GgaINT0087011 @ galGal3
Intron Retention
Gene
ENSGALG00000011136 | CAPN9
Description
NA
Coordinates
chr3:42378779-42379817:+
Coord C1 exon
chr3:42378779-42378936
Coord A exon
chr3:42378937-42379608
Coord C2 exon
chr3:42379609-42379817
Length
672 bp
Sequences
Splice sites
5' ss Seq
GAGGTGCTC
5' ss Score
2.13
3' ss Seq
CTGCCTTGAATCCCCCGTAGAGC
3' ss Score
7.42
Exon sequences
Seq C1 exon
ACACTTTCTGGACAAATCCACAAATCAAGCTGCATCTGACAGAGAAAGACGATGGTCAAGATGACTGCACGTTCATAGCAGCACTGATGCAAAAGGATCGCCGTAAACTCAGGAAGCTTGGTGCTGAAATGCTAAGCATCGGCTACTCCATTTATGAG
Seq A exon
GTGCTCTATTGCTTTTACAGTGCAGCAGCCACACCATCAATATTAGGATCTTTCTCCGGATTTGTAATCCTGCCAGTCATCAGATATTTTTAGGGCCCTTTCTCCTAAAATACTCCTCTTGGTTACATCAAACCCCATGGAGAATTTTGACTTGGTTAGGATGGAGTCCTTTCAAAGGAGGATTTAGGAGTCCCATGGGTATCCAGAGTAAACTCCTCAGCCCTGTGACTGTGTCATCCCCCTGCCTGGCTCCAGGAGAGGGGATGTTGCTTCATGTGAGCCTCTTGGGGCTCATTGTGCACAGTGGCTCCTGTTCTTGTGTTAAGTTTGGATTAGAAAATCTTTTGAGGCATGTTCTCTATCCAGAAGAGGACTGTGAAGACTCGTTGCTCTGTGACACCTCACTTGGGATTGTGATACTTACTAACAGGGAATGCTTATGCAGGAAGGTAGTGTCCTAGTGTCCCCTTAAACTTTCTTATGGGTGGGAGAGAAGCATTAGTAACAGGTCCTTGCCAAAAAGCATGAGCTAGGTTCTATGAGTGCTTGGGCAAGGGGGTGACAGTCAGGGTTGAGTTTTGTCAGGCAGAGTTTTGTGCATGACTGGGAAGAGGGTGGGGGTAGCCTTCAGTATACCACAGCCAATGCAGTGCTGCCTTGAATCCCCCGTAG
Seq C2 exon
AGCCCTGGTGGAGATGAACACTTGAGCAAAGACTTCTTCAGGTACCACGCCTCCAAGGCCAGGAGCAAAACCTACATCAATTTAAGGGAAGTGTCTGACAGATTCAAGCTGCCACCAGGTGACTACATCCTCATTCCAACCACATTTGAGCCACATCAGGAGGCAGATTTCTGCCTGAGAATCTTTTCAGAGAAGAAGGCCATCACTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011136:ENSGALT00000018152:10
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:
PF0106717=Calpain_III=FE(35.4=100)
A:
NA
C2:
PF0106717=Calpain_III=FE(46.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCAAGCTGCATCTGACAGAGA
R:
TCAGTGATGGCCTTCTTCTCTGA
Band lengths:
343-1015
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]