BtaINT0031372 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008868 | CAPN3
Description
Bos taurus calpain 3, (p94) (CAPN3), mRNA. [Source:RefSeq mRNA;Acc:NM_174260]
Coordinates
chr10:37872761-37874460:+
Coord C1 exon
chr10:37872761-37872921
Coord A exon
chr10:37872922-37874290
Coord C2 exon
chr10:37874291-37874460
Length
1369 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
TTCCTTTTGGGGGGGCACAGACA
3' ss Score
1.73
Exon sequences
Seq C1 exon
GATGTCCTACGATGATTTTATCTACCATTTCACAAAGCTGGAGATCTGCAACCTCACAGCTGATGCCCTGGAGTCCGACAAGCTTCAGACTTGGACAGTGTCCGTGAATGAGGGCCGCTGGGTGAGGGGCTGCTCTGCCGGAGGCTGCCGCAACTTCCCAG
Seq A exon
GTGAGAGATGCTCTGGATGGGGAAAGGGTCCAAGCAGAACAAGTTCCAGGCAGAATAATATTAACTAGCATCTGCTGAGTCTTTACTAACTTCCAGACATGCAATGTCTTATTAAACTGTCCCCATTTTACTGAGAGGTGACTTCCCTGGTGGCTCTATGGTAAAGAATCTGCCTGCCAGTGCAGGAGTTGCAGGTTTGATCCCTGGGTCAGGAAGATCCCCTTGAGAAGGAAATGGCAACCCACTCCAGTATTCTTACTTGGGAAAATTCTATGGACAGAGGAGACTGGTGGGCTATAGTCCGTGACGTCACAAAGAGACACAACAGTGACCAAACAACAATAACAACATTACTGAGAAGGAAATCTCCATTCTGAGTAGCTTACATTAAGGAGCTGGTAACAACTTTTAGGCAGGTTATTATGTCAGAACAGGACTGTGTTCATTATGCTGAGGATTGAACTGGAGAACTGAGTTAGCAGCAGCTACAAGAGTTTAAGCCAGAGATGATGAAAGCGAAGACCAAGTCAGGAGCAGCAGAGATGGGGAGAAGGGGCAGGTTGAGGGAAGGAAATATTGGTTGATCTGGAGAAGGAAGAATGACTTCAAAATTCTCTCATTGGGAGCCTGAGTAGATGATGTCAATGACATAACATGAAATGCACAGGAGAAAAAAAAAAGAAGGTTTTTTGTTTTTGACAGAGTTGGTTGTGGGCTTCTGCAGAGGAGTTTACTTTGGGACATGGGAAGTCTGAGGCATGTGTAGAATATCCAGGTGAAGATGCATGAAAGAGAACTCGATGCACAGATAAAAATGGCACTTGGCTCTATGACAGGGACTCAGTATGTATTTGTGGAAGGAAAGAAGGATGGAAAGACGAGAGGAAGGAAAGGAGGGAAGGAAGAAAGAAGGGATGACGGGAAGGAGTCAAAAGAGAGATTGAAGCTGGGATCTACAGCTTAGGAGTCAAGAGCATGTAGGGAGCAGTTAGAAAGTAGGAGTGGATAAGACAGCCTAGGGACGTGAGAGAAGAGGCCCAGGACCAAATCCCAGAGACTAGTAACACTGAAGGAGTAGGTGAGAAAAGTGAAGCCATCAGCAAAGACAGAGAATGAAAATTCACAGAGGAAGGAGGAGCCACATAGCCAATCAGTGCAGGTCCATCTGTATAAAGGTAAAAAGGCTACCCGCCCCCACCAACACACACACCAAATTAAATAAATGCCTGGATATTTTTTATTTTTCATACATATTTGAGCATGTAGATGAGGAGGCTAGAGATGAATAGGTTCCCTCCGTCTCATCTCCTGTCCTTTCCTTTCTCTGAGAGGCAGATCTGAAAGTGCAATTCCTTTTGGGGGGGCACAG
Seq C2 exon
ACACTTTCTGGACCAACCCACAGTACCGTCTGAAGCTCCTAGAGGAGGACGACGACCCCGATGATTCCGAGGTGATCTGTAGTTTCCTGGTGGCTCTGATGCAGAAGAACCGGAGGAAGGACCGGAAGCTGGGGGCTAACCTCTTCACCATCGGTTTCGCCATCTACGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008868:ENSBTAT00000011677:10
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=PD(12.8=34.5),PF0106717=Calpain_III=PU(15.5=43.6)
A:
NA
C2:
PF0106717=Calpain_III=FE(36.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTCCTACGATGATTTTATCTACCA
R:
CGTAGATGGCGAAACCGATGG
Band lengths:
327-1696
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development