RnoINT0028945 @ rn6
Intron Retention
Gene
ENSRNOG00000020935 | Capn1
Description
calpain 1 [Source:RGD Symbol;Acc:2267]
Coordinates
chr1:221368713-221369188:-
Coord C1 exon
chr1:221369119-221369188
Coord A exon
chr1:221368832-221369118
Coord C2 exon
chr1:221368713-221368831
Length
287 bp
Sequences
Splice sites
5' ss Seq
TGGGTAGGC
5' ss Score
6.03
3' ss Seq
AAGTGTCTTTCCTATCCCAGGGG
3' ss Score
7.14
Exon sequences
Seq C1 exon
GAACTGCTGTCAAACCCCCAGTTCATCGTGGATGGAGCCACCCGAACGGACATCTGCCAGGGAGCACTGG
Seq A exon
GTAGGCCCCCAGGGGTGGGGTTCTGGGTGTTTTCCTCATTGTCGTCCCCGTTCCCGTTCCATTGGGCACTGCCCCAACTCCGCCCTCCTGCAGGTCCAGACAGGCTTTGGCTATCAGCATAGGTGCTGGTTCGCCCAGATTCCTGGGTCTTTTCTGTAAGCGGAGGGGAGATGAAGGGTCCCCCACTCAGGGAATCCCAGGTGGTTCCCAGTATTCCGCATACACAGAACCTCCCTCCCTTGGGCAGATCTGAAGAGCAAGCCTAACAAGTGTCTTTCCTATCCCAG
Seq C2 exon
GGGACTGTTGGCTCCTGGCTGCCATTGCCTCGCTCACTCTCAACGAGACTATCCTCCACCGAGTGGTTCCCTACGGCCAGAGCTTCCAGGAGGGCTATGCTGGCATCTTTCATTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020935:ENSRNOT00000028431:3
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(23.2=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(13.0=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:
GAACTGCTGTCAAACCCCCAG
R:
CTGGAAATGAAAGATGCCAGCA
Band lengths:
189-476
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]