BtaINT0031390 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008868 | CAPN3
Description
Bos taurus calpain 3, (p94) (CAPN3), mRNA. [Source:RefSeq mRNA;Acc:NM_174260]
Coordinates
chr10:37864495-37866668:+
Coord C1 exon
chr10:37864495-37864641
Coord A exon
chr10:37864642-37866584
Coord C2 exon
chr10:37866585-37866668
Length
1943 bp
Sequences
Splice sites
5' ss Seq
CGGGTGTGT
5' ss Score
5.31
3' ss Seq
GTCCGGTTTTCACTCCACAGATG
3' ss Score
10.1
Exon sequences
Seq C1 exon
GATGGCACAAACATGACCTATGGAACCTCTCCTTCTGGGCTGAAAATGGGGGAGTTGATTGAGCGGATGGTGAGGAATATGGATAACTCGCGGCTCAGGGACTCAGACCTCATCCCTGAGGGATGCTCAGATGACAGACCAACTCGG
Seq A exon
GTGTGTACTCCTCCCACCTGCATGGCCCGGGTGTGTTGCGTGGTGTCAGACCTTCCTCAGCAGCCGGCACCGCCCACGTGGGCTCCTCCTGGGGCCTTCCAGGGGTCTGGGTTGGAATCTCTTGCTCGCTCGAAGGCTCCTGAGGCAAGGGGGGGAGACAGCTTTTGGAGGGAATCTCTGGCGGGGGAGGGGAAGGGGTTCCTTCATACTCCATGGTCCAGGCAGTTTCTCTGATAATGAATTAACTGGCATAAATATTTATGAGAGAGATTTCATTTATTTGTAAAGTATTTCTCTCCTTCTAGTTTGTTCATTTATGTATTTGACACTTATTTACTGAGCTCCTACTAGGCACTCTTCTAACAAACAAAGAAAATTCTCTCCCATTTGTGTCGGATTCTAAGGAACAAGCAGTTTCCACACACTCCCCCGGCCCCACCCCCCGAGCTTGTATTCTAGTAGTTTTGGAAGTAATACATGCTATACAGTAAAGCAGAGAAAAAATGAACCTATTTTTTCCCTATCTGAGGATAATAACATTTGGCATATGTCCTACTAGGGTTTTTCTATGCATACACCTAATCTAAATCTTTATTTTAAAAATGCAGTCATACTGTATGTACCTCTTTGCAGCATGCTTCTTTTTCAGTTAGCTTTATATACCTAATGTGTCAACAAGAATCACATTCTTAGTGTGTCTTCTATAACATTTTTCGTGGCTGTACAATAGTCCAACATGCAGATAAATTGTAGTTTTTTTACCCCATAACTTATTATTGGGAATTTAAATATTTTCTTTTTCTGTTTTGGCTGTAGTTTTTAAATGTTACAGCTAACATCCTATTAGATACATCTTTGTGTCCATCCAGGACACTTTCCTTTGGACAGATGGCCAGTAGTGGAATAGCTGGGAATGCATAATGTAATGCCACAAGAGTCATTTCAAGTGGTTTCCCTGGTCCAAAACTGAGAGGTTTATGAACCTCCTGCCCCCCTCCCTTTCTGTTCACATGGTCTGGGTCCTCTAAAGACTAAAATCTGGAAGAGTTTGAGATGTCAAAAGCCTTGGCTCCTCATATACCCCTCACTTTGAAAAGGGCTCCAGGCTACCTCTTAAAGCTGTCATATCACCAGGCAGAGTGAAGCCACAGAGATCCATCTAGGGCTCAGTGGGTTTTGGCCATTCTACCCTTCTCCCAAGGATCTCCTGTGGCTGCAAATCTCAGATGGAAGAGACTTCCCTGCTCCCTGAGGCACAGTCATGTCTGAGCAGGACTCTCCTCTAGCTGCCTTGGAATTCTCTGCCTGGGTACAGGAACTTTTAATTTCTTTCTTTTTTTTTAATTTTTTGCCACATGACATGGCACGTGGGATCTTCGTTCCCCCAATCAAGGATCAAACCCGCACCCCCTGCACTGCAGGTATGGAGTCCTAACCACTGGACCACTAAGGAAGTCTACTTTTAATTTCTTGAATATGTTCTAGGGTGGGTGGAGAAGGTGAGGGGATATAAAGATAAAAGGTTAGACCTCCATGTTTCATCTAACCCCCTTTCTCAATCCCTTTCTCTTCCAGGAATAGTCAACCCTGGGTGGGCTCAGGGAAGGGGAGCCTGACCCAAGGCAGCCTCCATCCACCCCCACTTCTTCCTTTGAAAGACCCAAGGGATCCAGAAAGGAGGGCCAGGCACGCTCTCACTCACCTCGTGGCCCCAGCCTCCACATTGTTCTCCAATGGTTAAGGGACCAGCTTGACGGAAACACCTTGTCTGGGCTGCATATTCTTGGCTCTCTTAAAGGGCTAGTGTGGGTCTTCTCATGGCTAGGAGGCACGCTTCCAGAGCATGGAGGAGTCCTTGTCCTCACTGAACCCAGGATGTGAACTAGTGTGAACTTTGTCTCAGGAAACAAGCCCTGACAGGCTGTCCGGTTTTCACTCCACAG
Seq C2 exon
ATGATTGTTCCAGTTCAGTTTGAGACAAGAATGGCCTGTGGGCTGGTCAAAGGCCATGCCTACTCAGTCACTGGGCTGGAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008868:ENSBTAT00000011677:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.204 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=PD(4.4=18.4),PF0064816=Peptidase_C2=PU(30.4=91.8)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(18.2=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:
TGGCACAAACATGACCTATGGA
R:
TCCAGCCCAGTGACTGAGTAG
Band lengths:
225-2168
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development