RnoINT0029055 @ rn6
Intron Retention
Gene
ENSRNOG00000034015 | Capn2
Description
calpain 2 [Source:RGD Symbol;Acc:2268]
Coordinates
chr13:100896139-100898451:-
Coord C1 exon
chr13:100898291-100898451
Coord A exon
chr13:100896309-100898290
Coord C2 exon
chr13:100896139-100896308
Length
1982 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
CCTCTGACCTTGTTCCACAGATA
3' ss Score
10.31
Exon sequences
Seq C1 exon
GATGTCCTTCAGTGACTTCCTGAGGCACTACTCTCGTCTAGAAATCTGCAACCTGACCCCGGACACCCTCACCTGTGACTCCTACAAGAAGTGGAAACTCACCAAGATGGATGGGAACTGGAGGCGAGGCTCCACTGCAGGGGGCTGCAGGAATTACCCAA
Seq A exon
GTAAGTGTTATGACCATGAGTGGTTGCAGTCCCATGGCCTCCTACCTGGAGAGAGACGCCACATCAGCCTGAAAGCCTGGGGGAGTTGGCTCCCACTCACCCAGGCCCTCGTTCTCTTCCCTCACCACCAGCCTTTGTCTCAGCATCTATTTTTCCATTTTCTCAGCCTTACTACTTCCTGCATTCGTTTGCTCTGGTACCCTTTGGACCCCACATCCACTGATGGCCTTCATCCAGTTTATGGAGGCAGTGCTAAGCCCCAGTTCATAACGAGCCACCCCAGGCCCTCATGCACTGCATCCTGGGACACACGAGCCTCTCGCTGTAGTCTGTCACCCTCTTGTGTGTCAAGTTTACTTATAAAATGTTTATAGCTGGGTGTTGGTAGCTGCGTGCCTTTAATCCCAACACTCAGGAGGCAGAGACAGGCAGATCTGAGAGCTGAAAGCCATTGTGCTGTACAGAGTGAGTTCTAGGACAGTCTACACAGAGAAATGCTATCTCAAAAAGACAGACAGACAGGAAGGAAGGAAGCAAGCGAGCAGGAGAGTGCTTCTCCTCTGTTCTGCTCTGTTGATTCCTTTGCTGATCTCTTCTGTTTTGATGGCTCAGTCCTCTCCTACTCTGTCCCATAGACACTGTCTGATCTCCATGACACTGCCAGTGATAGGGTGGGGTGTACAGAGAGTACTGGGAACTGTTCCAATGAGCTTCATCTGTGTATTAATCTTCTCGATGAACTCAACTATTTTCATTTCCAACTTGAGGATGATGGGACATGGGAAGTGGCTGGCCCAAGGTCACAGAGCTTTCTGGGGTTAGAACCCAGGCAGTACGGCTATGAAGTCACTCTTACTCTGGTGGCAGATCATGGCCATATTTTGATTCTCTGTTGCGGATGAGGAAACAGAGGCTGTAGGTCGTACACCAGGCCAACAGAGCAAGCAGACTAGCCGGCCAGCCCCTCCAGTCCCAGCATGCAGTTCCAAGTGCAGCTCTAGAGGCTTTAGCACCCACAAAAACACCCTGTACCCCTTAGGTGGGGAGTCTGCAGACACTCTCTCAAGGACCTCCGAGCGAATGCTCTTGCCCTTGGGGACGTCCTAACTCAACAGTACTTACTCAGTGACACTGAGGTAGCCTAGAGCTTCGTACACAAATGAGTATGTGCCAGTACAACTGAGATTAAAGAAGCAGTTGTGTCATGGCTGCCAACACTGCGAGACCATGCTTCCAATTCAACCCCAGAGGCCATTGTGTGAAGGATGGGAGGCACTCAGACAGGAGGGACTCAGTATCTGGCTGCATATGGGGTTTGGAAGTGTGGGTTGCAGAGGCACCATAAGATGTTTTCTGGCCTCTGCATTTGCAAAGGAATGGCAGGGCGAGGGGGAAGACAGGCACAGTGTGCAAAGATGTCCTTAGGGAGCACCAAGGCAAGCCAGCCTAAGGGCAAAAAAGTACCATTCCTGCTTTAGGTCCTCCTGAGGTGCACACTGTGCCAGGAGCCCAGTGGTCCTCCATTTGCTATGATGTGGGTGATAAGCCTTTGTGAAGACTTTGTAAGGGGACCAAGAATGTAACTCTGATGGGAGTGAATCCCTGGTTCAGTTTCTAGTACTTGCCATGCCTGCACTGAGCAGGTAGAGAGTCAGGAGGACCAGAAATTTGAGCTCATCCTCAGACACATAAGCAAGTTTGAGGCCAGCTTGAGCTGTAAGAACCCTTGTGCCAGAGGAGAGAACCCAAGGAAGCTGTCTCCTCACAGTAGCTGCAGGCAGATTTGACTCCGAAGCCCGTCTCTGTCAGTAGCCACTCCATCTAAGAGGTTGCCGTTGGCCTCTTCTGTGCTTCCTCTTTTCCCACCAGCTCCTTTTTTCTCATCCTTGACCCACCACCTCCAGCCACAAGGCCAGACCCACCGTGGTTCTCAGATCCTGGAAATTTATTCAGGGCTGGGTTCCTCTGACCTTGTTCCACAG
Seq C2 exon
ATACCTTCTGGATGAACCCTCAGTACCTAATCAAGCTGGAGGAAGAAGATGAAGATGATGAGGATGGGGAGAGGGGCTGTACCTTCCTGGTGGGCCTCATCCAGAAGCATCGGCGGCGGCAGAGGAAGATGGGTGAGGACATGCACACCATTGGCTTCGGCATCTATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000034015:ENSRNOT00000045326:9
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=0.035
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=PD(6.3=34.5),PF0106717=Calpain_III=PU(15.4=43.6)
A:
NA
C2:
PF0106717=Calpain_III=FE(35.9=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:
TCCTTCAGTGACTTCCTGAGGC
R:
TCATAGATGCCGAAGCCAATGG
Band lengths:
326-2308
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]