GgaINT0078831 @ galGal3
Intron Retention
Gene
ENSGALG00000009360 | CAPN2
Description
NA
Coordinates
chr3:18803738-18804604:-
Coord C1 exon
chr3:18804393-18804604
Coord A exon
chr3:18803775-18804392
Coord C2 exon
chr3:18803738-18803774
Length
618 bp
Sequences
Splice sites
5' ss Seq
AACGTACGT
5' ss Score
9.51
3' ss Seq
CAATTTCCGAATCTTTCTAGGGT
3' ss Score
6.52
Exon sequences
Seq C1 exon
TTCTCTGGCCAGACAAATATTCATCTGAGCAAAAATTTTTTCCTGACTAACAAAGCAAGAGAAAAATCCAACACCTTCATCAACCTCCGGGAGGTGCTGAACCGGTTCAAGCTCCCTGCAGGAGAATACATCATCGTGCCCTCTACCTTTGAGCCCAACTTGAATGGAGACTTCTGCCTCCGAGTCTTCTCGGAAAAAAATGCAAACTCAAC
Seq A exon
GTACGTATCTTTGTGCCACAGGTGATTTACCAGGAATGGGAGAGTTTGGTATGATTATTGTTTATTTTATAGCAATTTCTGTCTGGATAGAGGCTTTTAGTCTTTGGACTGTAGCCAGCTGGGTCCCACAGCCCAGGCTGATCCATGGAAACGAGAAAGCCACAGAAAGATGTGCTTTGCACGGGTGGTGAGCACACCGACTAGGAGAAACAGCCCACACCTCTGAAATCATGCTGGGAAAAATCCAAGACAATTGTTCAGCCAACTGCTGCCTTTACTAACACTGAGCTGGGTTTTAGTAGAGATGGCTCAAAGCACACCGTTGGCTGCAGATGTGGCATGTCCCATACAGCACATGGGCTGGGGCCTTGGGATGGGGTGGGAGATCTTTCACAGCAACTTACCTCCTTCACTGCAAGCACAAACCTTCTTCCCCTTGCGTATTTTCTATACCAATGAGAATACTGCCACGTCAGTGTGCGTGTGGTTCACCCCAGCAACCTCTCAGCTTTGAACATGTATTGTTATTACTGTAATTTAAAGAATTTGGATCTTAAAGTAATTGAATCAGAGAAGTGACTTATTTTGTTTTTAATATCAATTTCCGAATCTTTCTAG
Seq C2 exon
GGTTATAGATGATGAAATAGAGGCCAATTTTGAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009360:ENSGALT00000015241:12
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(44.9=100)
A:
NA
C2:
PF0106717=Calpain_III=PD(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTCTGGCCAGACAAATATTCA
R:
CTCTTCAAAATTGGCCTCTATTTCA
Band lengths:
248-866
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]