GgaINT0087020 @ galGal4
Intron Retention
Gene
ENSGALG00000011136 | CAPN9
Description
calpain 9 [Source:HGNC Symbol;Acc:HGNC:1486]
Coordinates
chr3:39841769-39843085:+
Coord C1 exon
chr3:39841769-39841827
Coord A exon
chr3:39841828-39842626
Coord C2 exon
chr3:39842627-39843085
Length
799 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGA
5' ss Score
8.55
3' ss Seq
GATCCTTCTTTCAATATTAGTTC
3' ss Score
6.24
Exon sequences
Seq C1 exon
GAGTATTCCAAGCATTGAGTGTGAAAAACAAGGATTTCATTAACTTGAATATTGGCGAG
Seq A exon
GTATGAGCACAGCTTCATAAACACCAGTAAAATGATGGGGCTTCTCTAGCGCTTGGTCTTCACAAAAGAACTGGAGGTGAAATCGGTGTCCATGAGAGCACAGGACTGTCTGCCACAGATTTCAGCAGGGCTCTGATTTTACAGCACACACCCTGGTTACATCTCCTTGGTGCTATTTCCTTCCTTGCCCTATTGCACACAGACAGCTTCCCATCCCCTCTTCTGGCTTTTCTGCTTTTACCTTCCTTGGGTGCCAGCTCACGGTGAGGGAAAGGAGAGGCAGCAAACTGGGATGGGACTCTTTCCCTCCCTGTGAATTGCTTAGGAGTTGAAATCAGCATCTCAGTTAATGTGCATCCTCAGCTTTTCAGCATAGGCTTGTTGTTTTCTTTGTGCTCTCTTTGTCTTCCTATTGCACACATGGTCTGTCTCTCATTTTACACTTACCCGAAGTTTCCTGGGGCAATGCACATTGAGTTTCTTGGCACAGCAAATGTGAAAGCTCAAGTGGGCTGTGGTGAAGGAAATAAACACACTGCTGTTATTGGCATCCAGTGCTCAAAGAGCTCTACCCTCTTCCCTCCAAGCACAGAAGTAAATGCTGGAAAGTCCTGCTTGCATACTAGCTAGGGTCTCCATGTAGCACCAGGACATAAAAGCTAGTGAACAAAGATCCCCTTCCCTGTGTGGGGTCAAATCTGAGCAAGGCATTGCTTTTGAACTTTTCTCTTTCATTTGGGGAGGCAGGTGAAGGGCCTGAAATTACTTATTGTAAATTTGATCCTTCTTTCAATATTAG
Seq C2 exon
TTCATCAACCTGGCAATGAACATCTGAGGAAGTCGGATTTGGATGCCAGGAGTCTCTTGTGCCATCGCTGCCATGACTTCTGCCCCAACAGCTGTGATGCCCTTCTCATGCAGACTTCATCAGGAGCTTTTGTGTGGAGGAAGACTCATGCTGCTCGTCTTTCTGGTCTCCAGCCCTGTTGCATTCAGGAGTTCAACAGTCAGATCTCATTTTGTTTTTAATTTCGATAAAAGCTATTGATGGATTTGTTACTGGGAGAGATATTTGGATGGGGCATACATGCCTCTCAAGCAGACTGAAACCGATGCCCCTGAGTGAACACAATCTTTTATGAAATAGGATTGTATTTAGTTTCAGCACAGCACCGTCTACAATGATTAAACATCTTTATTGCTGCTTGGCTACAGATTGCTGTAAGATGCTTTTAAAAATATAAGGTTGCATAAAATTTTGTTCGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011136:ENSGALT00000018152:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg19)
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:
AGCATTGAGTGTGAAAAACAAGGA
R:
GGCATCGGTTTCAGTCTGCTT
Band lengths:
358-1157
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]