GgaINT0000895 @ galGal3
Intron Retention
Gene
ENSGALG00000006060 | SCN8A
Description
NA
Coordinates
chrE22C19W28_E50C23:62943-63673:-
Coord C1 exon
chrE22C19W28_E50C23:63519-63673
Coord A exon
chrE22C19W28_E50C23:63117-63518
Coord C2 exon
chrE22C19W28_E50C23:62943-63116
Length
402 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
AGAATCTGGTTATTCCCCAGGCT
3' ss Score
5.33
Exon sequences
Seq C1 exon
GTTGCATGCAGCGCTGTAAGTGTTGTCAGGTCAATATTGAGGAGGGGCTGGGGAAGTCCTGGTGGACCTTGAGGAAGACGTGTTTTCTGATTGTGGAGCACAACTGGTTTGAGACTTTCATCATCTTCATGATCCTACTGAGCAGTGGAGCTCTG
Seq A exon
GTAAGTGGCACACAGAAGTACGTGTAGCTGGGGGATGTCCACGTGGGAAAACTGTGTGTAGGAAACGTGGTGAAAAAGGGAACTGTGATGGTTCTTATTTGGAAAACAACAGATCTGCGTTGTGGTAGGTGCTGTAGAAAAGTCTTTCTCAGTGAGTTTGTTTAGTTTAAACCAGAAATGAAGATTCTGAGCCTGGATGTCTGGGTTCTGCCCGTATTTTGAGTAGAAATGTACTGATTTGAGATAGTTGATGCAGCTACTAGAGCAGATGTATTGCACTGTGTAAGGAATGTCATCCCACTGCTCATCTCAGTATTGTCTGAATGAGCTTCTGGATTAATTACCACGTTGACCCGTGGAGTAAATCTGGTGTAATGACAGGAGAATCTGGTTATTCCCCAG
Seq C2 exon
GCTTTTGAGGATATTTACATAGAACAGAGGAAAACCATCCGGACCATCCTGGAGTACGCAGACAAGGTCTTCACGTACATTTTCATCCTGGAGATGTTGCTGAAATGGTGCGCCTATGGATTCGTCAAGTTCTTCACCAACGCCTGGTGCTGGCTGGATTTCCTCATTGTGGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006060:ENSGALT00000009776:19
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:
PF065128=Na_trans_assoc=PD(20.2=84.6)
A:
NA
C2:
PF0052026=Ion_trans=PU(17.0=67.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCATGCAGCGCTGTAAGTGTT
R:
AGCCACAATGAGGAAATCCAGC
Band lengths:
326-728
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]