RnoINT0028943 @ rn6
Intron Retention
Gene
ENSRNOG00000020935 | Capn1
Description
calpain 1 [Source:RGD Symbol;Acc:2267]
Coordinates
chr1:221347566-221348002:-
Coord C1 exon
chr1:221347886-221348002
Coord A exon
chr1:221347625-221347885
Coord C2 exon
chr1:221347566-221347624
Length
261 bp
Sequences
Splice sites
5' ss Seq
TCCGTGAGT
5' ss Score
8.93
3' ss Seq
TCATCTTGTCTTGAACACAGGGT
3' ss Score
5.36
Exon sequences
Seq C1 exon
GCTTCAAGCTTAACAAGAAGCTGCATGAGCTCATCATCACCCACTACTCAGAGCCCGACCTGGCCGTGGACTTTGACAACTTTGTGTGCTGCCTTGTGCGCCTGGAGACCATGTTCC
Seq A exon
GTGAGTGTCCCACTTCGCCACAGTGCACACAGTATTCCTCGAGAGACGTAGGGTGTGAATGGGGTGGAGGCTGAAGGAGGCCCGAGGACTCTTACATAGGTGCATGAAGTGTGGGCAGAGGAGAGCCTAAGGAGGCCTCTCTGGACAGGAAGCTTGGTGACTTTGAGGGACAGGGATACATGAGAGGTGGGAGGCAGTCTTGGCTGAATATCAACTGTCTGGCTGCTATATCGGATTTAACTCATCTTGTCTTGAACACAG
Seq C2 exon
GGTTTTTCAAAATTCTGGACACAGACCTGGATGGTGTTGTGACCTTTGATCTATTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020935:ENSRNOT00000028431:20
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:
PF134991=EF-hand_7=FE(43.3=100)
A:
NA
C2:
PF134991=EF-hand_7=FE(21.1=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:
GCTTAACAAGAAGCTGCATGAGC
R:
ATAGATCAAAGGTCACAACACCATCC
Band lengths:
164-425
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]