RnoINT0028942 @ rn6
Intron Retention
Gene
ENSRNOG00000020935 | Capn1
Description
calpain 1 [Source:RGD Symbol;Acc:2267]
Coordinates
chr1:221369119-221369600:-
Coord C1 exon
chr1:221369333-221369600
Coord A exon
chr1:221369189-221369332
Coord C2 exon
chr1:221369119-221369188
Length
144 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGA
5' ss Score
10.65
3' ss Seq
CAGGATTGTGGGTCTTGTAGGAA
3' ss Score
4.99
Exon sequences
Seq C1 exon
GATGGCAGAGGAGTTAATCACACCTGTGTACTGCACCGGGGTGTCAGCCCAAGTGCAGAAGCAACGGGACAAGGAGTTGGGCTTGGGCCGCCATGAAAATGCCATCAAGTACCTGGGCCAGGATTATGAAAATCTTCGTGCAAGATGCCTGCAGAACGGGGTCCTCTTCCAAGACGATGCCTTCCCTCCAGTTTCTCATAGCTTGGGCTTCAAGGAACTGGGTCCCAATTCCTCTAAAACCTATGGCATCAAGTGGAAGCGTCCTACG
Seq A exon
GTAAGAGGGCAGCTCTGGCTGGAACTTGGCTCTGATGATGGGTGGGCAACGGGAGAAGGAGAGGTGGGGCCCCCATTATTAGTGGTGTCTGGGTGCCAGTTTCTAGAAGGGACTGGCCCAGGAACAGGATTGTGGGTCTTGTAG
Seq C2 exon
GAACTGCTGTCAAACCCCCAGTTCATCGTGGATGGAGCCACCCGAACGGACATCTGCCAGGGAGCACTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020935:ENSRNOT00000028431:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.022 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=PU(11.3=38.2)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(23.2=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:
AAGCAACGGGACAAGGAGTTG
R:
GCTCCATCCACGATGAACTGG
Band lengths:
248-392
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]