RnoINT0029075 @ rn6
Intron Retention
Gene
ENSRNOG00000008609 | Capn3
Description
calpain 3 [Source:RGD Symbol;Acc:2269]
Coordinates
chr3:112258038-112259909:+
Coord C1 exon
chr3:112258038-112258181
Coord A exon
chr3:112258182-112259825
Coord C2 exon
chr3:112259826-112259909
Length
1644 bp
Sequences
Splice sites
5' ss Seq
CGGGTGTGT
5' ss Score
5.31
3' ss Seq
GTCTGGTTATTACTCTACAGACA
3' ss Score
5.79
Exon sequences
Seq C1 exon
GATGGCACCAACATGACTTATGGAACCTCTCCTTCTGGTCTGAACATGGGGGAATTGATTGCGCGGATGGTGAGAAATATGGATAACTCGCTGCTCAGAGACTCAGACCTGGACCCCAGGGCCTCAGATGACAGACCGTCACGG
Seq A exon
GTGTGTACATCTCCAAATGTCAAGACTGACTGGCACCCCCAGATCTACATAGCCCATCCTTCTGAAGTCCACTCCCCAGAGAGTCATTGTCAACAGAACAGGTTCCCTCCCTTTTGGTAACTCTCCTATAAAGGTCACAGGGCCCCTACCCTCTATAGTATTTGGGTCCTCCTGCTTGGAAGGCACATGTACTTACTGAAGGACTGAGACATACAGAAAATCACAGAGGGAAATTTAGTCTGTACTTTCCCATCCAAAGATAACTGTCCAGCATTTGGTATATGGTCCTTCTAGGCACATGCTTAATCTTTATTTTTGTTTTTAAAATTGTATCTTAGTTTATGTTACAACTTTGCAACCTGCTTTTTTTTTGTTCTTGTTGAGGTTCATATTTTTAAAATGCAACTAAGTATTCTTATATCATTTTAGCAATATTGTAATGTGCAATATATTGTAATTTACTTACTAACACTCTGTTATTGAAAAGTTAGAGGGCTTTTTTTTTTTCTTTTTCTTTTTTTTGGAGCTGGGGACTGAACCCAGGGCCTTGCGCTTCCTAGGCAAGCGCTCTACCACTGAGCTAAATCCCCAACCCCTAGAGGGCTTTTTTTTTTTTTCTTTTTCTTTTTTTTCGGAGCTGGGGACTGAACCCAGGGCCTTGCGTTTACTAGGCAAGCGCTCTACCACTGAGCTAGATCCCCAACCCCTAGAGGGCTTTTTTTAATCTGTTTTTCAAAAGTACTATAATAAGCATAAAGACAGTATTCACCCACAATGGCTTCCATAGGACAGAGTCTCAAGAGTAAAACTGTTGGGTCAAAATGATAGGCTGTGTAGATCCAGAAGCCAGCCCAGGCAGCCTCAGGTGAGCAGACCAGTGAGTGCCCTGCCCTAATCTGGGTCAAATGAATGAAATATAAGAGACTAAAATGAAAAAAGTTCCAAACTCGCCTACACCTGACACCCTGAAGACGGCTTCAGGAATTCACACCCATGTAGCCCCCAAAAGCTACCCCAAAGCTGTTGTTACTAGGCCAGCTGATGCTGAGATGCCTGTCAAGGGCTCAGAAGGCCTTGGTAATCTACCCTTGTGCTAAAGAACCCTCAAGAACTAGAACTTGAACATTTCTGCCCCTGGGCATAGTCATGTCACAGCAGGGAGCCACCCAGTATTCCCAGCACTGGGAGCAGGGACAGAGTTTTCTTGACTTTCATGTTCTAGGTAAGTGTGAGGGAGGTGAGGTAATGTCAAGAGAACTCCCTCTCTTAAGTCTTTCTTTGGGGAATAGTCAACTCTAGATGGGCTCGGAGGAAGGCACAGATCCTAAATGTCCCCTCTCCTCTGCTGAGGATGTTAGAAGAGAGGGGCAAATTCTTTTACTCACATCCTACTCCAGAACTCACCTTGCTTTATGGCCATCAGGGCAGTAAGGTCAGCTAGGAAGACTAAGGCAGCATCTTCCTGTTGCTTTTGAAAAACTATCGAGGGTCTAGTCCCAGCCATAAGGCATAGGGTCAAGGAAACAAGTCATTCTTAGTCTGAGATAGTTCAGAAATGGACCAGTATGAACCCTTGTCTTCAATGAGCTGAACTTCTGCCCTTTCCCCCAACTCCTGACAGGCTGTCTGGTTATTACTCTACAG
Seq C2 exon
ACAATTGTTCCGGTGCAGTATGAAACAAGAATGGCCTGTGGACTGGTGAAAGGGCACGCCTATTCAGTCACTGGGCTGGAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008609:ENSRNOT00000011761:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.312 A=NA C2=0.027
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=PD(4.4=18.8),PF0064816=Peptidase_C2=PU(30.4=93.8)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(18.2=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:
TGGCACCAACATGACTTATGGA
R:
CCTCCAGCCCAGTGACTGAAT
Band lengths:
224-1868
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]