BtaINT0031378 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008868 | CAPN3
Description
Bos taurus calpain 3, (p94) (CAPN3), mRNA. [Source:RefSeq mRNA;Acc:NM_174260]
Coordinates
chr10:37881705-37882859:+
Coord C1 exon
chr10:37881705-37881818
Coord A exon
chr10:37881819-37882781
Coord C2 exon
chr10:37882782-37882859
Length
963 bp
Sequences
Splice sites
5' ss Seq
CAGGTTTCT
5' ss Score
-0.33
3' ss Seq
TTTCCTTTGTGCCTCCACAGCTA
3' ss Score
10.71
Exon sequences
Seq C1 exon
CCCATCATCTTTGTTTCAGACCGAGCAAACAGCAACAAGGAGCTGGGTGTGGACCAGGAAACAGAGGAGGGAAAAGACAACACAAGCCCTGATAAGCAAGCAAAATCCCCACAG
Seq A exon
GTTTCTGAGCATGTGCATGAGTGGGGTGGCCTGCACACAACTGAGGCCTGTGCTCTTGGAGTGCATGGGGGTTGGAGGAGCCATAGGGGTGGGGTGTCCCTTTAACATCCAGAGGTTTAGGTTTGTCCCACTGACATTTTCCCTCATCAAATTCTCCTAAAATTTGGGGTGCTGCTTGGATGAATGTCTTGGGATTGGCTGCCACACCAAGCTGGTCCTGGGAAGGATGGGCTGAGCTTCCCTGCTGGAGCCCATCCAGCCAGGATGATGAAAGAAGAGGGATGCAAAGCCTGTGACAGACACTGAGACAGAACAGCTCATTTCCTGGTGTCATTAACAGGGAAGATAAAGAACAGTAGTGGGAGGGGGGTGACACCAGAGGTGGAGTCCTCCAGAGCTCAGGGGACAGTGTTAGATTGGAGTGAGGACAGGAGGTCATATAAAGTATATAGGAGGTGAGACTAGCAGGCAAGATTCCAGATAAACCCAGGGACATCTCTGTCCTGTGGTGCCCATGCAATGGCGGGGGAGGGGAGGAGGGTCCTCTGAGGATTTGGCCTTGATGGCAGAAATGGCTGGAGGTATCAGATTGGTCTGGTCTGCTTCATCCTGCTGGGGCTGGTTTGGTTGGGATGGTCAGGCTGTAAAAGGAGGAGAGGGCTCCAGCTGGTGCAGATGGGGGAAAGAGGACCAAGGGGGCTGTCTACATGTCTGCACAGCTGATATACCTCCTCTGGCTAGGCTGGGGAGGTACAGAGTGAAGGGTCCTTGGGGCCCAGATGATTCTTACTCCAGATCAGTAGGTTCAACCAAGAAAGAAGAGCATTGACTCTGTACCCAGCTCCTGCTGCCACCTATGGCTGGTTTAGTCACCCTGGCTCCTTCAGTCCAGAAGGAACTTTCCTCTCGGGTTTGTCCATCTCCCTGGTCCCTGCCAACCAGTTTTCCTTTGTGCCTCCACAG
Seq C2 exon
CTAGAGCCTGGCAACACCGACCAGGAAAGTGAGGAACAGCGGCAATTCCGGAATATTTTCAGGCAGATAGCAGGCGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008868:ENSBTAT00000011677:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.763 A=NA C2=0.673
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF138331=EF-hand_8=PU(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:
CCCATCATCTTTGTTTCAGACCGA
R:
CGCCTGCTATCTGCCTGAAAA
Band lengths:
190-1153
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development