RnoINT0029074 @ rn6
Intron Retention
Gene
ENSRNOG00000008609 | Capn3
Description
calpain 3 [Source:RGD Symbol;Acc:2269]
Coordinates
chr3:112256724-112258181:+
Coord C1 exon
chr3:112256724-112256892
Coord A exon
chr3:112256893-112258037
Coord C2 exon
chr3:112258038-112258181
Length
1145 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGT
5' ss Score
9.11
3' ss Seq
TCTTGCCTATCGGGGCTCAGGAT
3' ss Score
5.63
Exon sequences
Seq C1 exon
GCTCCATGGTTCCTATGAAGCTCTGAAAGGTGGGAACACCACAGAAGCCATGGAGGACTTCACAGGAGGGGTGACAGAGTTTTTTGAGATCAAGGATGCTCCGAGTGACATGTACAAGATCATGAGGAAAGCTATCGAGAGAGGCTCCCTCATGGGCTGCTCCATTGAT
Seq A exon
GTAAGTGTATTCCAGGGAAGCCTTTCACTCAGCTAACAACACACAGATTCCTTCTGAGATAGGTGGATGCTTGAAAACAAGAGCCATATGGATGAGATGGTTCACTGGTAAGGACACTTGCTGCTAAACCTGAGGACCTAAGTTTGATCCTTGGAATCCACATGGTAGAAAGACAATGGACTCCCAAAACTTGTTATCTGACTTCTGCATGCACTTCCTCCCGACACTACCGCAAACAAAGTCGTCACCCTCCAGAAAGTCACACAGCATTACTAAGCACATCCCCAAAAAGTGTACAATATGCACACTTGGAAAATACAAAATTAAAAAAAATGTAAGCAACAACTGAGCTTCACATTTATAAGAATGTGAAAAGAAGCCCCATTTTTAGCACTGAACAACTTATTTTTTTAAAGAAACTACCAGTAATTCCAGCAATTTAAAAGCTGAAGCCAACCTGGTTTGCATAGTGAGATCCTGCTTTTAAAAACAAAGAACATGGATGATTGTTGACTTTAAAATGGACAGTTTTTCAGTGGAAATGTATTCCTAAGAATGGGGTGCTTCCTAAGAAAAAGGCTGAGCGATGAAATGTCAAACCCTAGAATTCTGGTAGAAATAGGTCTCTTTTGTCCAGACTGCTCAGCACAAGCCCTGCAAGACAACCGCATCTCGGGCTATGAACCTTGGGGGCTGTGGACCCTGACCCTTAGAAAGCTCCCTGGTTGCTGAACTTTGACATCACCTCAGTCCTTAGGCTCTGTGCTGCTGTCAGGATGATCACTTTGACCCTCTCTCAGGGGATCAAAATCATATGAACTGAGACAGGAGCACAGAGAGGACCCACAATGGCCTGATTTCAAGAGCTACTTTGGGACTAGTAGTCTGGGATGGGGCAAGCCACCTCCTGCCTCTTTCTCTCCCAGTACTCCCTCTGGGTAGGGAGGCTTGGTTGTCACCACATGGGAACTCTCCTGTCCTACCACTGTCTTGCATCTTTTCTGCATTTGCTCCCTGTTGATGTCTCTCTCCTCTTTTGTTTTGCATGTCGTTCCTCCTTTCTGTCCCCTTCCCTTCCCACCCTCCCTTTTTTTGCTCTCTTTTTCTTTCCTGGGTTCTCTACTTTCTTGCCTATCGGGGCTCAG
Seq C2 exon
GATGGCACCAACATGACTTATGGAACCTCTCCTTCTGGTCTGAACATGGGGGAATTGATTGCGCGGATGGTGAGAAATATGGATAACTCGCTGCTCAGAGACTCAGACCTGGACCCCAGGGCCTCAGATGACAGACCGTCACGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008609:ENSRNOT00000011761:5
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=0.312
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(27.5=100)
A:
NA
C2:
PF0064816=Peptidase_C2=PD(4.4=18.8),PF0064816=Peptidase_C2=PU(30.4=93.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTCCATGGTTCCTATGAAGCT
R:
GGTCTGTCATCTGAGGCCCT
Band lengths:
306-1451
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]