BtaINT0129559 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002425 | SCN9A
Description
sodium channel, voltage gated, type IX alpha subunit [Source:HGNC Symbol;Acc:HGNC:10597]
Coordinates
chr2:30178629-30180355:+
Coord C1 exon
chr2:30178629-30178733
Coord A exon
chr2:30178734-30180084
Coord C2 exon
chr2:30180085-30180355
Length
1351 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAAA
5' ss Score
2.56
3' ss Seq
TCATTTTTGTTTCTTTGCAGAAC
3' ss Score
12.16
Exon sequences
Seq C1 exon
CTTGGAGGTCAAGATATCTTTATGACAGAAGAACAGAAGAAATATTATAATGCAATGAAAAAGCTGGGATCCAAGAAACCACAAAAGCCAATACCTCGGCCAGGG
Seq A exon
GTAAAAAATATTATATTTAGCATGTAAATTTTAAAATTATTTTAATTCATCTTTAATGTATAATTATTTCTTAAACATGAATGTATAATTTTAACATTTTAAAGAAAAGTCCTTATAAAACTGAATATATGTATTTTGAACACTATCACAGCTCTTAATAGTCTTTCATATATTTTCCTTTTCTATAAAAATGAAAAAATAATTATATATGCTTTTACTCTACATTAGCTGTACATCTTACTATTAGTACAAATGTTCTATAGAGAATCAAAATAAAATGTACTTTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCAGGTGTAAATAGTGAGTCTTAGCAGTTAAATAGTTTGTATTCCTCTAATAGTTAAAATAAATTTAAATGCATTTTATGTATCTCAATTTCTGTTTTGTATAACACTGTAGACCAAAGTTGTGGCTGAAGACAGAGCATCCTAAAAATGGGAATATGTTTAGTACCAGCTGCCTACATGAGGATTATCCAGCACTTTTTAAATGGACACATGGCCAGGTTTCATCCAGACCTACAGAACCATAATCTATGAATTTAAAGCTCTAGTATTTAATTTTCTCAGTACCCTACTTGATCTTGATAGAGTGTCTTAAAACTTGCTTATGTAACCAATAAAGTGATTTTGAAATTGAGTTTCATGAAAAGCACAGTACTGTTCAGTGAGCTTGATAAGAAAAGTGATATGTTAAATATGGATATGTTTGGAAGTATATATTCTATACATGGAAGAGACAGGAAAGTATAGATCTCTGATATTATAGCAGTAATACCAGTGTAAGACAATGATGCCAACACATTAGTCAAAATAAGGTGACAAAGTAGAAATTTAGAGATGTCATTTTATTACCTTGAAACACTCTAGGTAATGGAACTGAGATTTTCTTTTCTTTTTTTTTCTCTGAGAGTTTCTTAGTAAAAAAATTACCTTGTGATCCTGGCAATTCCTGTATGACATACTAGGGTGGATATACTTAAAAGCAAATGTTAGTTTACAAGGTTAATTGAAGAATTGGTACACTGAAAGTCAACAGCAAGTTGTCATGTACTCTGACTTAGATCTAGCCCATTAATCATATTCCTTAAACAAAGCAAGAGCTTATAACCAAGGATAATTTATGCAAGTTTTGAAGACAGGTACCTTTAAAATTTGTTTTGTTAATGTAATCATTTATGGATACTACTTGGAAAATTTACTGTACAATTTCCTATCATTTTTGTTTCTTTGCAG
Seq C2 exon
AACAAATTCCAAGGATGTATCTTTGACCTAGTAACAAACCAAGCTTTTGATATAGCCATCATGGTTCTGATCTGCCTCAACATGGTAACCATGATGGTGGAAAAAGAGGGACAAAGTGACTACGTGACTGAAGTTTTAAATTGGATCAATGTGGTTTTTATTATCCTGTTCTCTGGAGAATGCGTGCTGAAACTGATCTCCCTCAGATGCTACTACTTCACTGTAGGCTGGAACATCTTTGATTTTGTGGTTGTAATTCTCTCCATTGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002425:ENSBTAT00000003146:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.057 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(20.4=47.3)
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:
TGGAGGTCAAGATATCTTTATGACA
R:
AAGATGTTCCAGCCTACAGTGA
Band lengths:
342-1693
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]