FlyBase Gene Report: Dmel\Sce

OTHER RING DOMAIN UBIQUITIN LIGASES -: The RING (Really Interesting New Gene) finger domain co-ordinates two Zn²⁺ ions via conserved Cys and His residues. Most proteins which contain a RING finger are assumed to be ubiquitin (E3) ligases. The RING finger binds ubiquitin-conjugating enzymes (E2) and promotes direct transfer of ubiquitin to the target protein. (Adapted from FBrf0215242 and PMID:19489725).
dRING-ASSOCIATED FACTORS -: The Drosophila Polycomb group complex dRING-associated factors (dRAF) catalyzes histone H2A K119 ubiquitination and H3K36me2 removal. Therefore, dRAF removes an active mark from histone H3 and adds a repressive one to H2A. (Adapted from FBrf0215737).
POLYCOMB REPRESSIVE COMPLEX 1 (CORE SUBUNITS) -: The Polycomb repressive complex 1 (PRC1) is a Polycomb group complex. It binds to histone H3K27me3 (histone H3 K27 methylation is catalyzed by PRC2) and monoubiquitinates H2A on K119. This leads to chromatin compaction, RNA polymerase II stalling and gene silencing. (Adapted from FBrf0179742 and FBrf0228921).

Protein Function (UniProtKB)

E3 ubiquitin-protein ligase that mediates monoubiquitination of 'Lys-118' of histone H2A, thereby playing a central role in histone code and gene regulation. H2A 'Lys-118' ubiquitination gives a specific tag for epigenetic transcriptional repression. Polycomb group (PcG) protein. PcG proteins act by forming multiprotein complexes, which are required to maintain the transcriptionally repressive state of homeotic genes throughout development. PcG proteins are not required to initiate repression, but to maintain it during later stages of development. PcG complexes act via modification of histones, such as methylation, deacetylation, ubiquitination rendering chromatin heritably changed in its expressibility. May play a role in meiotic sister chromatid cohesion.

(UniProt, Q9VB08)

Phenotypic Description (Red Book; Lindsley and Zimm 1992)

Sce: Sex combs extra

A dominant enhancer of Mcp in the BXC. Sce/Sce zygotes from Sce/+ mothers die as first instar larvae with weak posteriorly directed transformations, i.e., A7 displays some A8 characteristics. Heterozygous offspring normal. Sce/Sce embryos from clones of homozygous oocytes produced by pole-cell transplantation display extreme posteriorly directed segmental transformation. Ventral setal belts of all abdominal and thoracic segments transformed toward A8; head involution blocked; abdominal type denticle belts also found anterior to T1 in the presumptive labial and maxillary segments; in addition an extensive belt of abdominal denticles of unknown derivation forms on the anterodorsal surface of the embryo. Keilin's organs and ventral pits suppressed in thoracic segments; wart-like sensilla normally found in A8 formed anteriorally as far as A2. Tracheal branches in A1-7 resemble those normally found more posteriorly. Sce/+ offspring from homozygous germ line clones in the mothers may survive to adulthood or die as pharate adults; they show patches of tissue transformed toward A8.

Summary (Interactive Fly)

Polycomb group - protein ubiquitination - a member of a protein complex, termed PRC1 (Polycomb repressive complex 1) - monoubiquitylates histone H2A, an activity thought to be crucial for repression by PRC1-type complexes

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the GBrowse view of Dmel\Sce or the JBrowse view of Dmel\Sce 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

Comments on Gene Model

Gene model reviewed during 5.44

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Sce-RA

FBtr0085245

NM_058161

1542

435

Additional Transcript Data and Comments

Reported size (kB)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

RefSeq ID

GenBank

Sce-PA

FBpp0084614

47.3

435

7.14

NP_477509

AAF56737

Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Subunit Structure (UniProtKB)

Interacts with ORD. Component of PRC1 complex, which contains many PcG proteins like Pc, ph, Scm, Psc, Sce and also chromatin remodeling proteins such as histone deacetylases. This complex is distinct from the Esc/E(z) complex, at least composed of esc, E(z), Su(z)12, Rpd3 and Caf1. The two complexes however cooperate and interact together during the first 3 hours of development to establish PcG silencing.

