GgaINT0079533 @ galGal4
Intron Retention
Gene
ENSGALG00000020084 | CAPN13
Description
calpain 13 [Source:HGNC Symbol;Acc:HGNC:16663]
Coordinates
chr3:7766800-7768390:+
Coord C1 exon
chr3:7766800-7766966
Coord A exon
chr3:7766967-7768244
Coord C2 exon
chr3:7768245-7768390
Length
1278 bp
Sequences
Splice sites
5' ss Seq
CTGGTAATG
5' ss Score
5.67
3' ss Seq
TAATAACACTTCCTCGGCAGGTG
3' ss Score
6.4
Exon sequences
Seq C1 exon
GATGTCCTATGAAAACTTTCGGGAGCAGTTTTCCTGGCTGTGTGTATGTAACTGCACCCCAACGTTTCTGGACTTCGGAGATCAGCGCCACACAGGATGGTCTGTGGAAAGACACATCAACCTGTGGAGCCCGCTGCTCGCTACTGGCAGGAGCAACTGGTCCTCTG
Seq A exon
GTAATGAATGCTCCCTGTGGTCACCCAGTCCTCTCCTCCTTCTACACCAGTGCTTACATTGAAACATTCACCACGAGCACCAGTTAGCAGAAATATTGATTGGTATTTGTTAACGCCCGCTCTTTCTCATTACAGCACCTATCAGCTAGAGAAACAGATAGGAAGAAAGCAGTGGCACCGGCTGCTGAGCTGGGGAGAATAAAAAAAAAAGGGGGGGGCTTGTGATTTAGAGATCCTAGGCTGCCTAAATCAATATGTGCTTGTCTATGCTCTTTCAGCCTGTTGAAGTAGGTGCTACAGGGGACCTCATCAGAAAGTCTGGTCTGGCAAATATGTGACTGGTCCCCCAGAGAAAGAGGTACTCTGGAATTAAATGGATATAAAATGAAAGAATTGTGCTACAAAGCTCAGTGTTCAAAGGCAAAAAAAGTCCTTTGACCAGATAAGACCATGCATTTTACTGGAGTGCCCGCAACACAGCATAACCATCTGATCAAAAGAGGTGATTCTCCCCTTATACTTAGTGCTGGTGCGGCCTCGCTTTGAGTACTGTATGCAGTACTGGGTTCCACAACACAGAATGGATGTTAAGGTCCTTAAAAATGCTCAGAGGAAGGCAGCAAAGCTGGTAACAGGGCTGGAAGGCACGTCCTGGAAGGAGAGGCTGAGGACTGGTCTGGAGAAGCTTTCAAGGCCACTCAAATACATGGCTTCAAGTCTAGGCTGACTTAAGTAGATGCTGGACACCTCAGACCTCTTCCTCCAGTTTCACTTCTTGTCAGGGATGCATCTTGTTAATTAAACCTTTGGCCTTTTTGTTCTGGTCCTCAGCGCCGTCTTCTGCATCACAAACAGTAATAGGTAGGAAGAGGAGGATATCTTTGGATCACTTTGGGTTTTTCATTTATGTGCTTATGATCTCCAAGACGCAGTGCTTTTCAGCTCAGTCACCAGGTCAGCCAGAGGACTGAAAATCACTGCCTTCCTGCTTGGGGAAAGTGTACCATGGAGGTGAAACAGAGGTGGGTGGGTGAGAAATCTGCCTGACATTTATGACTTTGCCAGAGATTTCTAAAATGACTAATGGGCAATTAATTTAACTCCAGATTCCTCAACTCCTACTAATAAGGTAGGGGCCGCAGTGCTTTGTTGCATCAAAAGCATTTTGGAGAAGTAATTACTTCTTCTTCTGAGTCTTTATAAGCAAGATCTAACACAAGAGGCTACTACTGAGGTCTTTGAGTGGCTATTGCTAATCTAATAACACTTCCTCGGCAG
Seq C2 exon
GTGCAGTTTCAAAGAACCCTCAGTATTTCTTCAAAGTGACAAAACATGACCCCAAATCCTACAATGTGGTCATTTCACTCATACAAAAAAATGCAGAGGGTGTGCATGATGCACAGAAATTGAAGATTGGCTTTTTCATCACCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000020084:ENSGALT00000014759:10
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=0.000
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=PD(6.4=33.3),PF0106717=Calpain_III=PU(18.9=42.1)
A:
NA
C2:
PF0106717=Calpain_III=FE(37.8=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:
GTCCTATGAAAACTTTCGGGAGCA
R:
CGTGGTGATGAAAAAGCCAATCT
Band lengths:
310-1588
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]