BtaINT0129562 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002425 | SCN9A
Description
sodium channel, voltage gated, type IX alpha subunit [Source:HGNC Symbol;Acc:HGNC:10597]
Coordinates
chr2:30101479-30103103:+
Coord C1 exon
chr2:30101479-30101607
Coord A exon
chr2:30101608-30103011
Coord C2 exon
chr2:30103012-30103103
Length
1404 bp
Sequences
Splice sites
5' ss Seq
TGCGTAAGT
5' ss Score
9.73
3' ss Seq
ACTCTGATTTAATTCTGCAGGTA
3' ss Score
9.48
Exon sequences
Seq C1 exon
GTACACTTTTACTGGAATATATACTTTTGAGTCACTTGTGAAAATCCTTGCAAGAGGATTCTGTGTAGGAGAATTCACTTTTCTTCGTGACCCATGGAACTGGCTTGATTTCATAGTCATTGTCTTTGC
Seq A exon
GTAAGTATTTATTTTTTGAAACTCCAAACTCATGAAAATCTCAGAGAGCACAGTGTCCCAGTGAGAAAGAACTTTGGGATCAGACTTTTCCTGCATATAATAGTTTGATTTAAAAGATACTGCATGGAAACTAGTCATCAAAAAATGGTAATAATTTTTCAGAAAGAGCATTTCCCACTCAAACATGTATATATGATATTGTTATAATAGAGGATCTTTCTCTGTGCTCAGCATGTGGATGGATAGCATATGTGGTGCCAGTTAGAGTCACACTTTTCCCAAGTTCCTATTTAATATCTGGTAAAACTGATAAGAGAAACAGAGAAAACTCAGGCATTTATTATTAGCATGGTGCTCTTTCTATTAATGTATATTATTCAAGAACTAATAAAATATAGAAGCAAATCTTTTCATAAGGACTGTCACTGCATACTGAACCTAACATTAATGCGTTGTGTATATATTACATAGGCATCTACAGTTTATTTTCATGGGAAAAATATCACATTAAGATATAATTTTAGCTTATTTATATTGCTGCTCTTTTCCTAACTATATTTGTCAGAACATTTCTTTAGTTTTAACATCTCAAACCTAAATGCAATATTTTCCCTCTGTCATTTTGAATTGTAAAAGTAATATATGTTCATTGGAGGGATTTAGACAATAGAAAGGGTCTTGAGATTTCTAGTCTCCAATTCTGTACACCTGCCCCACCTCTTTGTCCTTCATCCATGACTACTGTAGGTCCACCCACCACCTGCTAAGATAACACTGTGTCAAAGAAGGCTGCATCTTCTCAGGGGTCTCCTTTTTTATTGAGTATAAATTACATGCCATAAACTTTATCTTTTTTTAAAGTATAAAATTCAGTGTTTTATAGTATGTTCATAAAGTTATGCAACAATCACCGCCCTCTAACTCCAGAAAATTTTCATTATCCCAGAGAGCAGTCACTTTCCTTCCCTTCTTCCCCCAAGTCCCTGGAAAATACTCATCTATCTTCTGTATCTGGATTTGCCTAATGTAGACATTTCACATGAGTGGAACCTTAAAATATGTGGCCTTTTGTGGCTGGTTTCTTTTAATTAGCATACAGTTGTTAAGATTTGCTGATGGTGTTTTGTAGAACATTATCAATATTACCATAATATTGAAGTCTAGTCATTGAAGCATTTCATCGTTTATTTAGGCATTTAAGTGTATGAAGCCATTTTAATATTTGCATTTTGCTCACATCAAATGACTCAAATCAAATTAAATTAGTAATGATAGAAGCAAAAGATTTGCACAACTATAAATTTAAATAAGAAGTTCCAAGCATAGGAAACACCTTGACTAAAGGCACAGGTAAGTATCATAGACTATATCTAAATTCTGAATAACTCTGATTTAATTCTGCAG
Seq C2 exon
GTATTTAACAGAATTTGTAAACCTAGGCAATGTTTCAGCTCTTCGAACTTTCAGAGTGTTGAGAGCTTTGAAAACTATTTCTGTAATCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002425:ENSBTAT00000003146:5
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=FE(17.4=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(12.6=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:
TACTTTTGAGTCACTTGTGAAAATCC
R:
GGGATTACAGAAATAGTTTTCAAAGC
Band lengths:
198-1602
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]