BtaINT0031354 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012778 | CAPN2
Description
Bos taurus calpain 2, (m/II) large subunit (CAPN2), mRNA. [Source:RefSeq mRNA;Acc:NM_001103086]
Coordinates
chr16:27825578-27827650:+
Coord C1 exon
chr16:27825578-27825789
Coord A exon
chr16:27825790-27827613
Coord C2 exon
chr16:27827614-27827650
Length
1824 bp
Sequences
Splice sites
5' ss Seq
CCAGTAGGT
5' ss Score
5.41
3' ss Seq
CGCCTTCCTTCTGCTTCTAGAGT
3' ss Score
9.67
Exon sequences
Seq C1 exon
TTGACTGGACAGACCAACATCCACCTCAGCAAAAAATTCTTCCTGACAACCAGAGCGCGGGAGCGGTCGGACACCTTCATCAACCTGCGGGAGGTGCTCAACCGCTTCAAGCTGCCCCCCGGGGAGTACATCGTGGTGCCCTCCACCTTCGAGCCCAACAAGGACGGCGACTTCTGCATCCGGGTCTTTTCCGAGAAGAAAGCCGACTACCA
Seq A exon
GTAGGTCGTTCAGCCCTCCTCCTCCGCGCCCCTTGTTCCTGGCCTGCCTGGAGCAACCTCACTCCTCTGAATGTCAGTTTCTTTTTCTGTAACACCTGCCGGCTTCAGAGGCGAGTTATTGAAGGACTCTAGCGCTGTCATCACGTCAGCAAAGAAAATAGCCACTCAGGATCTTTGGGGTTAGAAAGGGGTGGTGGCAGAGCCAGTCGCAGAGCCTGACTTTACAGCCGTGTCTCCGAATGTCCACCAACTAGGGCAGTGCTGGTGGGATCCTTGTGTCCCCAGTCCGCCGGCCTGGCAGAGCCAAGGGTGTGAGTAAGTCTCCCCGCGGCAGTCACTAGGTCTCAAGGCGTTCCCCCTTCCTCACTGGAGCCCAGCTGTCCAGGATCCTTTTTAGCTGAAGCCACTGTCAGTACAGCCTCAATTCTAGTGGCTTCTGCTTCTCCGGCTGCTGCCCAACTGTGTCTGTTCATCTCGGCCCTTGACTGCATGCGATGTAATCAGCCTGGGGTAACTTAAGCAGATGGAGATTACTGGAAGGCCATGGAACTCTCTAGAACCTACGGGAGGCTGGACAACGGGATAGAAAAGTGCAGGGACCTCAGATGCTCCCGAGGACCAGGGTGTGGGAAGCAGGGGTTGTGGTGGCTGCCGTGTCCCCTCTGACCTGAGTCACATGCTCAAGGTCAAGAGACTCAGTAGAGTGTCTCCGTTGGATGGGCTCTAGAGGCTGCCTAGAAGGGGAGGGCAGCAGGCAGGAGGGCCAAGGATGATGGCCCAGGCTCCAAGACAGTGCACGGCAGAGAAGGAGTTCCTCTTGAGAAAACTGGGGTGTTGTTAAAGTGAGGGAAAGTGTCAGAGCTTCGAACGGGTAACAGCGCTGCCATGGCTGTAGCTTTCCTGCCTCTGACAGGCTCCCTTCCTCTGCTTAAGCTCGCCGTGGGGCAGGGCCTTGCTCTCAGCTCCTAGGATCCTCGGGGCTGGCCTGGTATTTAGCCTGTGGTCCCCACTGACAAGGAAATGGGGACATGACACAGTGCATTGGAATGACACGGTCCTATGTCAACCTCAGTCCCCTCCCGGGGAAACCTCAACCACCTCCTGCCCCGCCACCAACTCTGCCATCTCTTGGCGAGCTCCCTCCCCCAAGGGGACACGCCATCCCTCAAAGGTGTCCACCTTCTTGTCCCAGGATATTAATCCTGATTCTAACTGTCAGCACCAAGAAGTCTCCGCGTGCATCCTTCTGTGAGGCATCAGCACGGTAGACGGGACTCTTGGTGGTCTAGTTTGAGATCCCAGGGGCCGGAGGGAGACCCTCCTGGGCTTAACTTGCCTCACTGTAGAGCAGAAGGACCCAGCCCTTCACACAGGTGTGGGATAAACCAGCCAGTGCCCGAGCCTCATTTGAAATCTCCCCCAGGCCTCCCCGGCTGCCAGCCTCCTCCCGCCCTAGGCAGCAGGGTATGCTGATTCTCGGTGTGTTCACGAGGGCAAAGAGTGTTTCCAAGGGAACCTAAAAACTGTTCTCCAGGCCAGAGCACCACCGCCATAGTACATGGGAAGCCTGTGTTCTTTGATAAAGACCAAAAACTAGGGACCAAAAACATTCTGATGCTCCAAGTGTTTTTTGGTGATGACACTTTTTTAGATCGTTTCTGCTTTAATTTCTGCTGAAATTACGGGATGTGTTGTCACAGAAACTTGGGATGCAGAGAAACCCCCTGTGCCCACCCCATGCTGGGTGTAATATGCCAGTTCCATTTTAGCAGGGATTTCTGCCCACTCCCTCTGCAGTAACACACGCCTTCCTTCTGCTTCTAG
Seq C2 exon
AGTTGTCGACGATGAAATCGAGGCCAACATTGACGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012778:ENSBTAT00000047532:12
Average complexity
IR
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:
PF0106717=Calpain_III=FE(44.9=100)
A:
NA
C2:
PF0106717=Calpain_III=PD(0.1=0.0)
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:
TGGACAGACCAACATCCACCT
R:
CTCGTCAATGTTGGCCTCGAT
Band lengths:
244-2068
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development