GgaINT0054920 @ galGal4
Intron Retention
Gene
ENSGALG00000009050 | CAPN3
Description
calpain-3 [Source:RefSeq peptide;Acc:NP_001004405]
Coordinates
chr5:24949690-24950368:+
Coord C1 exon
chr5:24949690-24949767
Coord A exon
chr5:24949768-24950207
Coord C2 exon
chr5:24950208-24950368
Length
440 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAAT
5' ss Score
3.53
3' ss Seq
CTTCCCTTCAATTCTTCCAGGAT
3' ss Score
10.64
Exon sequences
Seq C1 exon
ATCAGAAGAGTGGAACTTCATTGATGAAGAAGAGAAAACCCGCCTGCAACACAAGATTGCAGAAGATGGGGAATTCTG
Seq A exon
GTGAATTATCTGTCAAAAAAAAAACGTGCTTCTATAGGAGATATGCAACTGTAACAAAACTGGGTCACACTGTAGGACTTAAACATGCTAAAACAATGGCATTAATTCCTTCATGTTCCCCAACAAGCCTTGTTCTGCAATCCTTTCACTCTCCCACCAGGGTATATTGAGTCCCACAGCCCATCTAATTATCCCATGCTTCACAAGCTCTCCATCCCCTTTCCTATGATCTGTCCCCTCACTCCAGTGTTCCCTAGTTTGGAGCTGTACCTGTGCTAATTGACCAATAGGCTAAATGCATTGGGAAATTGGAGCTCACACTGCAAACTTGTACTAGTAGAAGCAGTAATATGGGTCACTCTCCATGACCTCTTTAGGAACAGTGTATCTTTCAGACAACTACCTACCATGCAAATTCAGCTTCCCTTCAATTCTTCCAG
Seq C2 exon
GATATCATTTGAAGATTTCATGAGGCATTTCACAAAACTTGAGATCTGTAACCTCACACCTGATACTCTGGAAGCTGATAAGCTTCAGACCTGGACTGTGTCAGTCAACGAAGGACGCTGGGTGAGAGGCTGCTCAGCTGGAGGGTGCCGCAATTATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009050:ENSGALT00000032636:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.037 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(7.6=100)
A:
NA
C2:
PF0064816=Peptidase_C2=PD(5.5=34.5),PF0106717=Calpain_III=PU(15.5=43.6)
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:
TCAGAAGAGTGGAACTTCATTGA
R:
CTGGATAATTGCGGCACCCTC
Band lengths:
238-678
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]