HsaINT0032669 @ hg19
Intron Retention
Gene
ENSG00000136807 | CDK9
Description
cyclin-dependent kinase 9 [Source:HGNC Symbol;Acc:1780]
Coordinates
chr9:130549797-130550392:+
Coord C1 exon
chr9:130549797-130549887
Coord A exon
chr9:130549888-130550225
Coord C2 exon
chr9:130550226-130550392
Length
338 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
TCTTTCTATTCCTGCCTCAGCTT
3' ss Score
6.41
Exon sequences
Seq C1 exon
TTCCCCATTACAGCCTTGCGGGAGATCAAGATCCTTCAGCTTCTAAAACACGAGAATGTGGTCAACTTGATTGAGATTTGTCGAACCAAAG
Seq A exon
GTAAGTTATTTGGTTCTTACGAGAAGATGACACTTGTAGCCTAAGGTTTTGTTTGTAAACTTGGAACTAGGCACACCTAAACTGCCTCTTCTTAACTCAGATGGACCCATGGTGACTGCTTTTTCTGGTCCTCTTTCATCGTAGCTGGTGCTTCCTCGGGGCCTGCCCTGGCCCAGAAGAGGCACTCAGAAAATATTTGACCGGTGAAGGAAGGAACAGACAGATGCTCTGGAGGGCATGGGTGCCCGTGGGTTGGAGCAGGAAGAAAGAAGCTGGTTGTGGGAAAGTGTGTTGGGTGTGGTTTTCTTGACTTTTTCTTCTTTCTATTCCTGCCTCAG
Seq C2 exon
CTTCCCCCTATAACCGCTGCAAGGGTAGTATATACCTGGTGTTCGACTTCTGCGAGCATGACCTTGCTGGGCTGTTGAGCAATGTTTTGGTCAAGTTCACGCTGTCTGAGATCAAGAGGGTGATGCAGATGCTGCTTAACGGCCTCTACTACATCCACAGAAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136807-CDK9:NM_001261:3
Average complexity
IR-S
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=PD(30.5=90.0)
A:
NA
C2:
PF0006920=Pkinase=FE(18.5=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:
TTCCCCATTACAGCCTTGCG
R:
GTTTCTGTGGATGTAGTAGAGGCC
Band lengths:
255-593
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
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)