GgaINT0054921 @ galGal4
Intron Retention
Gene
ENSGALG00000009050 | CAPN3
Description
calpain-3 [Source:RefSeq peptide;Acc:NP_001004405]
Coordinates
chr5:24950208-24951099:+
Coord C1 exon
chr5:24950208-24950368
Coord A exon
chr5:24950369-24950929
Coord C2 exon
chr5:24950930-24951099
Length
561 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
TTGTTGGTGGCATTTCACAGATA
3' ss Score
5.71
Exon sequences
Seq C1 exon
GATATCATTTGAAGATTTCATGAGGCATTTCACAAAACTTGAGATCTGTAACCTCACACCTGATACTCTGGAAGCTGATAAGCTTCAGACCTGGACTGTGTCAGTCAACGAAGGACGCTGGGTGAGAGGCTGCTCAGCTGGAGGGTGCCGCAATTATCCAG
Seq A exon
GTGAGCAATGGGTCTTAAGAGATACCACCTCTCTGATGGGGGCTATGCTACATCCCACTGGCTAAATCTCACTACAGCCCGATCAATGCTCAGCTGCAGGAAAGCTTTGGTTCCTCAGTGGATGAGTCACATGATTTTATATCTAGTTGTCTTCTGCCACTATGTTTGTGACAGTGCCTCATAAGCCCAGAAGGCAAATCTGGCAAAGATAAATTCTTGTTTGAATACTTTGCATTGCAGGTAAGAGATATCAGTTTCTCTCTGTCAGCTAGATTTAACTTTGGAAATTCTCTGATAAGTTCTGCTATGTTAAGGTTCTCTGAAAGTTTATCAAATGCCAATTCTTCACTTTAAATCCTCTGTTGTACAGTTGTTAGAATTATATAAACCCCCAACACATTAAAATATATACATTATATATATATGAAAATAAAAGCCCAGCTTTATCCTTTCCCTCAGGAACTACACACAGGGAATAGTAAAAGTTCTCTTTGGTCAGAAGTATGGCTAGAAAACTGAAGATTTATATGTTTGCTTTGGGTTGTTGGTGGCATTTCACAG
Seq C2 exon
ATACATTTTGGACCAATCCCCAGTATCGCCTGAAGCTCCTAGAGGAAGATGATGATCCTGAAGATGAAGAGGTTATCTGCAGCTTCCTGGTAGCACTGATGCAGAAAAACAGGAGGAAAGAACGCAAGCTGGGAGCCAACCTCTACACCATTGGCTTTGCCATCTATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009050:ENSGALT00000032636:10
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=0.018
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=PD(5.5=34.5),PF0106717=Calpain_III=PU(15.5=43.6)
A:
NA
C2:
PF0106717=Calpain_III=FE(36.1=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:
ATCATTTGAAGATTTCATGAGGCA
R:
GCAAAGCCAATGGTGTAGAGGT
Band lengths:
318-879
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]