GgaINT0000893 @ galGal3
Intron Retention
Gene
ENSGALG00000006060 | SCN8A
Description
NA
Coordinates
chrE22C19W28_E50C23:64350-65344:-
Coord C1 exon
chrE22C19W28_E50C23:64874-65344
Coord A exon
chrE22C19W28_E50C23:64468-64873
Coord C2 exon
chrE22C19W28_E50C23:64350-64467
Length
406 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGT
5' ss Score
9.81
3' ss Seq
GGTTTTATTTTGTGTTCAAGAAA
3' ss Score
4.43
Exon sequences
Seq C1 exon
GTGCTGAACCTGTTCCTGGCTTTGCTGCTGAGCTCCTTCAGTGCAGACAACCTGGCAGCAACGGATGACGATGGGGAGATGAACAACCTGCAGATCTCTGTCATTCGCATCAAGAAGGGCATTGCCTGGACCAAGGCGAAAGTGCGTGAATTCATGCAGGCTCACTTCAAGCAGAGAGAGGCAGATGAGGTCAAACCCTTGGACGAGCTGTATGACAAGAAGGTGAACTGCATTGCCAACCACACGGGGGCTGATATCCACAGAGACATCGATTATCAGAAGAACGGCAATGGCACAACCAGTGGAATTGGGAGCAGCGTGGAGAAATACATCATCGATGAAGACCACATGTCCTTCATCAACAACCCCAACCTCACCGTCCGGGTGCCTATTGCTGTCGGGGAGTCAGACTTTGAAAATCTCAACACAGAAGATTTCAGCAGCGATACAGACCCTGATGGCAGCAAAGAG
Seq A exon
GTATGTTGTAATGCTAATTATCTATTCTTGTCATTTGACGTCTGAGCACCTGAAAGCATGTGGGGAGGGAGAGCTAGATAGTTCCAGCACCAGACCTCTGTTTGCATTCTGATGTTGTCTTGCACCTGAGACAGAAGCTCGTTGTGCTGGTTGCTTTATGGAGAACCGTGCATACTTCTGTATTTACTTTGTGCGTTTGGATATGTGATTAAAGGGACCAATTGAATGAGGTGTCTGTCCATCCTGCTGACATGAGATGTTAGCTGGGTCACGGTCTTAATGAGGTCAAGTGAGGAAACAGCTTTCTCTACAGTAAATGCGGTGAATGACTTGCTGAGTCACCACAAGCTTCGGTATTTGGTGGGAGCTAATTATAGGTTGGAATGGGTTTTATTTTGTGTTCAAG
Seq C2 exon
AAACTGGATGATACCAGCTCCTCCGAAGGCAGCACCATTGATATAAAGCCTGAAGTGGAAGAAGTCCCTGTGGAGGCACCAGAAGAGTATCTGGACCCGGATGCATGCTTCACTGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006060:ENSGALT00000009776:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.197 A=NA C2=0.550
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.2=5.1),PF065128=Na_trans_assoc=PU(61.0=84.7)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(17.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAACTGCATTGCCAACCACAC
R:
GCATCCGGGTCCAGATACTCT
Band lengths:
351-757
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]