RnoINT0029150 @ rn6
Intron Retention
Gene
ENSRNOG00000018480 | Capn9
Description
calpain 9 [Source:RGD Symbol;Acc:70965]
Coordinates
chr19:57362400-57364110:+
Coord C1 exon
chr19:57362400-57362560
Coord A exon
chr19:57362561-57363952
Coord C2 exon
chr19:57363953-57364110
Length
1392 bp
Sequences
Splice sites
5' ss Seq
TGGGTGGGT
5' ss Score
3.82
3' ss Seq
TGCCCCCTTTCAAATGGCAGACA
3' ss Score
6.43
Exon sequences
Seq C1 exon
GATGGCATTTGAGGACTTCAAGACCCATTTTGACAAAGTGGAGATCTGCAACCTCACGCCTGATGCCCTGGAGGACAACACCCTCCACAAGTGGGAGGTGACCATCCACCAAGGAAGCTGGGTTCGTGGCTCCACCGCCGGCGGCTGCCGCAACTTCCTGG
Seq A exon
GTGGGTGGCTTCTCTGTCCTTCTCTCTCCTATCCCCATAGCAAATCTGTCTGGGGACATGGAAAGGGGTAGTGTGTGTGGAGCTGGACAGCAAAGTTGGGATGACCAGGGAGACAACAGCTGAGCCTTAGGCAGGACGCTGGTAGGGGAGCTCGGGAAATGCTCTGTTATGAGGTTCAGGAACATACATAAAGTGGATGACAAGTCACACCAGGCTGGCGGGAACGAGGGTCTGTTGTCCAACCGCACCTCAGAGAGGTGGGGCAGGTGTTGGAGTCTTTAAAGGCTGCGTGGGTGATGACAGAAAAGTTGGAGGAAGTATGAGGCAGGAGCTTGGAAGGTTGCTGAGGATGAAGGAAGTAGGGTGAGAGGGCTGATGGGAAAAGGGAGGGAAAAGACCACCTTTTCGGGATTAGAAGCTGTTCATGAGGTACCAGGGAGAGTGTGTCCTGAAAAGGTTGGATCTTGTAACTTTCTTCGTTGTGTCGGTGTTAGGTGTGCTGGACTCATGCATCTTACTTTTATTTTTGTCAGTTTTTTTTTCCTGCGTTCATTTGAGTATAGAGACAAAGGCAAACCTTGGCTGTCAGTCCTCAAATGTTTTTGACACAGGGTTTCTCCCTGTTCAGAAGAGCCTGCCAAGTAGGCTAGTCTGGCTGGCCAGTGACCACCAGGCTGCCTGGCTCCACATCTGAGCACTAAATGCACGCTGGGACACCTTGTGTTTCCATTTACCACGTTTATTCAGTGTGTGTGTGTGTGTGTGTGTGCGTGCATGCGTATTTGTGTTTGTGTTGGTGTGTATTACATGTGTGTGTGTGTTTGTGTGTGCAGGCTCCTGTCTTTGTGTGCATGTGTGTGCATATGTGTGTTTGTGTATGTGTGTTTGTCTGTGTGTTTATGTGTATGTGCATGTGTAGTTTGTGTATGTGTGTTCATGTGTGCACATGCATGCATATGTGCATGTGTGTGCATGCATGCATGCATGTGTGTTAGTGTGTATGTGCATGCATGTGTGTGTTTGTGTGTATGTGCATGTGTGCATGCATTCATGCGTGTGTGTGTTTGTGTGCATGTTTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGCGCGCAGGTTAGGGGACAGCTGCTGGCAGTTGGCTTTCTGCCTCTCCCTGAGAGGACCCAGGTCATCAGCCTTGACAGAAAATGCCTTTCTCTACTGAGCCTTCTTGCCGGGCTTTTTGTTTGTTTATTTTTGTTTTGTCAGTTGTGGGGTTTGGGAGTAGATTCCTGGGAATCGAACTCAGGTGCCAGTACATCAAGCACCTGGCCATCTGTGCTCTGATTTTGTATTTTTAAGGACGTGATAGTAATTCTGCCCCCTTTCAAATGGCAG
Seq C2 exon
ACACCTTCTGGACCAACCCACAGATAAAGCTGTCTCTGACAGAGAGGGATGAGGGCCAGGAGGGCTGCACTTTCCTAGCAGCCTTGATGCAGAAAGACCGCAGGAGGCTCAAGAGGTTTGGTGCCAACATGCTGACCATTGGCTATGCCATTTACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018480:ENSRNOT00000025357:9
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(6.4=34.5),PF0106717=Calpain_III=PU(16.3=43.6)
A:
NA
C2:
PF0106717=Calpain_III=FE(35.4=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:
TGGCATTTGAGGACTTCAAGACC
R:
AGCCAATGGTCAGCATGTTGG
Band lengths:
303-1695
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]