RnoINT0028940 @ rn6
Intron Retention
Gene
ENSRNOG00000020935 | Capn1
Description
calpain 1 [Source:RGD Symbol;Acc:2267]
Coordinates
chr1:221348889-221349307:-
Coord C1 exon
chr1:221349239-221349307
Coord A exon
chr1:221348968-221349238
Coord C2 exon
chr1:221348889-221348967
Length
271 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGT
5' ss Score
8.37
3' ss Seq
ACTCTTTACCCTTCATACAGACC
3' ss Score
7.92
Exon sequences
Seq C1 exon
CGAGACGGTAATGGGAAACTGGGCCTGGTGGAGTTCAACATCCTGTGGAACCGCATCCGAAATTACCTG
Seq A exon
GTAGGTTGTCCCCTGACTGGGTTCTCCTGCCCACTGTGGCCTCAGTCGGGCATGGTATGCCCAGTCCAGTCGCAGAGCCCAGGCTTGCTGTATAGCCAGGGTTTCCCACAGAACTTCCTTTCCGCATGTGACTCCTTTCCCATCCAAGCCCACAGGTCTCTCCAAATGACCCCCTTCCTGGCCATTCCCCTCCTCCCTCACTCTGCCTAGGGGCAAGAGGCCATGATGAGGAGCTGCTGACTCACTTCCCCACTCTTTACCCTTCATACAG
Seq C2 exon
ACCATCTTCCGAAAGTTTGACCTGGACAAGTCTGGCAGCATGAGTGCTTATGAGATGAGGATGGCCATCGAGGCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020935:ENSRNOT00000028431:18
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:
PF138331=EF-hand_8=PD(29.5=78.3),PF134991=EF-hand_7=PU(4.4=17.4)
A:
NA
C2:
PF134991=EF-hand_7=FE(28.9=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:
CGAGACGGTAATGGGAAACTGG
R:
TCGATGGCCATCCTCATCTCA
Band lengths:
140-411
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]