Special

DmeINT0018068 @ dm6

Intron Retention

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:4880294-4882492:-
Coord C1 exon
chr2L:4881215-4882492
Coord A exon
chr2L:4880473-4881214
Coord C2 exon
chr2L:4880294-4880472
Length
742 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAAT
5' ss Score
1.19
3' ss Seq
CCGAACCGCAACTCCGACAGCGC
3' ss Score
1.91
Exon sequences
Seq C1 exon
CGCATATCGCCTTCTTTAACCGCCAATTGCTCCTGCTCCTGCCCACTAACCAAGTCAAACCAAAAGAAGCGATTACTCTCCAAGCGCCAGCGGAAGTGAAATGATAAAGTCCACCACGAATCCACAGGAACAGCGTCTGCCACGCCCCGAGGATCAGTCGCCAGCGCCGCCGCCGCCGCCCCCCTCCTCAGCCACCACCTCCACCGCCGCCCCAGCCACGCCCACGCACCAAGTGGCCACCGTGATAGCCAACATGGACACCCTGAAGACAGCCTTTCTGCCCAATCTCAGCATGGACCCCAATGTGCACGTGTCGCCGCACTATTGTCCCATGTGTCACCAGCAGTTTGAGCGACCGCAGCACGTCGCGGATCACATGCAGCTGTGCCACGGGATCACGCTGAACGCCCAGGGAGCCATTGCCACGCTGGACGGCGGTCATCCGCAGGCACAGCAGCACCCCAAGCTCAGCCACCCCTGCTTCAATTGTGATGAAAAGTTTGGCAACGCCGTCGATTTAGACGAACACCATCGGCTGGCCCATCAGACGCCCGCCTTCCTGTCCCGCTGCCTTATGTGCAGCATCTATGGCATCCACTCGGCCACCCAGCAGCCCAACGAGTACAAATGCACGCAGTGCGGCTCCATTTGCACCACCGCCATGCTGGCTGCCGGACAGCAGGGCTTTATGGAACAGCAGGAGGCGGCGGTGACGCCCGACGATCAGCTGCCGGCAATGGCGCCCCGTGATATGAGACTGACGCCCGAGGAGCAGCACCATCAGCAGCAACTGCAGGCGGAGCACCACCATCAGCAACAGCACCAACAACAACAACAGCAGCAGCAGCAGCAGCAGGAACTGCTGGAGCAGCAGCAGCGTGAAATGCAGGAGCAGGCGCAACAGCAGCAGGTGCACCATCACCAGCAGGATCAGGATCTCGCCGGCGACCAGGTGGCGCTGAAGGTGCCACCACTCACCGTCAAGCTAAACAAGAACGCCAACGGTGGCGCCATTGTGTCGCATCCGCAGGTCATTATCAAGGAGGAGCCACTCAGCCTGAGCGACAGTGGTGATGTTGTCAACTCTGTGCCTGTCTATGCCATACAAGCCAATCCCGGTGTACCCGCTCCGGCCAGTTCGGGTGTGCTAGTCGGCACACAAACGGTACCTGCCGATCTGGCGCACAAGATCCGGCACAAATGTCCGGATTGTCCAAAGACCTTCAAGACGCCCGGCACGCTGGCCATGCACCGCAAGATACACACAGGCGAAGCAGA
Seq A exon
GTAAATCCATTTTATATGCATCTTACGGACTGGGTATTCCGGCAATGATAGCTACTGGACAGCGACTTTAAAAGCTCTAGTCGAGTAACTGGCATTTGATGATCTTATAGATATTTTAATGATAGTAGTTAGTTTGTTAGTTAGTTAGAAGTGATGGGATATTGTCGTGCAAAGAAGAATTTATAAAATATTGATAGATATAGTATAGATCGCAGTGTAATCTCAACAAGATTAAGTGTCTTTGCATCCAGGAAAGCTTTCAGTTGCAATGCTTTAAGATAAGAATGCTTCCTAGCTCATTGCCGGATTACCTGTTATTCATTCCAAGGCATTGCCCGCTCTAGCTCAAAGGGGGGGATACCCACGTAGTTTTTTGTGGGTCTTCCTTTGCGACTGGGGCGGCGTGATCGCCGAACTAACCCCAATAATCTTACCACCTTGTATATATATATATATATATATTATTTTTGATTTCCTTCGGGCCAGCTGGGCGCATGGGCGCGCCCTCGAAGCTCTGGGACGAGGCCCATGCGTTCGTGTGTCGTTTGTTTTGCAACTTATTTTTAAATCGAGTGTTACTAATAATATAATTTAAATTTCTTTCTTTTCTCCCGCGCCCACTCTCTCTCTCTCTCTCTCTCTGTATCTTTTTCCTCTCCGTTTCTGCGCGGTATTTTGTGAATATGAATATAAATAATTGTTAACTCTCGAATCTCCACTCTCCGAACCGCAACTCCGACAG
Seq C2 exon
CGCCACGCCCAAAGAACGCCCCTACACGTGCTCCTACTGCGGCAAGTCCTTCACTCAATCGAATACACTAAAACAGCACACTCGCATACATACAGGTGAGAAACCATTTAGATGTGGCTATTGTGGCAGGGCGTTCACTGTTAAGGATTACCTGAACAAACATTTAACGACTCACACGG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0000286:FBtr0089649:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact

ORF disruption upon sequence inclusion (1st CDS intron)

No structure available
Features
Disorder rate (Iupred):
  C1=0.612 A=NA C2=0.138
Domain overlap (PFAM):

C1:
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)
A:
NA
C2:
PF057587=Ycf1=PD(11.5=44.3),PF134651=zf-H2C2_2=PD(57.6=31.1),PF134651=zf-H2C2_2=WD(100=42.6),PF134651=zf-H2C2_2=PU(38.5=16.4)


Main Inclusion Isoform:
NA


Main Skipping Isoform:
FBpp0088592


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
FBpp0088590, 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:
AGCGACAGTGGTGATGTTGTC
R:
CCCTGCCACAATAGCCACATC
Band lengths:
349-1091
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)