GgaINT0000901 @ galGal3
Intron Retention
Gene
ENSGALG00000006060 | SCN8A
Description
NA
Coordinates
chrE22C19W28_E50C23:52737-53658:-
Coord C1 exon
chrE22C19W28_E50C23:53554-53658
Coord A exon
chrE22C19W28_E50C23:53008-53553
Coord C2 exon
chrE22C19W28_E50C23:52737-53007
Length
546 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
GCCTCTCTCCTGTTGCACAGAAC
3' ss Score
7.35
Exon sequences
Seq C1 exon
TTTGGAGGTCAAGATATTTTCATGACAGAAGAACAAAAGAAATACTACAATGCCATGAAAAAACTGGGCTCCAAGAAGCCTCAAAAGCCAATTCCCCGGCCTCTG
Seq A exon
GTGAGTATGTTAGAAAGGGAAAAAAATGCAGAACAGACTTCTGAAGGAGCTTCAGCTCCAAAAGCATCCTTTGTTCTAACTCATGCTGGACAGCACATCATCATCTTGTCTCCTCCCCTTAGAGTAGGGTCTTGGGCCATATGGTTACACCAGTCAGAACCTAGGCACGTTTCCCTGCTTTGTGAAAGGCTTTGCATGGTGAGTTCTGTAGGTAATGCCATGGGTAAGTCATCCTGAGGTCACTGCTGCAGGGCAGACCTGGCTGCTTCCTCCAGCTGTGAATGGAATAGTCAGCCTGCGTTTGCTCCCACCGAAGAGCGAGACATGCTGGTAATAGGGCTGCTCATCTGGGATATAAATAATAGCATCTTCCTACCTTTCCCCCACACAGATTGATCTGTGGCTAGAGTGTGCCTTGAAAGCTTCAAAGGGTACCGAGAAGCAATGTCCTCATCCCTGTTTCTACCAACAGGAAAGCAATCTGTTGACTGATGGCAGATTTTTGTTCCAACCTGTTTGGCTCACGGCCTCTCTCCTGTTGCACAG
Seq C2 exon
AACCGCATTCAGGGAGCTGTCTTTGACTTTGTCACTCAGCAAGCATTCGACATCGTCATCATGATGCTCATCTGCCTCAACATGGTGACCATGATGGTGGAGACGGACACACAGAGCAAGCAGATGGAGGACATCCTCTACTGGATCAACCTGGTGTTCGTCATCTTCTTCACCTGCGAGTGTGTGCTGAAGATGTTCGCCTTGCGGCACTACTACTTCACCATTGGGTGGAACATCTTTGACTTCGTTGTTGTGATTCTGTCCATTGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006060:ENSGALT00000009776:25
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:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(20.5=47.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAAAAGAAATACTACAATGCCATGA
R:
CCACAATGGACAGAATCACAACA
Band lengths:
344-890
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]