BtaINT0031375 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008868 | CAPN3
Description
Bos taurus calpain 3, (p94) (CAPN3), mRNA. [Source:RefSeq mRNA;Acc:NM_174260]
Coordinates
chr10:37875470-37876472:+
Coord C1 exon
chr10:37875470-37875678
Coord A exon
chr10:37875679-37876435
Coord C2 exon
chr10:37876436-37876472
Length
757 bp
Sequences
Splice sites
5' ss Seq
TGAGTGAGT
5' ss Score
6.51
3' ss Seq
CTTGTTTGTGTTCCTCACAGGGA
3' ss Score
10.1
Exon sequences
Seq C1 exon
ATGCACGGCAACAAGCAGCACCTGCAGAAGGACTTCTTCCTGTACAATGCCTCCAAGGCTAGGAGCAGAACCTACATCAACATGCGGGAGGTGTCTGAGCGCTTCCGCCTGCCTCCCAGCGAGTACGTCATTGTGCCCTCCACTTACGAGCCCCACCAGGAGGGCGAGTTCATCCTCCGGGTCTTCTCGGAAAAGAGGAACCTCTCTGA
Seq A exon
GTGAGTCCCAGCCTGGCTTTCCCCACCTGTCCCTAAGAGCCCACATGACCCATACCAGAGACTAGAGGTGTGAGATAACCGGACAGGTCTCTCCAGGAGTCCTGTTGACCAGGACCTCTTCCCCTGTTCCTGAGCCACTGGGAACATCTCCCCTACATCCATCCGCCCACCCATTCATCCCACAGATAGCTACTGAGCACCTGCTTTGTCCCAGGCACTCTTCTAGGCACTAAGAACAGAGCAATGAATTAAACAGAAATCCCTGCCTTCGTGGAATTTAACATTTTAGCATGAGATGACAATGTAATAGAAAAAAGTATATAGAGATTATTAGATTTACATAAGTGATAAGGAGAAAAAATAAAGTGGGAAGAAGGATAGGAGCAGTTGGGGGGTGACTGAACTTTTAGGTACGGTGACCAGGGAAGCCAGCAAGGCCACATCCTGCCCTCTTTGTCACTGGAGATAAGTTCATAGGCCCTTGCCACTTTGACCTCTGTCCCTAAACGAAACATAAGGTCCATGAATAGGTGTCTGGGTCATGCATCTGGGAAACCTAGACAAAGCCAAAAAGAAGCCCTGTGTCTGCACTTGGCTTCAGGGAATGGCACCTGTGGTAGGGGGTATTAGTCCCTGGGGTTCTCTTGAGGTCAGTCCAGACTTGGCTCCGAGAAGCCAGGTGGCCTGAGCAAAAGCCCTCTGCTTCCTACTTGTTCTTGGTGACACTGAGACCCCCTCTTGTTTGTGTTCCTCACAG
Seq C2 exon
GGAAGTTGAGAATACAATCTCTGTGGATCGGCCAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008868:ENSBTAT00000011677:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.029 A=NA C2=0.462
Domain overlap (PFAM):
C1:
PF0106717=Calpain_III=FE(44.5=100)
A:
NA
C2:
PF0106717=Calpain_III=PD(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGACTTCTTCCTGTACAATGCCT
R:
CTGGCCGATCCACAGAGATTG
Band lengths:
215-972
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development