RnoINT0029067 @ rn6
Intron Retention
Gene
ENSRNOG00000008609 | Capn3
Description
calpain 3 [Source:RGD Symbol;Acc:2269]
Coordinates
chr3:112250990-112252443:+
Coord C1 exon
chr3:112250990-112251059
Coord A exon
chr3:112251060-112252324
Coord C2 exon
chr3:112252325-112252443
Length
1265 bp
Sequences
Splice sites
5' ss Seq
TAGGTAGGA
5' ss Score
7
3' ss Seq
TGGTCTGCGTTTACTTGCAGGGG
3' ss Score
8.38
Exon sequences
Seq C1 exon
GAAATTTGTGAGAATCCCCGATTTATCATTGGTGGAGCCAACAGGACTGACATCTGCCAAGGAGATCTAG
Seq A exon
GTAGGAAAACTCCCTCCACCATGTCCTGCCAGATTACCCAGGGCTAGTTAACCCAAGAGATCTCTATTCAGGATGTGAAGAGATAAATTCTGGATTTTCTTTTAGTGCATCTCCTAATCTTTTAAAGATTATGTATTTATTTAATTTGTATGTGTGTCTGTCTGTCTGTCTGTCTGTGTGTGTGCTTCTGTGTGCACATACCATAGCATATACCTGTGAGAGTTAGAGGACAGCTCATGGGGTCAGCTTTTTCCTTCTTCCATGTTGGATCTGGAGGTCAAACTCAGGTTGTCAGTCAGGCATCTCTCTACACTAAAGGAAGCCTTTGACAGAGGTGGCATTTGCCATGTAGGGAGAGGTCAAGGTTCTGTCAGCTTGTTGGCTTGGCTGTTCCACGTCCCTTCCTTTCCTTCCACCTTTTGTTCTGGAAGCATCCTCCTTGGGCAGACTGTAAGCTAGCTCTGTGAAGAGAAACTGGAGAGACATTAACAGACTATTTAAAACTTGACCCAAAAAGGCAGGAACAACTGAAAAATACTGCTACTTTGTTCCAGAAAGAGAGGCCGAGAACACCTCCTGCCCAGTGGCTTCCAGTACCCGAGCGGCACTGCCTGCGCAAACTAAGCCCTGAGCCCTTCAAACCAATACACTGCTTTTGAGCTGATTCAAGGGAGGGAGATGGCTGGTTTGGGTGGTTGTCAGCCTCTCTCCCCACCAACAGCGTGGCAGCTAGCCTGTGCCCCCAGTAGATAGCTGTGGGACTGTCAGGGTACCAGGTATGCCCCTTTGCCAGTTTAAATGCCCTGTGTAGAATGGTTCTGGGGCAGCTAGCTACCCAGCACCCTGCCTTCTGACACACATCTGCTTAGCTGATGGTTCTCTGATACAGTTTTCCTTGATGCCAGAAGGGAAAATGGGCTCAGCACACAAAGACTGAGGGCAGCCATAATTACCACTGCTGTCTCCACTGAGACCATAGAAGGAAGTGTTTTGTAGAAGGACGAATCAGTTGACCTTAGGAAAGCATCTAGTCCTGAGGGAATGAGTTACCCTGCTCCTCATGCTGTGGAGAAGCTCCTGTCCCCTCTGTCACTCTCCTTGCCTGGGCTCACATCTAGTTGAGGGCAGGCTGGAAGTAGGGCAGTGGGCACTAATTCATGAGCATCCCAAGTCAATAGCTATGGGGAACTTCTGGTTGGGGCTGGGCCGTCTCTTCCCAGAGAGGAAGCCTCCATCTGACTACCTTGGTCTGCGTTTACTTGCAG
Seq C2 exon
GGGACTGCTGGTTTCTTGCAGCCATTGCCTGTCTGACCCTGAATGAGCGACTGCTTTTCCGAGTTATACCTCATGATCAAAGTTTCACTGAAAACTACGCAGGGATCTTCCACTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008609:ENSRNOT00000011761:2
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(11.3=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(19.1=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:
GTGAGAATCCCCGATTTATCATTGG
R:
CTGGAAGTGGAAGATCCCTGC
Band lengths:
182-1447
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]