BtaINT0129563 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002425 | SCN9A
Description
sodium channel, voltage gated, type IX alpha subunit [Source:HGNC Symbol;Acc:HGNC:10597]
Coordinates
chr2:30103012-30104289:+
Coord C1 exon
chr2:30103012-30103103
Coord A exon
chr2:30103104-30104079
Coord C2 exon
chr2:30104080-30104289
Length
976 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
CTTTTCTTCGCTGTATTCAGGCC
3' ss Score
9.06
Exon sequences
Seq C1 exon
GTATTTAACAGAATTTGTAAACCTAGGCAATGTTTCAGCTCTTCGAACTTTCAGAGTGTTGAGAGCTTTGAAAACTATTTCTGTAATCCCAG
Seq A exon
GTAAGAAGTAACTGGTGCGAAGCATTAGGTCACTCATAACTCCAACTATTTGGGAGTTGTTCTTTGTGTGTGTGTGTGTGTGTGGGTGTGTGTTGTCACCGTGTTTGTGTATAAACTCCCCTATTTCAGATATGTGACAGAGTTTGTGGACCTGGGCAATGTCTCAGCGTTGAGAACCTTCAGAGTTCTCCGAGCTTTGAAAACAATTTCAGTCATTCCAGGTGAGAGTGGGGTTAAACACCAGGGCTGACTTTGATCTTTTGAAGGAAAAAACAATAAAAACTTAATCTTAACATAATTTTAATTAAATTTGATCTCATGTCTTTCATAATTGTTATGAAAAGTCAGCCTTTGAGTTTAATCAATTGCATGAGTCTTAGAGGATGAAGATGGCCATTTGGTTCACATCTCAACTTGAAATTTTTCCTCCTGTTTAACAGTTTATTTTCCATTTTGCTTATCCAGGAATAAAAATTTCAATTTGTTTTACTGCTTTTCTTAGAGTGAAGAAAAGAGATATAAAAATATTAGCATGGGGAGGATTGCATGACACAATGCTTTTTTCTTTCCTCAACAAACCATTTCTTTACTGAAAACAGTTGTCACTGTATCCTGTAATTCAGCCTCTGTTTTGGTCATCACAAAGAGATGGTTTGTCTGACAGACATGTACTGAACTGACACAAGTTATTTTTTCAAGTGAGTGTGGCTATGATTTGAGCAACCAAATTATTCATTTTGACTGGTTATTCTCTGGAAATACTTTAAAGTTTTTAGTCACTTGCTGCAATATACAGAAACAAAATATATAAAACAGCAGATCCCCCTTTTGAGCTGGTAGACTTTTTTTGAACTAGGTTATTTAAGATCGTTGATTTGATAAAGTGCATGCACTTCTAGGAAAGCTTGTATTTTGCTTTTGTTTTTCATTTAGAAACTTTATTTCATTTTGAACACCTTTTCTTCGCTGTATTCAG
Seq C2 exon
GCCTGAAGACCATTGTGGGGGCCCTGATCCAGTCTGTGAAAAAGCTCTCAGATGTCATGATCCTGACTGTGTTCTGTCTGAGCGTGTTTGCCCTGATTGGGCTGCAGCTCTTTATGGGCAACCTGAAGCATAAATGCGTGCAGAGTTCACTTGCAAATAATGAAACAATGGAAAACATATTGAACACCCTCGATGAAGAAGAATATGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002425:ENSBTAT00000003146:6
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(12.6=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(28.3=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:
ACAGAATTTGTAAACCTAGGCAATGT
R:
TGCATATTCTTCTTCATCGAGGGTG
Band lengths:
294-1270
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]