BtaINT0031600 @ bosTau6
Intron Retention
Gene
ENSBTAG00000006572 | CARD9
Description
Bos taurus caspase recruitment domain family, member 9 (CARD9), mRNA. [Source:RefSeq mRNA;Acc:NM_001077111]
Coordinates
chr11:103881320-103881834:-
Coord C1 exon
chr11:103881649-103881834
Coord A exon
chr11:103881458-103881648
Coord C2 exon
chr11:103881320-103881457
Length
191 bp
Sequences
Splice sites
5' ss Seq
TGGGTCAGT
5' ss Score
4.68
3' ss Seq
GCGTCCTCTCTGAGTCACAGGAG
3' ss Score
0.02
Exon sequences
Seq C1 exon
CCATGTCCGACTATGAGAACGAGGACGCATGCTGGAGCGCCCTGGAGGGCTTCCGGGTGAAGCTCATCTCTGCCATCGACCCCGCCCGCGTGACGCCCTACCTGCGCCAGTGCAACGTGCTGAGCCCCGACGACGAGGAGCAGGTGCTCAGCGACCCCAGCCTGGTCACCCGCAAGCGGAAAGTGG
Seq A exon
GTCAGTGCCGCGGGCGGCCGCACTCTGCCCCCACCCTGGTCCCCCGACCCTCACCCTGCCTCCGCCCCGTCTGCCTGCCACTATGCCCGCTCCCCACACGGCAGACGCCCCTGGGAGCGCCCCAAGGTGGGGCCAGGCTGGCCCCCTCTGCAGCCTCGTGGGCCACCACATGCGTCCTCTCTGAGTCACAG
Seq C2 exon
GAGTGCTCCTGGACATCCTGCAGCGGACGGGCCACAAGGGCTACGTGGCCTTCCTCGAGAGCCTGGAGCTGTACTACCCGCAGCTCTACAGGAAAGTCACGGGCAAGGAGCCCACCCGCGTCTTCTCCGTGATCATCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000006572:ENSBTAT00000008634:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.032 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0061916=CARD=PU(58.6=82.3)
A:
NA
C2:
PF0061916=CARD=PD(40.2=74.5)
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:
CTTCCGGGTGAAGCTCATCTC
R:
TGCCCGTGACTTTCCTGTAGA
Band lengths:
242-433
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development