BtaINT0031364 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012778 | CAPN2
Description
Bos taurus calpain 2, (m/II) large subunit (CAPN2), mRNA. [Source:RefSeq mRNA;Acc:NM_001103086]
Coordinates
chr16:27812962-27814191:+
Coord C1 exon
chr16:27812962-27813080
Coord A exon
chr16:27813081-27814057
Coord C2 exon
chr16:27814058-27814191
Length
977 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACT
5' ss Score
8.63
3' ss Seq
TCTCTCTCCCTGCCCTGCAGTTC
3' ss Score
9.71
Exon sequences
Seq C1 exon
GTGACTGCTGGCTGCTGGCCGCAATTGCCTCCCTCACTTTGAATGAAGAAATCCTGGCTCGAGTCGTCCCCCTGGACCAGAGCTTCCAGGAGAACTATGCGGGGATCTTCCACTTCCAG
Seq A exon
GTAACTTAATAGTTGGCTCAATCATTCTCATCACGTCCTGGTTGTTGTTATTCAGTTGCTCAGTCATGTCTGACTCTTTGCAACTCCATGGACTGCAGCACACCAGGCTTCCTTGTCCTTCACTATCTCCTGAGTTTGCTCAAACTCATGTCCATTGAATCAGTGATGCCATCCAACCATCTCATTCCCTTCAATCTTTTCTGGCATCAGGGTCTTTTCCAGTGAGTCGGCTCTTTGCATCAGGTGGCCAAAGTATTGGAGCTTTAGCATCAGTCCTTCCAATGAATATTCAGTGTTGATTTGCTTTAGGATTGATTGGATTGATTTCCTTTCAGTCCAAGGGACTCTCAAAAGTCTTCTCCAATACCACAATTCGAACAGGTCCTGAGGGCCAGGATCATGTCCTGGGTACTAGGAGCAAGTGTGGAGGTTAGGAATGGATCCTGGGGGCCAGGAGCAGATGCTAGGGGCCGAGAACAATACTCTTCTACTAAGCACCCTGAGGAACATCAGGAAGCTCCCTGACCTGCGACCAACCTGGGACCCTGTGAGGACAGCAAAGGCGAGGAGGGTGGTAGGGCAGGGTTCTCAGGAAGTGGTTCCCAAGTTTTTAAAAAAGTGTGCTATTTGGGATCTGAGACAAAATGTTAAGGTAAGGCTCACTGTCCTCCTTGTATGCTGGTAAATGAGAAATAGTATTTTTTAAAGTATAAGGTGCAGGCTAGAGGGTAGGAGGGGAGGGTGTGGCCTCGGAGGGAGGGGCAAGCATGTGTCCTTGGTTTCTCAGTGAGGATGAACCTGCAGGACGAGGGCTGGAGGGAGCACCTCTTCTCAGGGTGGGCTCATGGAGCCTATGCCCAGGGCCTCCTACGGGAGGAACCAGGTGCAGCTGAGGCTCGTGGGGTGGGAAGGACCCCAGGCTGCCACCTACCACCAGCTCCCTCTCCAGGCCAGCCCTCTCTCTCCCTGCCCTGCAG
Seq C2 exon
TTCTGGCAGTACGGCGAGTGGGTGGAGGTGGTGGTGGACGACAGGCTGCCCACCAAGGACGGGGAGCTGCTCTTCGTGCACTCGGCAGAGGGCAGCGAGTTCTGGAGTGCGCTGCTGGAGAAGGCCTACGCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012778:ENSBTAT00000047532:3
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:
PF0064816=Peptidase_C2=FE(13.0=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(14.7=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:
GTGACTGCTGGCTGCTGG
R:
TAGGCCTTCTCCAGCAGCG
Band lengths:
247-1224
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development