BtaINT0129561 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002425 | SCN9A
Description
sodium channel, voltage gated, type IX alpha subunit [Source:HGNC Symbol;Acc:HGNC:10597]
Coordinates
chr2:30100830-30101607:+
Coord C1 exon
chr2:30100830-30100918
Coord A exon
chr2:30100919-30101478
Coord C2 exon
chr2:30101479-30101607
Length
560 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
CAATGGACTCTTTTACCTAGGTA
3' ss Score
5.53
Exon sequences
Seq C1 exon
GCATTCAGCATGCTTATCATGTGCACTATTCTGACGAACTGCATATTTATGACCATGAGTAATCCTCCAGACTGGACCAAGAATGTAGA
Seq A exon
GTAAGTGGGTATAAGTACATTTTAATATAGTCTTACTATGGTTGTTATCCTTCCTTTTTCATACCAGGAAGTTATTGCATGTATAAAAATTGTGGTGATTATCTTCCCATGTTCTATAGTTACTGTACTTTCAATTAGTTTTTCTCCTTTATTAACCTGCTAACATTAGAAAAGAATAATACATGTTACAGTCTTTTCTAGAAAAAAAGATCTTACCAGATACCCTGCCTGTTCTTAGACATGTCACGTCCTTGGATGTATTTCAGATAGGAACAATACAGGAATTTTCTAGGCAGATCTCATACCTGTGTTCTTAGTAAATACCTTTACTTTAAAATACCTCTACTTTCTGGGAGTGTTTCTGACATATACATTTTAAGATTTTCTGGAAAGATCTTAATTGTAATTTATTCTAATAGTTAGAATGGGCCCCTTAATCATCAGCCATACTCTAATCAGTGTCTTCCTTTGGTTGATCTGAGAAAAATAATTATAAAGGCTTACCTGGTACCATGTTCTTTTCACAATGGATTAATATCACAATGGACTCTTTTACCTAG
Seq C2 exon
GTACACTTTTACTGGAATATATACTTTTGAGTCACTTGTGAAAATCCTTGCAAGAGGATTCTGTGTAGGAGAATTCACTTTTCTTCGTGACCCATGGAACTGGCTTGATTTCATAGTCATTGTCTTTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002425:ENSBTAT00000003146:4
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:
PF0052026=Ion_trans=PU(0.8=6.7)
A:
NA
C2:
PF0052026=Ion_trans=FE(17.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATGCTTATCATGTGCACTATTCTGA
R:
AGACAATGACTATGAAATCAAGCCA
Band lengths:
206-766
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]