GgaINT0054922 @ galGal3
Intron Retention
Gene
ENSGALG00000009050 | CAPN3
Description
NA
Coordinates
chr5:27832248-27834404:+
Coord C1 exon
chr5:27832248-27832435
Coord A exon
chr5:27832436-27834195
Coord C2 exon
chr5:27834196-27834404
Length
1760 bp
Sequences
Splice sites
5' ss Seq
CTTGTTCTT
5' ss Score
-19.04
3' ss Seq
TTGACTCCATTGTTCTGCAGATG
3' ss Score
9.41
Exon sequences
Seq C1 exon
ATACATTTTGGACCAATCCCCAGTATCGCCTGAAGCTCCTAGAGGAAGATGATGATCCTGAAGATGAAGAGGTTATCTGCAGCTTCCTGGTAGCACTGATGCAGAAAAACAGGAGGAAAGAACGCAAGCTGGGAGCCAACCTCTACACCATTGGCTTTGCCATCTATGAGGTACCAGTTCTAGACCTT
Seq A exon
GTTCTTAGTGCCAGATTCCCAGCCCTTACAGTATGTTTACCAAGGGAGTCATTGAACTGTTCATCCTGATCACATGAATTGCAGTTTCTCCTTTGCAAGGAAATGTGGAAGAGAGGAAAAAAAATTCAAAGCTTTAGTACTATTTAGCCCATAGTAACCTCAGGGTTTATCCCATCTATAAGTAACACACTTAACAGGTTTTTATGGTGATTTTATGTCAGATTTTAGCATATTCTTCCCCATATCTACTTCGGTCTCCACACTTCCTTAATCCATGCTGAAACTAAACATCTAATTGGCAGAACCGTGTAAAAAGGGAAACAGTCAAGACACAAAAGTAGTGATCAACATCTGTCCCTCTAGTGACTTCAGGTAGAAGTTGATTTACTCAGCTCTTTGCACAAAAATATTTGGTTCAAATCTTACTGGATCTTGTGTAGGTCACAAGAAATCTGAAAAGGAAGGTGGGATTTTCTTAGAAAGCTTATATAAATTGAGGTAACTTAAGGTTGTAACTAGCTGCAACCCCAGAAATCCCTTCTGTTAGATTTATAAGCAAGTAGACTCACCTAGAACTTCTGTTTCTTCTCTTTGTTACTCTCTAAGGTACCCAAAGAGGTATGAGCTGAATGGGGACAGACTGACAACTTGGTGTATGCTCACAGCTAGTGTCACTGTTGCTCCTGTCTGTAAGTCAGTGGGAAACTGTCCATTCAAGTTTGTTTTCAGGGATGTTACAGATGTGAAACTGCTAACCATTATGCTTTGAGTGTTTAGTAACATTTTCTGAGTCATTTTAAATTCTTTCTCACTTGTTCCCTGTTTTCACCTGCACCTGGTCCTTTTCTGTTCTATACGTGAGCTGGCCACTGCTTTCACTGTCCCGTAGTGAACCTGGACTACAGGAAGAAGCGTCAGCTAGCACTTAAGACATCACACCCCACAAAGAAGACCCCTAAAGCACTTCTGTATCCTCCTGCAAACAATGCCAGCAACTTATAACCTGTAGCCACAGAGTTTGTTCTACAGTATCAGATTTTTTGTTGCTATTATTAACAAATGGTATTTTCAGCCGTTGAAGAAAACATATTAGAAGTGCACAGACTGAGTTTTTCTGAGCCTGCCAATAGCTGAATCATTGGTACCAGAAGTTTGCAAGTGAGTTCACATAAAAGCTTTTGCTGGAAAATATAAAGATGACCATCTGAACGTTGTGTTTACAAACCTATTTTATAGGCAGTTATTTCTGTAGAAAGCAACTGTAAGCACTTGTTCTTAGCCCACAGGCATTGACTTATTTTTCATGTTTACATGAATGCAATGCCACTTTGGTAGATACAGAATTCATATTTTCCCAGGTAAGTTACCACTGAAAACACCTTCACCTTACTGTGCAGTACGTAGGAGCCTGCAGATACCATTCCCTGCCACACCACCCTCAAAGCAACTAACTGAACTTTTGGTTACATGCAATTAGCATCCAACAAAACATAAGATCATGGACACAGCAGAACAGCCAGCCAGCAGTGTCTGTGTGGGATGTTGGGCAGCTCACAGAAGCCAACTAAACCCAGCTAGCAGCAGCTTATAAAGATGACAGACTGTAACTGGTAACAAGCTAGCAGCCCCCATCAAATCCCTGCTTGCTAAGCTGCCGCTGCTTCATTTGTGTTTTCTGTCCCAAGTGCTGCCTGCATGACAAGCCACCTGGGGAACGGGTAAGACTTCCTTGCAGATGAGTTGACTCCATTGTTCTGCAG
Seq C2 exon
ATGCACGGTACTAAGCACCACTTGCAAAAGGATTTTTTCCTCTACAATGCTTCCAAAGCTAGAAGTAAGACCTATATAAACATGCGAGAAATCTCTGAGCGCTTCCGGCTGCCTCCCAGCGAGTACGTTATCATCCCATCCACATACGAACCCCACCAGGAGGGAGAATTCATCCTGAGGGTTTTCTCAGAGAAAAGAAGTCTTTCAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009050:ENSGALT00000032636:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.016 A=NA C2=0.014
Domain overlap (PFAM):
C1:
PF0106717=Calpain_III=FE(36.1=100)
A:
NA
C2:
PF0106717=Calpain_III=FE(44.5=100)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAATCCCCAGTATCGCCTGA
R:
TGAATTCTCCCTCCTGGTGGG
Band lengths:
348-2108
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]