BtaINT0031370 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012778 | CAPN2
Description
Bos taurus calpain 2, (m/II) large subunit (CAPN2), mRNA. [Source:RefSeq mRNA;Acc:NM_001103086]
Coordinates
chr16:27820553-27822638:+
Coord C1 exon
chr16:27820553-27820713
Coord A exon
chr16:27820714-27822468
Coord C2 exon
chr16:27822469-27822638
Length
1755 bp
Sequences
Splice sites
5' ss Seq
CGAGTGAGC
5' ss Score
5.16
3' ss Seq
CCGCCCCTCTCTGTCTGCAGACA
3' ss Score
11.73
Exon sequences
Seq C1 exon
GATGTCTTTCAACGACTTCCTGAGACACTATTCCCGCCTGGAAATCTGCAACCTGACCCCTGACACACTCACCAGTGACAGCTACAAGAAGTGGAAACTCACCAAGATGGATGGGAACTGGAGGCGGGGCTCCACCGCGGGCGGCTGCAGGAACTACCCGA
Seq A exon
GTGAGCCCCCCTCAACCTTACCCTGGGGTGCTGCACCCCAGCCTGGCTGCTCCTACCACTGGGGCCCTCTGTCTCTCCTTCCTGAGTCTCCATCTCAACACCCTCTCGGTCTCCTCAGCCCCTTCCCTTCTGTACTCACCTTTCTACCTGCCTGGGCAGAACCCAAGACGTGCTGAGTCTGTGATTCCTCTCCAGGCCCTAGATTCCCTGATGCCATGACCTCACACTGAGGTAGCACTAACCCCACTTCATGCCCATGGGCTACTTTATCCACCCAAAGCCCAAGCAGCTTAGCCCAGCAGAGGTTCTCACCCAGTGGGTCTCTGCACGTCCAGGCCCTGGTTGTTGCCTGGCAACACTTTTGTGCCCAATTCACTCAGCCAATGCTGATGGGGCCCTGCTCAGAGGAGGTGGCAGTGAGGATTCCTCTAGTGGTTCATCCTTTGTTGATTCCCTTGACTCTTCTGCCTCGATGACCCAGTCCTCCCCTGCCCTCTCTACCTCAGAAACTGTCTCATCACGATGACATCTGCCGATTGTGGAAGACACATTGGGTGCTAGTCTTCACAGAAGACTTCTGGGGCAGGCACTTTATTATCATCTCCATCCTTAAGATGAGGGGACTTGGTGAAATTAAATGTCTTGCCCAAGGGCCACAGAGCCTTGACTGTGCCTAGGGTTAAGAACCCAAGCAGTCTGGCTGTGAAGTCAGCCTTTAAGCACTACAGTGGCAAGTCATGGTCATATATGGATTCTCTGTTACAGATGAAGAAACCGAGGCTCTGAGTGGCATGCTCGGGCCACAGAACAAGTAGTCAGACTGGGACTAGCTGGTGCCTGTAGCTCTGGTGCTTTTAATCCTTCACCTCATGTGTGCAGCCACCAAGCAAGTTCCAGAGGTTCTAGGAGACTGTCCTCTGCCTCAGACAAGACTATCTTCCACCCCTTATTTCAGGGGTTGGTAAACTCTCTCTTGGGGGACAGATAGTTGATACCTGGCTCTGTGGACCACCCAGTCTCTATGGTAACTATCAACTGTTGCTGTAGCCCAAAGGCAGCCATACTTAATGAATGGATGTGGCTGTGTGCTAATAAAACTTTATTTGTAAAAACAGGCATCCAGCAGCTCATAGAGCCATAGTTTGCCAAGCCCTATACTAGATGTTTGGAGAGGGCAATGGCAACCCTCTCCAGTATTCTTGTCTAGAGAATCCCATGGACAGAGGAGTCTGGCAACCTATAGTCCATGGGGTCGCAAAGAGTCAGACACGACTGAATGACTAACACATACTAGATGATGCCTTTATTTCCAGAATCCAAGTATTATCCCATCAAGGAAGGGGAGGCAATCATATTAATTATCCTTAAAATGAATGAATCTCAGCTCCTTCCAGCACCATGGGAGTGGGCAAGGGCACAGGCCCAGGAGGACGGGGACACAGAACAAGAGGCTGAGATTGTGCACTGATGTTCCTGGCCCTTAGTTCATTGAGGGGGCTGCAGAGCTAGTCCCCAAGTCTCCCTAGCCATGCCGTCCGAGCCATCTCTGACCCCCGAGTTAGAGCCTGGTGAGGGGAGGAAAAAGTAGGGGATGTCATAGCTGATCCAAAGGAGATCTGGGCCTCAGCTCTGACCACCCTGTTCCAGGGTGAGAAATGCACGCCCCCCTCCAGTCCTGGTCTCTGGTTCCTCGTCCATCTCCCCCACCCATGTGTTGTGTGTTGGGTGACTGACCCCGCCCCTCTCTGTCTGCAG
Seq C2 exon
ACACGTTCTGGATGAATCCTCAGTACCTGATCAAGCTGGAGGAAGAGGACGAGGACCAGGAGGACGGGGAGAGCGGCTGCACCTTCCTGGTGGGCCTCATCCAGAAGCACCGGCGGCGGCAGAGGAAGATGGGCGAGGACATGCACACCATTGGCTTCGGCATCTATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012778:ENSBTAT00000047532:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.036 A=NA C2=0.053
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=PD(6.3=34.5),PF0106717=Calpain_III=PU(15.4=43.6)
A:
NA
C2:
PF0106717=Calpain_III=FE(35.9=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:
ATGTCTTTCAACGACTTCCTGAGAC
R:
TAGATGCCGAAGCCAATGGTG
Band lengths:
326-2081
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development