Special

DmeEX6012807 @ dm6

Exon Skipping

Gene
FBgn0019949 | Cdk9
Description
The gene Cyclin-dependent kinase 9 is referred to in FlyBase by the symbol DmelCdk9 (CG5179, FBgn0019949). It is a protein_coding_gene from Dmel. It has 2 annotated transcripts and 2 polypeptides (1 unique). Gene sequence location is 2R:22636063..22637727. Its molecular function is described by 6 unique terms, many of which group under: protein binding; catalytic activity, acting on a protein; heterocyclic compound binding; catalytic activity; phosphotransferase activity, alcohol group as acceptor. It is involved in the biological process described with 8 unique terms, many of which group under: response to stimulus; defense response to other organism; positive regulation of defense response to virus by host; response to temperature stimulus; regulation of defense response to virus. 23 alleles are reported. The phenotypes of these alleles manifest in: anatomical structure; multicellular structure; organism; material anatomical entity; somatic cell. The phenotypic classes of alleles include: phenotype; increased mortality; female semi-sterile; cell number defective. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of moderate expression. Peak expression observed within 00-18 hour embryonic stages, at stages throughout the pupal period.
Coordinates
chr2R:22636063-22637343:-
Coord C1 exon
chr2R:22637259-22637343
Coord A exon
chr2R:22636942-22637199
Coord C2 exon
chr2R:22636063-22636873
Length
258 bp
Sequences
Splice sites
3' ss Seq
TTATATATGTGCTCCCCTAGTTT
3' ss Score
7.6
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
Exon sequences
Seq C1 exon
AGAGGTTTTTAAGGCTCGCGAGAAAAAGGGCAACAAGAAGTTTGTGGCCATGAAGAAGGTGCTGATGGACAACGAAAAGGAGGGC
Seq A exon
TTTCCCATCACGGCTCTGCGAGAGATCCGCATCCTGCAGCTGCTAAAGCACGAGAACGTGGTGAATCTGATCGAGATCTGCCGCACCAAGGCCACCGCCACGAATGGTTACAGATCCACCTTCTATTTGGTCTTTGATTTCTGCGAACACGATTTGGCAGGTCTTCTGTCCAACATGAACGTCAAGTTCAGTCTGGGCGAGATTAAGAAGGTTATGCAGCAGCTTTTAAACGGTTTGTATTACATCCACAGCAACAAG
Seq C2 exon
ATCCTGCACCGAGACATGAAAGCTGCCAACGTGCTGATTACCAAGCATGGCATCTTAAAGCTGGCTGACTTTGGCTTGGCCCGTGCTTTTAGCATTCCAAAGAACGAGAGTAAGAATCGCTATACCAATCGCGTAGTAACCTTGTGGTACCGGCCGCCTGAGCTGCTACTTGGTGACCGCAACTATGGTCCACCCGTGGACATGTGGGGAGCCGGCTGCATAATGGCCGAGATGTGGACACGCTCGCCCATCATGCAAGGCAATACGGAGCAGCAGCAGCTAACCTTTATCTCGCAGCTATGCGGCTCCTTTACGCCGGACGTGTGGCCGGGAGTGGAGGAGCTGGAGCTGTACAAATCCATCGAGCTGCCAAAGAACCAGAAGCGTCGAGTCAAGGAGCGCCTGCGTCCGTATGTCAAGGATCAAACCGGCTGTGATCTATTGGACAAATTGCTGACCCTTGATCCCAAGAAACGCATCGATGCGGACACAGCTCTGAA
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0019949-'2-2,'2-1,4-2=AN
Average complexity
A_S
Mappability confidence:
100%=100=100%
Protein Impact

Alternative protein isoforms (Ref)

No structure available
Features
Disorder rate (Iupred):
  C1=0.000 A=0.000 C2=0.118
Domain overlap (PFAM):

C1:
PF0006920=Pkinase=FE(9.4=100)
A:
PF0006920=Pkinase=FE(28.5=100)
C2:
PF0006920=Pkinase=PD(57.0=74.2)


Main Inclusion Isoform:
FBpp0071848


Main Skipping Isoform:
NA


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal4)
HIGH PSI
Zebrafish
(danRer10)
HIGH PSI
Primers PCR
Suggestions for RT-PCR validation
F:
CGCGAGAAAAAGGGCAACAAG
R:
ACATCTCGGCCATTATGCAGC
Band lengths:
304-562
Functional annotations
There are 1 annotated functions for this event
PMID: 23140174
Partially encodes an experimentally validated Eukaryotic Linear Motif (ELM). Method: alanine scanning, protein kinase assay, western blot. ELM ID: ELMI003213; ELM sequence: TKASPYNR; Overlap: PARTIAL_LEFT


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]


SPECIAL DATASETS

  • Neural diversity
  • Neurogenesis
  • Neuronal activity
  • Splicing factor regulation (brain)
  • Splicing factor regulation (SL2)