990, Lasko and Ashburner, 1988, Ashburner et al., 1982, Ashburner et al., 1982)

Df(2L)A379

(Fossett et al., 1994, Ashburner et al., 1982, Ashburner et al., 1982)

Df(2L)A400

(Ashburner et al., 1982)

Df(2L)A445

(Fossett et al., 1994, Ashburner et al., 1982)

Df(2L)Adh-nBR100

(Fossett et al., 1994)

Df(2L)Adh-nBR106

(Fossett et al., 1994)

Df(2L)Adh-nBR107

(Fossett et al., 1994)

Df(2L)Adh-nBR117

(Fossett et al., 1994)

Df(2L)Adh-nBR119

(Fossett et al., 1994)

Df(2L)Adh-nBR121

(Fossett et al., 1994)

Df(2L)Adh-nBR127

(Fossett et al., 1994)

Df(2L)ARR1

(Furukawa et al., 1992, Ashburner et al., 1990, Ashburner, 1982)

Df(2L)b80e3

(Ashburner et al., 1982)

Df(2L)b81a1

(Ashburner et al., 1982)

Df(2L)b84a3

(Furukawa et al., 1992)

Df(2L)b84a7

(Furukawa et al., 1992)

Df(2L)b87e25

(Zhu et al., 2005, Roote, 1996.8)

Df(2L)b89e80a

(Roote, 2000.7.3)

Df(2L)fn2

(Grau et al., 1984, Ashburner et al., 1982, Ashburner et al., 1982)

Df(2L)fn3

(Ashburner, 1982, Ashburner et al., 1982)

Df(2L)fn7

(Ashburner, 1982, Ashburner et al., 1982)

Df(2L)fn12

(Ashburner et al., 1990, Ashburner et al., 1982)

Df(2L)fn15

(Ashburner et al., 1982)

Df(2L)fn30

(Ashburner et al., 1982)

Df(2L)fn31

(Ashburner, 1982, Ashburner et al., 1982)

Df(2L)fn36

(Ashburner et al., 1982)

Df(2L)H20

(Ashburner et al., 1990)

Df(2L)osp144

(Ashburner et al., 1982)

Df(2L)PA4

(Ashburner et al., 1983)

Df(2L)PZ07130-mr2

(Roote, 2000.6.13)

Df(2L)PZ07130-mr7

(Roote, 2000.6.13)

Df(2L)r10

(Zhu et al., 2005, Ashburner et al., 1990)

Df(2L)RA5

(Ashburner et al., 1990)

Df(2L)rd9

(Zhu et al., 2005, Roote, 1996.8, Furukawa et al., 1992, Ashburner et al., 1990)

Df(2L)RM5

(Ashburner et al., 1990)

Df(2L)RN2

(Ashburner et al., 1990)

Df(2L)Sco-1

(Ashburner, 1982)

Df(2L)Sco^rv10

(Grau et al., 1984, Ashburner et al., 1983)

Df(2L)Sco^rv14

(Ashburner et al., 1983)

Df(2L)Sco^rv16

(Ashburner et al., 1990, Grau et al., 1984, Ashburner et al., 1983)

Df(2L)Sco^rv18

(Ashburner et al., 1990, Ashburner et al., 1983)

Df(2L)Sco^rv19

(Ashburner et al., 1990, Grau et al., 1984, Ashburner et al., 1983)

Df(2L)Sco^rv25

(Ashburner et al., 1990, Grau et al., 1984, Ashburner et al., 1983)

Df(2L)SS1

(Ashburner et al., 1990, Grau et al., 1984)

Df(2L)TE35B-3

(Gubb et al., 1985)

Df(2L)TE35B-4

(Gubb et al., 1985)

Df(2L)TE35B-5

(Lasko and Ashburner, 1988)

Df(2L)TE35B-7

(Gubb et al., 1985)

Df(2L)TE35B-8

(Gubb et al., 1985)

Df(2L)TE35B-9

(Gubb et al., 1985)

Df(2L)TE35B-10

(Gubb et al., 1985)

Df(2L)TE35B-11

(Gubb et al., 1985)

Df(2L)TE35B-12

(Gubb et al., 1985)

Df(2L)TE35B-15

(Gubb et al., 1985)

