BtaINT0035812 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004695 | CDK9
Description
Bos taurus cyclin-dependent kinase 9 (CDK9), mRNA. [Source:RefSeq mRNA;Acc:NM_001014935]
Coordinates
chr11:98474464-98475158:+
Coord C1 exon
chr11:98474464-98474590
Coord A exon
chr11:98474591-98475076
Coord C2 exon
chr11:98475077-98475158
Length
486 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGG
5' ss Score
10.17
3' ss Seq
TCTCCCCTCTCCGCCTGCAGGGA
3' ss Score
12.61
Exon sequences
Seq C1 exon
CTGGAAGTGGCGGCGGCGGCGTACTGGAGTCAGCCATGGCAAAGCAGTACGACTCGGTGGAGTGCCCTTTTTGTGATGAGGTGACCAAATATGAGAAGCTCGCTAAAATCGGCCAAGGCACCTTCGG
Seq A exon
GTAAGGCTGGGCACCCCCCGCTCCCCAACCCCCAGGGACCGGGAGCCTCCTGAACCTGCACCCCTCCGGGCCGACGTCGGGACGCCCAGACCCGGGCCCGGTTTGTCGGGAAGCCACTTAGACGCAAACTTATCGCCTGGTCTCGCTAGGCCGCACCGCAACCCCGCCGGGGCCTGAAGGAGTCGGCCGGCGGGGAGGAGCCTGAGGCCCTTGATGGGGGGGCAGGGAGGGGTTGCAGAGAGGAGCCTGTGAGTGGAGCGGGATCTCTCCGCGAGACGCCCTACTGAGGCGCAAAGAGCAGAGGGAAGGAGGCTGAGACTCGAGAAGGGACCGGAGTCACCGCGTGGTGGGGTAGCCGAGTGCCCTGGGAGACCCGGCCCAGCCCCGCCCGGGATTCCCTTTCCGGCCCTCCTCTGGTGGGGGAGGGGCGGGCTCTGCGGAGACGTCCTCTAAGATCCCTCTTGGGTCTCCCCTCTCCGCCTGCAG
Seq C2 exon
GGAGGTGTTTAAGGCAAAGCACCGCAAGACTGGCCAAAAGGTGGCCCTGAAGAAGGTACTGATGGAGAACGAGAAAGAGGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004695:ENSBTAT00000006162:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006920=Pkinase=PU(4.0=38.7)
A:
NA
C2:
PF0006920=Pkinase=FE(9.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCGTACTGGAGTCAGCCATG
R:
CCCCTCTTTCTCGTTCTCCAT
Band lengths:
191-677
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development