Special

DmeALTA0004627-3/3 @ dm6

Alternative 3'ss

Gene
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:4881215-4883107:-
Coord C1 exon
chr2L:4882865-4883107
Coord A exon
chr2L:4882360-4882492
Coord C2 exon
chr2L:4881215-4882359
Length
133 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
GATTTTTATTACTCCTGCAGCGC
3' ss Score
7.52
Exon sequences
Seq C1 exon
ACGTTGCCATCGTAGTTTCGATGCCAGTAATCGATACTTTTTGTTGTAGTTGTACATTTTTCGCCAAAAATAATAATAAAAGTGAAAAATTTTTTTTGTTAATATACGTTTATTTGTTGTACAAAGGAGAAAATGTTATTAAACTGATTGGCCGCCCCAGCATTTTCGTGACCCCCGCTCCAAATACAACAAAATCGAACGGCCGCCAGCAACAACAAGGTGCAGTAAATATTCAGTGCGCTG
Seq A exon
CGCATATCGCCTTCTTTAACCGCCAATTGCTCCTGCTCCTGCCCACTAACCAAGTCAAACCAAAAGAAGCGATTACTCTCCAAGCGCCAGCGGAAGTGAAATGATAAAGTCCACCACGAATCCACAGGAACAG
Seq C2 exon
CGTCTGCCACGCCCCGAGGATCAGTCGCCAGCGCCGCCGCCGCCGCCCCCCTCCTCAGCCACCACCTCCACCGCCGCCCCAGCCACGCCCACGCACCAAGTGGCCACCGTGATAGCCAACATGGACACCCTGAAGACAGCCTTTCTGCCCAATCTCAGCATGGACCCCAATGTGCACGTGTCGCCGCACTATTGTCCCATGTGTCACCAGCAGTTTGAGCGACCGCAGCACGTCGCGGATCACATGCAGCTGTGCCACGGGATCACGCTGAACGCCCAGGGAGCCATTGCCACGCTGGACGGCGGTCATCCGCAGGCACAGCAGCACCCCAAGCTCAGCCACCCCTGCTTCAATTGTGATGAAAAGTTTGGCAACGCCGTCGATTTAGACGAACACCATCGGCTGGCCCATCAGACGCCCGCCTTCCTGTCCCGCTGCCTTATGTGCAGCATCTATGGCATCCACTCGGCCACCCAGCAGCCCAACGAGTACAAATGCAC
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0000286-1-4,1-3,1-2-3/3
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact

5' UTR

No structure available
Features
Disorder rate (Iupred):
  C1=NA A=NA C2=0.601
Domain overlap (PFAM):

C1:
NA
A:
NA
C2:
PF127562=zf-C2H2_2=WD(100=23.1),PF096065=Med15=WD(100=62.6),PF057587=Ycf1=PU(85.5=60.5),PF134651=zf-H2C2_2=PU(39.4=3.8)


Main Inclusion Isoform:
FBpp0088592


Main Skipping Isoform:
FBpp0293426


Other Inclusion Isoforms:
FBpp0088590, FBpp0088591


Other Skipping Isoforms:
FBpp0307799
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:
ATTAAACTGATTGGCCGCCCC
R:
GCTGTCTTCAGGGTGTCCATG
Band lengths:
246-379
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)