HsaINT0032671 @ hg38
Intron Retention
Gene
ENSG00000136807 | CDK9
Description
cyclin dependent kinase 9 [Source:HGNC Symbol;Acc:HGNC:1780]
Coordinates
chr9:127788214-127788692:+
Coord C1 exon
chr9:127788214-127788385
Coord A exon
chr9:127788386-127788543
Coord C2 exon
chr9:127788544-127788692
Length
158 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGG
5' ss Score
8.99
3' ss Seq
TGGTGCGCTCTTCTTCCCAGGGG
3' ss Score
8.76
Exon sequences
Seq C1 exon
ATCCTGCATAGGGACATGAAGGCTGCTAATGTGCTTATCACTCGTGATGGGGTCCTGAAGCTGGCAGACTTTGGGCTGGCCCGGGCCTTCAGCCTGGCCAAGAACAGCCAGCCCAACCGCTACACCAACCGTGTGGTGACACTCTGGTACCGGCCCCCGGAGCTGTTGCTCG
Seq A exon
GTGAGGACTCCCGAGCGGGCCAAGGGGGGTGAGGGCCAGGCATCTACCTGGCCCCTTCCCCCCAACTGCCAGGGCTTCTTGAGCTGCCGGCCCTGGGGCATTGAGCCTCAGGAGGCCCTCGGGCTCAAGGGGCCCTCCTGGTGCGCTCTTCTTCCCAG
Seq C2 exon
GGGAGCGGGACTACGGCCCCCCCATTGACCTGTGGGGTGCTGGGTGCATCATGGCAGAGATGTGGACCCGCAGCCCCATCATGCAGGGCAACACGGAGCAGCACCAACTCGCCCTCATCAGTCAGCTCTGCGGCTCCATCACCCCTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136807:ENST00000373264:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006920=Pkinase=FE(19.2=100)
A:
NA
C2:
PF0006920=Pkinase=FE(16.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCTGAAGCTGGCAGACTTT
R:
CTGACTGATGAGGGCGAGTTG
Band lengths:
246-404
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development