Df(2L)TE35BC-1

(Gubb et al., 1984, Ashburner, 1982)

Df(2L)TE35BC-7

(Furukawa et al., 1992, Gubb et al., 1984)

Df(2L)TE35BC-23

(Gubb et al., 1984)

Df(2L)TE35BC-28

(Furukawa et al., 1992, Gubb et al., 1984)

Df(2L)TE35BC-29

(Gubb et al., 1984)

Df(2L)TE35BC-31

(Gubb et al., 1984)

Df(2L)TE35D-1

(Ashburner et al., 1990)

Df(2L)TE35D-2

(Furukawa et al., 1992, Ashburner et al., 1990)

Df(2L)TE35D-3

(Ashburner et al., 1990)

Df(2L)TE35D-6

(Stroumbakis et al., 1996, Furukawa et al., 1992, Ashburner et al., 1990)

Df(2L)TE35D-13

(Furukawa et al., 1992, Ashburner et al., 1990)

Df(2L)TE35D-14

(Ashburner et al., 1990)

Df(2L)TE35D-15

(Furukawa et al., 1992, Ashburner et al., 1990)

Df(2L)TE35D-19

(Ashburner et al., 1990)

Df(2L)TE35D-21

(Ashburner et al., 1990)

Df(2L)TE35D-22

(Cai et al., 2001, Ashburner et al., 1990)

Df(2L)W

(Ashburner et al., 1982)

In(2LR)Sco^rv1-DV7

(Ashburner et al., 1990)

T(2;3)Sco^rv7

(Ashburner et al., 1990, Ashburner and Harrington, 1984, Grau et al., 1984, Ashburner et al., 1983)

T(Y;2)A80^DR15^P

(Ashburner et al., 1982)

Ts(Y;2Lt)el⁴+Ts(YSt;2Rt)R15

(Ashburner et al., 1982)

Gene not duplicated in

Dp(2;2)Adh3

(Ashburner, 1982)

Inferred from location ( 8 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Lethality

Allele

lethal | recessive

lethal - all die during embryonic stage | maternal effect | recessive

stc³

lethal - all die during embryonic stage | recessive

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

stc^GD1543

viable, with Scer\GAL4^Mef2.PR

stc^GD1543

viable, with Scer\GAL4^pnr-MD237

stc^GD1543

viable, with Scer\GAL4^tin.CΔ4

stc^GD1543

Other Phenotypes

Allele

short lived | female limited

stc^KG01230

some die during embryonic stage | recessive

some die during embryonic stage | recessive | maternal effect | recessive

stc³

Phenotype manifest in

Allele

central nervous system

stc³

embryonic/first instar larval cuticle | maternal effect

stc³

larval abdominal segmental nerve

stc³

larval abdominal segmental nerve | embryonic stage | maternal effect

stc³

larval intersegmental nerve

stc³

larval intersegmental nerve | embryonic stage | maternal effect

stc³

larval ventral nerve cord | maternal effect

stc³

presumptive embryonic/larval central nervous system | maternal effect

stc³

ventral denticle belt | maternal effect

stc³

ventral nerve cord & abdominal segment 4 | maternal effect

stc³

ventral nerve cord & abdominal segment 5 | maternal effect

stc³

ventral nerve cord & abdominal segment 6 | maternal effect

stc³

ventral nerve cord & abdominal segment 7 | maternal effect

stc³

ventral nerve cord & abdominal segment 8 | maternal effect

stc³

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (4)

Hsap\NFX1

14 of 14

Yes

Hsap\NFXL1

3 of 14

Hsap\TNXB

1 of 14

Hsap\ZNFX1

1 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (3)

Rnor\Nfx1

14 of 14

Yes

Rnor\Nfxl1

2 of 14

Rnor\Znfx1

1 of 14

Mus musculus (laboratory mouse) (3)

Mmus\Nfx1

13 of 14

Yes

Mmus\Nfxl1

3 of 14

Mmus\Znfx1

1 of 14

Xenopus tropicalis (Western clawed frog) (3)

Xtro\nfx1

11 of 13

Yes

Xtro\nfxl1

2 of 13

Xtro\znfx1

1 of 13

Danio rerio (Zebrafish) (2)

Drer\nfx1

13 of 14

Yes

Drer\nfxl1

3 of 14

Caenorhabditis elegans (Nematode, roundworm) (2)

