GgaINT0087006 @ galGal4
Intron Retention
Gene
ENSGALG00000011136 | CAPN9
Description
calpain 9 [Source:HGNC Symbol;Acc:HGNC:1486]
Coordinates
chr3:39822724-39824131:+
Coord C1 exon
chr3:39822724-39822892
Coord A exon
chr3:39822893-39824047
Coord C2 exon
chr3:39824048-39824131
Length
1155 bp
Sequences
Splice sites
5' ss Seq
GATGTGAGT
5' ss Score
7.77
3' ss Seq
CATTGTTTTCCATATTTCAGACC
3' ss Score
8.56
Exon sequences
Seq C1 exon
GCTGAATGGCAGCTATGAGGCTCTGAAAGGAGGCAGTACAATAGAAGCCATGGAGGATTTCACTGGGGGAGTGGGAGAAATGTATGAGGTTAAAAAAGCTCCTGACAATTTCTATGAAATCCTAGAGAAAGCTCTGAAAAGATCGTCAATGGTGGGCTGCTCTATCGAT
Seq A exon
GTGAGTAAGAAATGGGTTCTGATTTTCTCAGCTTAGTTTTATGGTTTCTGCATTTAAAAATATGCACTGGATATGCACTGGACTCTGCAAATAATAGCTATGAAATGATAGATATGTAATATTAATATAATCCCTAGTTTAAAAGTTGTTTAAAAGAAAAGAAGATTCAGCACATTTTATCAGGTGATAGCCACGGTATTTAAGGCAGTAATGACATAAGAATGAGCACCTGGGGAAAGTGAACTTTATTTCCTGACTTACATGGCCATTAAAACTAGCCATAGCTTTGTGAGGACTTAAAGGCTCCAGAGACTAAAAATTGGTTTTCTTCATCCCTAGATTCTGTAACATATGTTGTGTCTTGGGGAACTCAAGTCACTTTTCAGAATCAGTGTGTTAGTTTGTAAACAGTGACCGGGCTTTTGGGTGTGTCAGATTTATCTCTCCGGATACTGGAATCTTCCCCTTTCCCCAAGAAAAGGTTTCAGGCACGTAGCAGATGTGTGAGTGGCCATACAGTGCTTCGACAGCATGTCTGACATGGAGGAGCCACCCATGTGTCCTTGGCTTTCTGGTGTAAAAAGCCCAAGCTGCTCAGCACCGAGAATGAAAGCCCCATTGCTGTTCCCTGTCCACTGTGCCCAATGGGAATGGCAATTCAGAAATAAAGGTGTGCCAGGTTTCTTCACCAGAATGAGCAACTGGAGAGGAAGGTTTCGGGGCAAATGAAAAATCCCATCAGGCACAAAATGAGACTGTATCAACACCAACCCAAGAGCACCTTTCCTTATCCCTTAACTTACTCAAACTACATTTTAGTGTACATTTTAGTGGTAGTTTATATCAATTTCCAGGAGCTGTGGGTGATGTTGATACAAAATCTCAGGCACATAGAAGCGATCTGAGCTGGGAACTACCTTGTTTTCCTTCAGAGTGCACAACGCCCCAAAAAAGAAAACCACACAGCTCTAAGGAGTTCCCTTTCAGAGGGCACCGTTGCACCATCGCTGCTTGCATAGAGCAGAAAGACAAACTCCCTGTTTACAATGCTGTTTAGCCACTGGTCTCCCATCTGATGCTTGGAAGAGACCAAGTGGCACCACTTGCAGTCTCATCACGAAAAGAGATATATTCACATTGTTTTCCATATTTCAG
Seq C2 exon
ACCAGCAGTGCTGCAGAGTCAGAAGCCAGGACACCCTTTGGCCTCATAAAAGGCCATGCTTACTCTGTAACCGGCATTGATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011136:ENSGALT00000018152:5
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(18.9=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(9.1=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:
ATGGCAGCTATGAGGCTCTGA
R:
TCATCAATGCCGGTTACAGAGT
Band lengths:
247-1402
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]