GgaINT0079548 @ galGal4
Intron Retention
Gene
ENSGALG00000020084 | CAPN13
Description
calpain 13 [Source:HGNC Symbol;Acc:HGNC:16663]
Coordinates
chr3:7778040-7780089:+
Coord C1 exon
chr3:7778040-7778118
Coord A exon
chr3:7778119-7779972
Coord C2 exon
chr3:7779973-7780089
Length
1854 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
CCTTCTGCTCTCCCCCACAGGCC
3' ss Score
13.75
Exon sequences
Seq C1 exon
GATCTCTTCAGGAGGGAAGACAGAAATTGTTCTGGATTTCTTGATGTATACGAGCTGAAGAGTGCGATACAGACAGCAG
Seq A exon
GTATGTCCAGGTGTGCTGAGCAGCTCCTGTCCCTGCGGAAAAGGGTGAAAAGAAGAAAGGGCTTCAGGAGTAAAGCAGTTTGGAGCGCACAGAAGTGCCAGTTAGATCACAGCTCTGCTCACAATACTGCATTGTCTCAGGGCACCGAGACAGAAAGCTCATTTTGCACAGAACCCTTTTCTTTGCTGCACGGCCCCGTGCCCACCTGCCCCCGCCCATACCGAAGCATCCACCCTTTGAATCACAGCAAGGGAAACAACAGAGATGCAGAGAAGCACAGCCTGCAGGGTCTCTCTAAGTCGCAGACAAAACACACAGCCAGGGAGAGGAGCAGGGAGCTCGCACATAATCCAATTCCTGCAGTTTCTCATGGAGGCAGTGACTAAGTCTATTATGGAAAGCCACAGTGGCAGGCATTTATTTAGTTTGCACTGACCTCTGTTGGCTACGCGAATGCTGAAACTTGCAGTGAGTGCATGGTGACCCTTTGCACAAAGAAGGCATTCTGGCTGGGTATCTCTCCGGAGACTTTGTGCATGAAATACAGCTCACAGACAGCAAACCTGCTGGTAATCATACAGCAGAGGAACTCCCATCGGTGTGCCTGGAGAGCTTGGGGTGGGTGCTGTCCCTGGGGGGAGCATGGTGAAGAAGCACTGTCCACGGGAATCATCAGCTCAGAATGGATGTGTAACTTGCTGAGAGGTAAGCAGTGCATTTGCATAAGCCTGAGCAGTGCAGCACTGATGTGCCAAATGTCAGTGAAGGAGCTGCCAGGCCACTTCTGCTAGAGCGTAAAGTGGGAGAAGTGGCAGCCAAAATGGTGCAGCTATTGGAAGGGACAAGCACAGACGTATTTCCGTTACTTAACTATTGGACATTGTATGTGTGATTCCTGCTGGAGACCTTCTCCGGGTAGGCTTGTACAAACAGGGTTTGGCATCGTGCTAACCCACATCCATCAGTTGCATCTACTCCATAAAGCTGTAGAGAAACCATTCCCTTCTTTTCTGCTCACTCAACTAATTGGCTGTGTTAAGAGTTCATTTAAAACCAAAAAGTCTAGAACTGGTTGGTAAAGGGGGGAAAGGCACTTCCCTTCCTTGCCACTGAGCTGCTAAAAACTGGGGGTGAGCAAATGAGACTTTCTGGAGTCACAAAGAATGCGTCAACCTGAAGCTATCAGTGCATAGCATTTCTCTTTTATTTAGTAAATCAGCTTTTAGACCAAAAAATATTTAAATCACGTCTTGGGTAGCCAGCATATTTAGGGTAGTTTTATTTAACTTATAAAAGAATCATTCTAATAGGCAACTTTTGCTCATTCAGTTGAATACCAATTTCCATCCAAATAGACTGTGACACAAATACTGAATAACCAGCTAATAAAAACCGAAATGCCCCTTTCACCATTTTCTGATATAAGAGAAAATGTAAAAATTAAGAATCCTGGGCATGCTGTACTGCATAATAGCAGTGTGCCCTATTCCTGCATAGCAGAAACGCCGGTGGTATTGTGAGCGCTGCGCTCAGACTGTAGCGGTTATGCAGCGTAGAAAAGAAAATCACCATTTATTAGAGAAAATAAAAGCTAAAAATGCAAAGTAAGGCAACCCTAGAATCCTTAATTCCGCAATAACCACAATTCATGTGATGAGAAGGGCTTGGATTCCCCACCACCCTGACCCTATTCTTGCTACCACAGCTGGGGGAAGGCATGCGGCTGTGCGGGGGGCCCAGAGGGCACCAAGTCTGACAGGGAGGAGGGCTTATCTATGGGAGCACGAGGCCAGCAGGGCCAGTCTGTCACCCCGCAGTGACCCCCAGGTGCCGTCCTTCTGCTCTCCCCCACAG
Seq C2 exon
GCCTGCCCGTCAATGAGCAGATCCTGCACCTGATGGCCCTGCGCTATGGCAACGTGTACAAGAGAATGGGCTTTGCTGACTTCGTGAGCTGCATGCTGCGCCTTGAAACCATGACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000020084:ENSGALT00000014759:18
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:
PF134991=EF-hand_7=FE(42.6=100)
A:
NA
C2:
PF134991=EF-hand_7=PD(50.8=77.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTCTTCAGGAGGGAAGACAGA
R:
AGGTCATGGTTTCAAGGCGC
Band lengths:
194-2048
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]