Special

DmeINT0002251 @ dm6

Intron Retention

Gene
FBgn0030408 | CG11085
Description
This gene is referred to in FlyBase by the symbol DmelCG11085 (FBgn0030408). It is a protein_coding_gene from Dmel. It has 2 annotated transcripts and 2 polypeptides (1 unique). Gene sequence location is X:12616316..12621216. Its molecular function is described by: RNA polymerase II cis-regulatory region sequence-specific DNA binding; DNA-binding transcription activator activity, RNA polymerase II-specific. It is involved in the biological process described with: regulation of transcription by RNA polymerase II; animal organ development. 6 alleles are reported. No phenotypic data is available. The phenotypic class of alleles includes: viable. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of very low expression to a trough of no expression detected. Peak expression observed during late larval stages, at stages throughout the pupal period, in adult male stages.
Coordinates
chrX:12619652-12621216:+
Coord C1 exon
chrX:12619652-12620213
Coord A exon
chrX:12620214-12620668
Coord C2 exon
chrX:12620669-12621216
Length
455 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
ATTTGCCTTTTCCATTGCAGGAC
3' ss Score
12.55
Exon sequences
Seq C1 exon
AACTGGAGCTCTCCAACGACGATTCGGATATAGACATTGAGGATCGATCTACGCCGGACTCGACGGCTGCGGGCTGCCAGCAGGAGCTACTGCTGTCGCACCATCACCGCAGATTCACCCACCACGACGAATCCAGTGTGGAGTCCTGCCTATCGGCCACAAGGGGCCCCGGCTCTGGCACAGGATCGGGTGGTGGCGGAGGTGGTGGTGGTGGAGGAGGAGTAGCCAGCGGACTGAGCGCCGCTGCAGCGGCGGCGGGCGTGGCTGCTGGACTCCTGGCAGCGGCGGCCAGTGGTGCCAATGGGGATCGGGATGCCAACGGTGGCAGTGGCCCGGGATCCGGTGGCGGTACAAGTGGCGGCTATGCGGAGCACAAGCTGCAGCTGAGCAAAAGTGGCCGGAAGCCGCGACGCCGCCGAACCGCCTTCACCCACGCCCAGCTCGCCTACTTGGAGCGGAAGTTCCGGTGCCAGAAGTACCTGAGCGTGGCCGATCGCAGCGATGTGGCCGAAACGCTCAATCTGTCCGAGACGCAGGTGAAAACCTGGTACCAGAATCGCCG
Seq A exon
GTGAGTGTTGATCGAGAGCAAATCCCCAAGTTGGAAAGGAGCCACTTTATTAATTGCTTTTTAAATTAAAACGATAATGGATAATGAAACAATAAGTTTTGATTAGAAAAGAATCAAATATCTTCCATTCGCGGATAGAATAATGAACTATTTGATTTTGTTTCACTATTTTAAATTGCAGTAAGTACAGTTGCGCTCATAGTGCTTCAACCGATCGCAAACGTCTGGCAACGCAAAACCTTGTATTTTGCGCAGTACAAATTGTATTTTTAAGTATATACATATTAATATTAATAATGGCTTGTTATTATAGTTTACCAAAGCCAATTTTATGTTGAGTAAGATTACTAAAAAAATATAGAATTTATTGGTACAATCACGCTAAAGTGATCCCATATTCAATTCTAACCGTGTGGCAACGATTGTAAGCGCTTCATTTGCCTTTTCCATTGCAG
Seq C2 exon
GACCAAATGGAAGCGACAGAATCAACTGCGTCTGGAGCAGCTGCGTCATCAGGCGACCATGGAGAAGGATTTTGTGGTCCAGGATGGCGGCGGTGCGGGCGGACTCGGCTGCTGTCCCAGCGGACTGAGCAGTTCTTTTAGTGCCGCCGCCGCTGCTGCAGCGGCTGCCAGCAATCCTTGCAATTTTCTCACTTCCGCCGCAGCGGCGGCCATTTTCCGTAATGTCGGCTATGTCCACGGATGTCCCATGTAGGAGCCACGCCCCAAACTCTCCCATAATACCATTTTCCCCAGCTGCCTGTGTATATAATGCGTATGAAGAAAACCGTTTTTGTGCAATAACCGATCGGGACAAATTAATGAAAGTCAAGCGATGTGCTGATATTTACCAAGCATACCCGATATTATTATTATAATACGTACTTAACAATATAATCATAAAAATAAGCGTAGTCGAATTAATTAATTGTATTATAAAACTAAAAAATTTTTTTTTTCACATCGCACTCTATGGAATTTTTTTTTGGCCAGAATAAACATTCAATTGC
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0030408:FBtr0073656:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact

Alternative protein isoforms

No structure available
Features
Disorder rate (Iupred):
  C1=0.691 A=NA C2=0.131
Domain overlap (PFAM):

C1:
PF0004624=Homeobox=PU(89.5=27.1)
A:
NA
C2:
PF0004624=Homeobox=PD(8.8=5.9)


Main Inclusion Isoform:
NA


Main Skipping Isoform:
FBpp0073489


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
NA
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:
CTCAATCTGTCCGAGACGCAG
R:
TATACACAGGCAGCTGGGGAA
Band lengths:
354-809
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)