GgaINT0079532 @ galGal4
Intron Retention
Gene
ENSGALG00000020084 | CAPN13
Description
calpain 13 [Source:HGNC Symbol;Acc:HGNC:16663]
Coordinates
chr3:7765887-7766966:+
Coord C1 exon
chr3:7765887-7765961
Coord A exon
chr3:7765962-7766799
Coord C2 exon
chr3:7766800-7766966
Length
838 bp
Sequences
Splice sites
5' ss Seq
CTGGTATTT
5' ss Score
3.5
3' ss Seq
TGCAGCTTTCTCCTTTGCAGGAT
3' ss Score
10.53
Exon sequences
Seq C1 exon
CTCTCCAGAATGGGACTATGTTGAGCCTGAAATTAAGGAAGAGCTCTACAGAAAGAAAAATGATGGAGAATTCTG
Seq A exon
GTATTTCCCAACTGATCCTTTTGTCTATCAGGCTTTCTCTTTGTGTTGGTTATAAAAGAAGGGTCATCTGGGCATTTGTTTTCTCTGCTCTTAGTGATGGTTCGAAGCACTCCTGTGTTAGCTGTGGGCAGACAACAAATTGTTGCAATGGTGTCAGAGAAAACAAGGCTTGGAGAAGTGAAACTGGCCAATACTATGCAACAAGCTGACGGGAAGAAAAAGAAGTAGTAGTAGTGAAGATCCAGCTTGGTGAGACTTAGTGGTTTTGTCACTCTCTCCAGGTGACCAGCTTGAACTTCAGACTGCTCAGAGGAATAAGTAGCTGAGGTCTTAGGGCTTGTGCACCTGACTGCTCTGCAGGTGCTTGTGGCTTTTCACAGCCTCTGGTTACTCTCAGATCCAGTTAGCCACGGGTCAGCCATTCTCTATAAAAGCCCTTATTCTTCAGAAAGTGCATGCTTGCCCTGTGAGGCTCTGAGGAAGACGGGGGAATGAACAGCAAGCTAGTCTGGGATGGACACTGCAGGCTTGAGCAAAGCATGGAAGGCAGGACAGGACACCAAAGTGAGGTAGTACAAGGCATTACAACAGGGATGTGCTGGGGATAGCAGGACTCCATCAAGGCACTACTGAATGTGCCCTTTAATTTCACCGGGGCTCTACGTGCATTTAGGGCAGCCCAAATGCATTAAGAGCTAACTTCTACTGCTAAGCATCCGCCAGCTTGTCTGCACCCTTCTACCACTGCTCCGTAACCCTGTTTTGAAGACGCCGAGGGGTTAAACAGGAATACCCCACTGGTGTCTCAGACTGAAAGGTGCAGCTTTCTCCTTTGCAG
Seq C2 exon
GATGTCCTATGAAAACTTTCGGGAGCAGTTTTCCTGGCTGTGTGTATGTAACTGCACCCCAACGTTTCTGGACTTCGGAGATCAGCGCCACACAGGATGGTCTGTGGAAAGACACATCAACCTGTGGAGCCCGCTGCTCGCTACTGGCAGGAGCAACTGGTCCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000020084:ENSGALT00000014759:9
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(8.5=100)
A:
NA
C2:
PF0064816=Peptidase_C2=PD(6.4=33.3),PF0106717=Calpain_III=PU(18.9=42.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGAATGGGACTATGTTGAGCC
R:
CAGAGGACCAGTTGCTCCTG
Band lengths:
238-1076
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]