GgaINT0087004 @ galGal4
Intron Retention
Gene
ENSGALG00000011136 | CAPN9
Description
calpain 9 [Source:HGNC Symbol;Acc:HGNC:1486]
Coordinates
chr3:39821436-39822141:+
Coord C1 exon
chr3:39821436-39821554
Coord A exon
chr3:39821555-39822007
Coord C2 exon
chr3:39822008-39822141
Length
453 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
GTTCCATCCTTTCTAAATAGTTC
3' ss Score
7.5
Exon sequences
Seq C1 exon
GTGACTGCTGGCTATTAGCCGCCATAGCTTCTCTCACACTGAATGAGAAAACACTAGCAAGAGTAGTACCGCTGGATCAAAATTTTGGGCCAGGTTATGCTGGGATATTTCACTTCCAG
Seq A exon
GTAAGATGAACTTCTGGCACAGCATGACAGCATTTCTGGCCAGTTGATTGTTGCATGTTGTGGTTTGCTTTGTGGTGGGGCTATCACTTATTCCAGAGGAAACTTCACAAAAAGTGAGATTGCTGAACTCACTTTGCTGTTTGCATTTTGAGGAACAGCCTCTTACAGGCATATATGTAGCCAGTTTCTGTGAAGAAAAATATGGCTTTATAAGTCATTTTCCACCCTAACCTCGCTTAGGATATAAGGTGTTAAAGATGAATCAAGAGTTGAACTGTGTCCTTCCTTCAGACCAACCTAGCATGACACAGTGAGAATAGATGGATTATCTTTGACTTCTGAGCAAGCCTTTGATTGTCACTAACTTACGCTTAGAAGCACCGGGACACCAAATTCTTATGCTCAGGAAATGACATGCTGTCAACCAACTCATGTTCCATCCTTTCTAAATAG
Seq C2 exon
TTCTGGCAGCACAATGAGTGGCTGGATGTTGTGATTGATGATCGATTGCCCACCTTCAAAGACCGGTTGGTATTCGTACATTCAGCAGAACACAATGAATTTTGGAGTGCTTTACTAGAGAAAGCCTATGCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011136:ENSGALT00000018152:3
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:
PF0064816=Peptidase_C2=FE(13.2=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(14.9=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:
TAGCCGCCATAGCTTCTCTCA
R:
TTGGCATAGGCTTTCTCTAGTAAAGC
Band lengths:
238-691
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]