HsaINT0032667 @ hg19
Intron Retention
Gene
ENSG00000136807 | CDK9
Description
cyclin-dependent kinase 9 [Source:HGNC Symbol;Acc:1780]
Coordinates
chr9:130548305-130549061:+
Coord C1 exon
chr9:130548305-130548519
Coord A exon
chr9:130548520-130548979
Coord C2 exon
chr9:130548980-130549061
Length
460 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGG
5' ss Score
10.17
3' ss Seq
GTCTCCCTTTCCGCCTGCAGGGA
3' ss Score
11.53
Exon sequences
Seq C1 exon
AAGTGGCCGTGGAGGCGGAAGTGGCGCGGCCGCGGAGGGGCCTGGAGTGCGGCGGCGGCGGGACCCGGAGCAGGAGCGGCGGCAGCAGCGACTGGGGGCGGCGGCGGCGCGTTGGAGGCGGCCATGGCAAAGCAGTACGACTCGGTGGAGTGCCCTTTTTGTGATGAAGTTTCCAAATACGAGAAGCTCGCCAAGATCGGCCAAGGCACCTTCGG
Seq A exon
GTAAGGCTGGGCCCCTCGGGGCCGGGAGCCCTGGGCCTGCACCCCTAGGGCCGACGTCGGGATGCCCGGGCCCCCCCCGAGTTGGTAGAGAAGTCGTCTGTCCCCGGGCTTGCCTGCTGGTCTCTAGGCCGCGCCGCACCCCGCCCCGGCCTGACGGAGCCGGCTGGTGGGGAGGAGCCTGAGGCCCGTGGTGGGGGCGGGGAGGGGCTGCAGAGAGGCGCCCGTGAGGGGAGCGGGATCTCTCCAAGGGACGCCCAAGTGAGGAGAAGGGACTGAGGGAAGGAAGCAGAGGCTCCGAACGAGACAGGCTGCCGGGTGGCGGGGTAGCCGCGTGCCCTGGGTACCTAGCCCAGCCCCGCCCGGGAATCTCTTTGCTGCTGCCCCTCCTCCTGTAGTGGGGGAGGGGCGGGCCCTGCGGAAATGGCCTGATGAGTTCTCGGGTCTCCCTTTCCGCCTGCAG
Seq C2 exon
GGAGGTGTTCAAGGCCAGGCACCGCAAGACCGGCCAGAAGGTGGCTCTGAAGAAGGTGCTGATGGAAAACGAGAAGGAGGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136807-CDK9:NM_001261:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.679 A=NA C2=0.083
Domain overlap (PFAM):
C1:
PF0006920=Pkinase=PU(4.0=38.7)
A:
NA
C2:
PF0006920=Pkinase=FE(45.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGGCGGCCATGGCAAAG
R:
CCCCTCCTTCTCGTTTTCCAT
Band lengths:
183-643
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)