GgaINT0087010 @ galGal4
Intron Retention
Gene
ENSGALG00000011136 | CAPN9
Description
calpain 9 [Source:HGNC Symbol;Acc:HGNC:1486]
Coordinates
chr3:39830527-39831522:+
Coord C1 exon
chr3:39830527-39830687
Coord A exon
chr3:39830688-39831364
Coord C2 exon
chr3:39831365-39831522
Length
677 bp
Sequences
Splice sites
5' ss Seq
TAGGCAAGT
5' ss Score
1.91
3' ss Seq
GGTGTTCTTTACTTTGGCAGACA
3' ss Score
5.78
Exon sequences
Seq C1 exon
GATGAAATTTGAAGATTTCAAAGTGCATTTTGATAAGGTTGAGATCTGCAACCTGACTCCAGATTCCCTGGAAGACAACACTACCCAAAAGTGGGAGGTGACCATCCATGAGGGGAGCTGGGTCCGGGGATCCACTGCAGGAGGATGCAGAAATTTTCTAG
Seq A exon
GCAAGTAGATACTGCTTTGAAAATGCAGAATAGGCACGGAAGCCCTTCACCTCTCTCAGCCCCCCTCCTGTTACCCTAGAGCCACAACTGTGGAAATAGGACAGACCAGCTGAGTCTCAGCCAGTAGAAGCCAGCCAAAGGTACAAATACAGTCCTACTTGAGACTTGGGGTAAAAGAACTGCTTTCTTCGCTCTCAAGTTTGTTGGATCTGATTTGTCTCTTACTTACATTTGTACAAGCTGTACTAGCTCTAAATAAGTCACTTAAAATGCAGCAGTAAGTGTAAAATGAGACAAAAATCCAGCTCAGCCAGCATGTTTATGTGGCTCTGAAGTAGCATTGTGGATCTGAACTGTGTTACTCCATATTGGCACCAGTACTATGGGATCATTGTAACTATGTGAACAAAATCCCAGCTGACAGCTTTATTTAAACCACGGTAACTTAATAAAATATCAGCCCTAAAATCTTTTCTACACCTAACTCCATGAAGAGCTTTGGGATTTGGCTAATTTTCTGCAGAGTTGAGTGGAAAGAAGCACGACAACTAATGGAAAAAATAATTTAGAGCAAAACCTCAGCTTAATTGTCCTCTTTGTTTACTTTTTGTGTGTGTGTGTGTGATTGTGGTATTATTCTGAGGCGAGAAATGTTCTGGTGTTCTTTACTTTGGCAG
Seq C2 exon
ACACTTTCTGGACAAATCCACAAATCAAGCTGCATCTGACAGAGAAAGACGATGGTCAAGATGACTGCACGTTCATAGCAGCACTGATGCAAAAGGATCGCCGTAAACTCAGGAAGCTTGGTGCTGAAATGCTAAGCATCGGCTACTCCATTTATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011136:ENSGALT00000018152:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.018 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=PD(6.4=34.5),PF0106717=Calpain_III=PU(16.3=43.6)
A:
NA
C2:
PF0106717=Calpain_III=FE(35.4=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:
TCAAAGTGCATTTTGATAAGGTTGA
R:
CTCATAAATGGAGTAGCCGATGC
Band lengths:
302-979
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]