Cele\nfx-1

14 of 14

Yes

Cele\znfx-1

1 of 14

Anopheles gambiae (African malaria mosquito) (2)

Agam\AgaP_AGAP008728

12 of 12

Yes

Agam\AgaP_AGAP005362

3 of 12

Arabidopsis thaliana (thale-cress) (2)

Atha\NFXL1

11 of 13

Yes

Atha\NFXL2

3 of 13

Saccharomyces cerevisiae (Brewer's yeast) (1)

Scer\FAP1

13 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\SPCC18.03

12 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:stc. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (1)

CG15011

5 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 0 )

Allele

Disease

Evidence

References

Potential Models Based on Orthology ( 0 )

Human Ortholog

Disease

Evidence

References

Modifiers Based on Experimental Evidence ( 0 )

Allele

Disease

Interaction

References

Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)

Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.

Homo sapiens (Human)

Gene name

Score

OMIM

OMIM Phenotype

DO term

Complementation?

Transgene?

NFX1; nuclear transcription factor, X-box binding 1

14 of 14

603255

NFXL1; nuclear transcription factor, X-box binding like 1

3 of 14

620488

Functional Complementation Data

Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.

Interactions

Summary of Physical Interactions

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

stc - Ada2b

anti tag coimmunoprecipitation, peptide massfingerprinting

(Weake et al., 2011)

stc - drm

two hybrid array

(Shokri et al., 2019)

stc - kel

proximity-dependent biotin identification, Identification by mass spectrometry

(Mannix et al., 2019)

Summary of Genetic Interactions

Interaction Browsers

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

60906

DroID - A comprehensive database of gene and protein interactions.

FBgn0001978

MIST (protein-protein) - An integrated Molecular Interaction Database

34888

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-51

Cytogenetic map

35C2-35C2

Sequence location

2L:15,113,480..15,118,069 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

35C2-35C2

Limits computationally determined from genome sequence between P{EP}vig^EP812&P{PZ}stc⁰⁵⁴⁴¹ and P{EP}esg^EP633&P{PZ}esg⁰⁷⁰⁸²

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

34C4-36A7

(Oh et al., 2003)

35C1-35C2

(determined by in situ hybridisation)

(Ashburner et al., 1999, Spradling et al., 1999)

35C-35C

(determined by in situ hybridisation)

(Stroumbakis et al., 1996)

35C1-35C2

(BDGP Project Members, 1994-1999)

Experimentally Determined Recombination Data

Location

2-51

(FlyBase, 2016)

2-47.9

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (16)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

92626

y¹ w^*; P{stc-GFP.FPTB}attP40

25139

In(2L)dpp^s22, dpp^s22 stc⁶/CyO

13413

y¹ w^67c23; P{SUPor-P}stc^KG01230

30472

Adc^b-1 stc³ pr¹ cn¹ bw¹/SM5

43208

y¹ sc^* v¹ sev²¹; P{TRiP.GL01553}attP40

Kyoto

130377

P{PZ}stc⁰⁵⁴⁴¹ cn¹ / CyO; ry⁵⁰⁶

NIG-Fly

HMJ21103

y¹ v¹; P{TRiP.HMJ21103}attP40/CyO

M2L-2745

y¹ w¹¹¹⁸; stc^SK2 P{neoFRT}40A/CyO-Tb

M2L-2746

y¹ w¹¹¹⁸; stc^SK7 P{neoFRT}40A/CyO-Tb

VDRC

v47973

w¹¹¹⁸; P{GD1543}v47973

v47974

w¹¹¹⁸; P{GD1543}v47974/TM3

v342386

P{hsFLP}1, y¹ w¹¹¹⁸; P{HD_CFD00207}attP40/CyO-GFP

More stocks available...

Genomic Clones (19)

Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

cDNA Clones (91)

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 JBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

Other clones

Drosophila Genomics Resource Center cDNA clones

For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

FBgn0001978

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0001978

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Stroumbakis et al., 1996)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Expression is enriched in embryonic gonads.

(Shigenobu et al., 2006)

0 alleles of stc recovered in a P-insertion screen.

(Oh et al., 2003)

A maternally derived source of stc protein is required during embryogenesis but not oogenesis.