(UniProt, Q9VB08)

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Mapped Features

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

External Data

Crossreferences

Linkouts

Gene Ontology (21 terms)

Molecular Function (5 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

protein binding

inferred from physical interaction with UniProtKB:Q24434

(assigned by UniProt )

(Balicky et al., 2004)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

chromatin binding

inferred from biological aspect of ancestor with PANTHER:PTN000743780

(assigned by GO_Central )

(Gaudet et al., 2011)

ubiquitin protein ligase activity

inferred from biological aspect of ancestor with PANTHER:PTN000743780

(assigned by GO_Central )

(Gaudet et al., 2011)

contributes_to ubiquitin-protein transferase activity

inferred from sequence or structural similarity with HGNC:10061

(FlyBase Curators, 2008--)

zinc ion binding

inferred from sequence model

(Ying et al., 2011)

Biological Process (8 terms)

Terms Based on Experimental Evidence (8 terms)

CV Term

Evidence

References

chromatin silencing

inferred from direct assay

(assigned by UniProt )

(Fritsch et al., 2003)

germarium-derived female germ-line cyst encapsulation

inferred from mutant phenotype

(Narbonne et al., 2004)

histone H2A monoubiquitination

inferred from mutant phenotype

(Gutiérrez et al., 2012)

multicellular organism development

inferred from direct assay

(assigned by UniProt )

(Simon et al., 1992)

neurogenesis

inferred from mutant phenotype

(Bello et al., 2007)

ovarian follicle cell stalk formation

inferred from mutant phenotype

(Narbonne et al., 2004)

sex comb development

inferred from direct assay

(assigned by UniProt )

(Simon et al., 1992)

ventral cord development

inferred from high throughput mutant phenotype

(Bivik et al., 2015)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

histone H2A monoubiquitination

inferred from biological aspect of ancestor with PANTHER:PTN000743780

(assigned by GO_Central )

(Gaudet et al., 2011)

Cellular Component (8 terms)

Terms Based on Experimental Evidence (7 terms)

CV Term

Evidence

References

NOT condensed chromosome, centromeric region

inferred from direct assay

(assigned by UniProt )

(Balicky et al., 2004)

nuclear chromatin

inferred from direct assay

(assigned by UniProt )

(Balicky et al., 2004)

nuclear envelope

inferred from direct assay

(assigned by UniProt )

(Balicky et al., 2004)

nucleolus

inferred from direct assay

(Chen et al., 2005)

nucleus

inferred from direct assay

(Balicky et al., 2004, Mulholland et al., 2003)

PcG protein complex

inferred from direct assay

(Lagarou et al., 2008)

PRC1 complex

inferred from direct assay

(Francis et al., 2001)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

PcG protein complex

inferred from biological aspect of ancestor with PANTHER:PTN000743780

(assigned by GO_Central )

(Gaudet et al., 2011)

PRC1 complex

traceable author statement

(Levine et al., 2004)

ubiquitin ligase complex

inferred from biological aspect of ancestor with PANTHER:PTN000743780

(assigned by GO_Central )

(Gaudet et al., 2011)

Expression Data

Expression Summary Ribbons

Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.

For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 5 -- 11

organism

Comment: maternal component at stage 5

(Gorfinkiel et al., 2004)

embryonic stage 13

ventral nerve cord primordium

Comment: NOT expressed in epidermis

(Gorfinkiel et al., 2004)

embryonic stage 15

central nervous system

Comment: expressed ONLY in CNS

(Gorfinkiel et al., 2004)

larval stage

imaginal disc

Comment: Ubiquitous Sce expression observed in all imaginal discs.

(Gorfinkiel et al., 2004)

imaginal disc | ubiquitous

(Gorfinkiel et al., 2004)

embryonic stage 1 -- 11

organism | ubiquitous

(Gorfinkiel et al., 2004)

embryonic stage 15 -- 16

central nervous system

(Gorfinkiel et al., 2004)

embryonic stage 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism

(Fisher et al., 2012)

embryonic stage 7 -- 8

anterior endoderm anlage

(Fisher et al., 2012)

head mesoderm

(Fisher et al., 2012)

hindgut anlage

(Fisher et al., 2012)

posterior endoderm

(Fisher et al., 2012)

trunk mesoderm

(Fisher et al., 2012)

ventral ectoderm

(Fisher et al., 2012)

embryonic stage 9 -- 10

antennal primordium