DmeALTD0004325-2/2 @ dm6
Alternative 5'ss
Gene
FBgn0000286 | Cf2
Description
The gene Chorion factor 2 is referred to in FlyBase by the symbol DmelCf2 (CG11924, FBgn0000286). It is a protein_coding_gene from Dmel. It has 7 annotated transcripts and 7 polypeptides (4 unique). Gene sequence location is 2L:4876891..4883107. Its molecular function is described by: DNA-binding transcription factor activity; DNA binding; DNA-binding transcription activator activity, RNA polymerase II-specific; sequence-specific DNA binding; protein binding. It is involved in the biological process described with: dorsal appendage formation; regulation of transcription, DNA-templated; adult somatic muscle development; dorsal/ventral pattern formation; positive regulation of transcription elongation from RNA polymerase II promoter. 20 alleles are reported. The phenotypes of these alleles manifest in: embryonic/larval cuticle; epithelium; larva; cellular anatomical entity; supramolecular complex. The phenotypic classes of alleles include: increased mortality during development; flight defective; phenotype; increased mortality. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of low expression. Peak expression observed within 00-06 hour embryonic stages, during late larval stages, during early pupal stages, in stages of adults of both sexes.
Coordinates
chr2L:4876891-4880472:-
Coord C1 exon
chr2L:4880378-4880472
Coord A exon
chr2L:4880294-4880377
Coord C2 exon
chr2L:4876891-4879196
Length
84 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGA
5' ss Score
7.62
3' ss Seq
CAATCGTGGCTGTTTTGCAGGAG
3' ss Score
5.91
Exon sequences
Seq C1 exon
CGCCACGCCCAAAGAACGCCCCTACACGTGCTCCTACTGCGGCAAGTCCTTCACTCAATCGAATACACTAAAACAGCACACTCGCATACATACAG
Seq A exon
GTGAGAAACCATTTAGATGTGGCTATTGTGGCAGGGCGTTCACTGTTAAGGATTACCTGAACAAACATTTAACGACTCACACGG
Seq C2 exon
GAGAGAAGCCGTTCCACTGCGGTTACTGCGAGAAGTCCTTCAGCGTGAAGGACTATCTGACCAAGCACATACGGACGCACACCGGCGAGAAGCCGTACACCTGTCCGTATTGCGACAAGCGCTTCACGCAGCGCAGCGCCCTCACTGTGCACACGACCAAGCTGCATCCGCTCTAGGGAAGGCCGGGCGGTGGCCGCCAGTTACCCGTTCCTGCCCCAGCCGCTCCTCCTCCTCCTACTCATCCTCCAAATCCTTCTGGTCCTGGTGCGCCGCCGCCGTTGTCCGCCGACACGGATACAGATCCCAAGAAGCCATCTGCGGCGGCTGCGGCATCGGCTTAGGACGAACTGCAGCGGAAACGGGATGAGCAAACCATAAATGAAAGACCATTTCAAAGACGAGACACACTCACGTAGACGGGAGTTATGCAACTGCAGCGGATGCAACAACTGCAACCAACGACTGGCAAATCTCTTCGCAGTGCTGCTAGATTAAATTAC
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0000286-5-6,6-6-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.159 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF057587=Ycf1=PD(13.0=93.9),PF134651=zf-H2C2_2=PD(57.6=57.6),PF134651=zf-H2C2_2=PU(38.5=30.3)
A:
NA
C2:
PF134651=zf-H2C2_2=PD(57.7=25.4),PF134651=zf-H2C2_2=WD(100=44.1),PF102764=zf-CHCC=WD(100=35.6)
Main Inclusion Isoform:
FBpp0088592

Main Skipping Isoform:
FBpp0088590

Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0088591, FBpp0293426, FBpp0307799
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCGGCAAGTCCTTCACTCAAT
R:
TTGTCGCAATACGGACAGGTG
Band lengths:
175-259
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Neural diversity
- Neurogenesis
- Neuronal activity
- Splicing factor regulation (brain)
- Splicing factor regulation (SL2)