(Tolias and Stroumbakis, 1998)

FlyBase curator comment: Authors state "stc is the sole transcription unit in this region". Subsequent genome annotation identified adjacent CG15269, in which the 05441 insertion FBti0005150 identified with stc⁰⁵⁴⁴¹ (FBal0008509) maps.

(Stroumbakis et al., 1996)

Mutants fail to coordinate the contractions required for hatching and die during late embryogenesis.

(Stroumbakis et al., 1995)

5 additional alleles are discussed but are not named.

(Ashburner et al., 1990)

Relationship to Other Genes

Source for database merge of

Source for merge of: stc l(2)SH1565

(Roote, 2005.1.24)

Source for merge of: stc BcDNA:LD22726

(FlyBase, 1996-)

Additional comments

Source for merge of stc BcDNA:LD22726 was sequence comparison ( date:990717 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Source for identity of: stc CG3647

(Kodira, 1999.11)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (18)

Reported As

Symbol Synonym

151662_s_at

(Kristensen et al., 2005)

BG:DS04929.4

(Ashburner et al., 1999, Ashburner et al., 1999.10.12)

BcDNA.LD22726

(Rubin, 1999.4.23)

BcDNA:LD22726

CG3647

(National Institute of Genetics Fly Stocks, 2023-, National Institute of Genetics Fly Stocks, 2022-, Ying et al., 2011, Ni et al., 2010.12.1, Bell et al., 2007, Wirbelauer et al., 2005, Whitfield, 2000.5.3)

Cf4

LD22726

(Pilot et al., 2006)

br33

(Furukawa et al., 1992, Gubb et al., 1985, Ashburner and Harrington, 1984, Grau et al., 1984)

l(2)35Cb

(Ashburner et al., 1999, The Moscow Regional Drosophila melanogaster Stock Center, Dubna, Alexandrova et al., 1996, Roote, 1995.5.4, Roote, 1995.5.15, Lindsley and Zimm, 1992, Ashburner et al., 1990)

l(2)SH1565

l(2)SH2 1565

(Oh et al., 2002.3.26)

l(2)br33

(Gubb et al., 1984, Ashburner et al., 1983, Ashburner, 1982, Ashburner et al., 1982, Ashburner et al., 1982)

l35Cb

(Fossett et al., 1994)

stc

(Hurtado et al., 2022, Symonenko et al., 2022, Flatt, 2020, Mannix et al., 2019, Shokri et al., 2019, Gene Disruption Project members, 2018-, Roshina et al., 2014, Du et al., 2011, Gerhold et al., 2011, Weake et al., 2011, Salzer et al., 2010, Roshina et al., 2008, Jordan et al., 2006, Negre et al., 2006, Shigenobu et al., 2006, Roote, 2005.1.24, Zhu et al., 2005, Pasyukova et al., 2004)

Name Synonyms

Chorion-factor-4

SHUTTLECRAFT

(Boucher et al., 2001)

shuttle craft

(Roshina et al., 2014, Salzer et al., 2010, Roshina et al., 2008, Negre et al., 2006, Harbison et al., 2005, Pasyukova et al., 2004)

shuttlecraft

(Gerhold et al., 2011, Jordan et al., 2006)

Secondary FlyBase IDs

FBgn0065412

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 63 )

Sequence Crossreferences

NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.

34888

GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.

GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.

RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.

UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.

P40798

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

P40798

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

Other crossreferences

AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.

P40798

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0001978

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

34888/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0001978

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0001978

FlyMine - An integrated database for Drosophila genomics

FBgn0001978

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

KEGG Genes - Molecular building blocks of life in the genomic space.

dme:Dmel_CG3647

MARRVEL_MODEL - MARRVEL (model organism gene)

34888

Linkouts

BioGRID - A database of protein and genetic interactions.

60906

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0001978

DroID - A comprehensive database of gene and protein interactions.

FBgn0001978

DRSC - Results frm RNAi screens

FBgn0001978

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

stc_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0001978

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0001978

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

Flygut - An atlas of the Drosophila adult midgut

FBgn0001978

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

TC030607

Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution

Interactive Fly

MIST (protein-protein) - An integrated Molecular Interaction Database

34888

References (125)

The following external sites may use different assemblies or annotations than FlyBase.

1.14

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