BtaINT0031366 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012778 | CAPN2
Description
Bos taurus calpain 2, (m/II) large subunit (CAPN2), mRNA. [Source:RefSeq mRNA;Acc:NM_001103086]
Coordinates
chr16:27815292-27816884:+
Coord C1 exon
chr16:27815292-27815460
Coord A exon
chr16:27815461-27816800
Coord C2 exon
chr16:27816801-27816884
Length
1340 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGT
5' ss Score
9.11
3' ss Seq
TGATTCTCCCGCGTTTGCAGATC
3' ss Score
10.06
Exon sequences
Seq C1 exon
GATCAATGGGTGTTATGAAGCACTTTCGGGGGGCGCCACCACCGAGGGCTTCGAGGACTTCACTGGAGGCATCGCTGAGTGGTATGAGTTGAGGAAGGCCCCTCCCAACCTGTTCAGGATCATCCAGAAGGCTCTGCAGAAAGGCTCTCTCCTGGGCTGCTCCATCGAT
Seq A exon
GTAAGTCCAGGCCTCCCTCCCTAGCCACATCCCAATCTGCTCTAGTGGAAGTGAGCTTCCACGGTGACTGAAAAGTCCCACTGCCCTTACTCCCCGAACGACTAGCCCATCTTTTGTCCGCCCAGGGGTGGCTAGGCAACAGTCAGGCTGGCTGGGGGTACAACTGTTGCCCAAATGGTGACTCCAGCCTCCAGCTGTTCTCTCTCCAGCCCACATACAACCCTCAGCCTCCTGTGACTCACCACCCAGATCACAGCTTCTGTGAGAGTCCCCTGCCCTCTGCTGGGCCCAAGGGCAGCACCATCCCATTCACCTTCAGCCCACCTGCAGGGCCTATGCCCAGAGCCCAGCAGCCTCCCCCAAACTGGTGCAGGGTTAGCAGATCTGTAGGAAGACTTTAGGAGGCACAGGGAGGAACCATCTCCTCATGCAAGCCTTGCTGGCACACCTTGCCAGGGGAAGGGAGGTGGGTGCGACATCCTGTCAGCAAGGAGCCGCCAGGCTTTGGCTGTGCCCAGCAGCCCAGCCCTGTCCTAACCAGGAGGAGCTGGTTGCTCTGGGATCAGGCATAAGAAGCCTGGCTCTGGGGGGTCCAAGTCTGTGTGCGACTCTAGGCGGAGATTTGCAAACCTTCTCTGCAGACCATGTCCAGGCATAGACCCTTTCTACTAGCAGCCCTTCTCATTGACTCAGACAAAAATAACCACCTCCATCACAACAAATGGGGAATGGGATCCCTGGGGAAGCCTTTTTTTTTTTTAATTTTATTTTTAAACTTTACAAAATTGTATTAGTTTTGCCAAATATCAAAATGAATCCACCACAGGTATACATATGTTCCCCATCCTGAACCCTCCTCCCTCCTCCCTCCCCATACCATCCCTCTGGGTCGTCCCAGTGCACTAGCCCCAAGCATCCAGTATCGTGCATTGAACCTGGACTGGCCAGACTCCAATTCTGAAGTCAGGCAGAAACGGAGGACTGCCCTCGTGTAAACCCTGCAGCGGGGCGGGGCAGGGCGATCCGCGCGGTTTCCGGAGACCCAGCGCATTTGGGCCGCCCAGGTGTGTGCCCTGAGCCCCCTCTGCACGGCGTGCCCTTTTCCTGCGGGAATTTGTGACTGCGCGGGGCACACACACGAGTGCAGGTGCGGCGCCCCCCGAGGGCTGCTTGCAGCCTCTCCTCTGGTTGTAAATAACGGCGGGAGGGCTCTGGGCGGGAGTGGGGCGGCTCTCTCACCCACCACCCAGGCCCCCCGCCCTGCGGTAGGACCCGAGCGAGGGAGGGAAGGAGGGAGAATGCGGGATGTGGAGGCCGGACTGATTCTCCCGCGTTTGCAG
Seq C2 exon
ATCACCAGCGCTGCGGACTCGGAGGCCATCACGTTCCAGAAGCTGGTGAAGGGGCACGCGTACTCGGTGACCGGTGCCGAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012778:ENSBTAT00000047532:5
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(18.7=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(9.0=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:
GGGTGTTATGAAGCACTTTCGG
R:
CTCCTCGGCACCGGTCAC
Band lengths:
246-1586
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development