RnoINT0029146 @ rn6
Intron Retention
Gene
ENSRNOG00000018480 | Capn9
Description
calpain 9 [Source:RGD Symbol;Acc:70965]
Coordinates
chr19:57356017-57357386:+
Coord C1 exon
chr19:57356017-57356185
Coord A exon
chr19:57356186-57357302
Coord C2 exon
chr19:57357303-57357386
Length
1117 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGG
5' ss Score
6.35
3' ss Seq
CTGGTCTTCCTCTGTTCTAGACC
3' ss Score
10.59
Exon sequences
Seq C1 exon
GCTGAACGGGAGTTACGAGGCACTGAAGGGGGGCAGCGCCATCGAAGCCATGGAGGACTTCACCGGGGGTGTGGCTGAGAACTTCCAAATCCGAGAGGCACCAGAGGATTTCTACGAGATTCTGGAGAAGGCCCTGCGGCGTGGTTCCTTGCTGGGCTGCTCCATAGAT
Seq A exon
GTAAGGGGTTGGCCGGCCCTGTGTAAACACCAACAGACAGAAATAGCAACCCAGAGGGGACATGAGTATCTGGAAGGGGGTCATCTTTAATTAAAACACACGTTGGTGGAACGCTTACCTAGCACACAGGCAGCCCTCGGGTCCAGCCCCAGCACTGTGTAAACCAGGCTAGTGAAATATACCTGTTATTGCCAGCACTCAAGAGACAGTGGCTGGAGAGCCCTAACCTCAAAGTCGTCTTCCATTACATGCCAGAACGAGCTGACACGACATGACACGAGACTGTCTCTAACGGACAAGCAAACACAAACTCGTATTAACACTTGTTGGGTGGCAATGGGCAAATACACCTGCTGCCAGGTGGAACTCCGCATGGTGCCTGGAGGCAGAGTTGTCTGTCTCTCCTGTCATGCTCGGGGCTGCTTCCCCAGTACCACACCAGCCAGGGCCCTGGCCGCCCTCAGAACCACTGCTGTTGGGCAGGATTTACCCACTGAAGGGAATCCACAGCTCTTCTGAAACATGTTCCTTTTATTTCTACACTGTGAAAAATCCACTGGAAAGAAAGCTAAGGGGGGTTTTCTAATTCCCCTATGCATAGAAATACACATAGAGATAAAATTTCATACCCTCTGTTTTTGAAATCTAATCAAGTTTCCCCTTTCTTCTTGGATTAACTGCAAAGATCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAATCATTCACTTTTCCTATAGGTTCACATTCATGAGCAAATCACATGTCACCAAGGAAGGCCTCTCCCCGTGTGACTGTGGGTGTCAGTCACTAAACTATCACTCGGGTGGCTGGTTTCTGTTTGGGGTCAGAAAGGTAGACTCATTGCAGTTGTGGGAGTCCCCCACTCTGGAAAGAGATTAGCTTTGCTGTGCGTCATTGATTAGCCTATTAGCGAGTCCTGTCCTCCCAGTTTCTAAGGCCTACATACATGGCTGCCCTTGAGGAGCTGAGGGCTGGGATGTGCTGAGGTAGGCGTGGGATGAGGCTGGGCCTGACACAGGGGAAAGCTGGCATAGATGACGGACCTAACTCTGGTCTTCCTCTGTTCTAG
Seq C2 exon
ACCCTGAATGCCTCAGAATCTGAAGCCCGCACACCTTTGGGCCTCATTAAGGGCCATGCCTACACTGTGACTGGACTCGACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018480:ENSRNOT00000025357:5
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(18.9=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(9.1=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:
GGGAGTTACGAGGCACTGAAG
R:
CTGGTCGAGTCCAGTCACAGT
Band lengths:
246-1363
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]