BtaINT0129546 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002425 | SCN9A
Description
sodium channel, voltage gated, type IX alpha subunit [Source:HGNC Symbol;Acc:HGNC:10597]
Coordinates
chr2:30120058-30123356:+
Coord C1 exon
chr2:30120058-30120429
Coord A exon
chr2:30120430-30123226
Coord C2 exon
chr2:30123227-30123356
Length
2797 bp
Sequences
Splice sites
5' ss Seq
AGCGTAAGG
5' ss Score
5.87
3' ss Seq
ATCATCTTTTTTTTTTTCAGGGT
3' ss Score
11.86
Exon sequences
Seq C1 exon
TCACCACTGAGCATCCGTGGCTCCTTGTTTTCTGCAAGGCGGAGCAGCAGAACAAGTCTTTTCAGCTTCAAAGGTCGAGGAAGAGATATTGGATCTGAGACTGAATTTGCCGACGACGAGCACAGCATCTTTGGTGACAACGAGAGCAGAAGGGGCTCCCTGTTTGTGCCCCACAGACCTCGGGAGCGGCGCAGCAGTAACATCAGCCAAGCCAGTAGGTCTCCCCCAGTGCTGCCAGTGAACGGGAAGATGCACAGCGCTGTCGACTGCAATGGCGTGGTCTCCTTGGTGGATGGACCCTCCGCCCTCATGCTACCCAATGGACAGCTCCTGCCAGAGGTGATAATAGATAAGGCAACTTCTGATGACAGC
Seq A exon
GTAAGGACGTTTTAAATAGCTCAGGCATGGTTTGGCTCTTATTCTTGCATCCATCACTCTCTCTGCTGGAGGGGCCTTCTCTCTGGTCCTCTGAATGGCTCTGCATCTTGCAATACTTTTTATGCTAGAAACACACCTTTAACTGATTAATGTAATCCTTATACTATTGTTGTAGGTATCCAATGCCAACATATTTAAAATCCCATTTTTGAAAAAATAGTACTTATCTACTGATATTATACTTGATTATGACTCACCCCCTTAGAAAACAATATATATATCAGCATAAAATGCATTGATAATGCTAACATTATTAGTTGATAATAGGTTCCATGTCTGTAAGGAGATTTGGGTTATTTGCCACCTACTGCTATTTTTTCAAGTCACTACTTTATATATACCTTGCTCCAAGGGATCTTATTTGAGTTCTTAATAATTAATAATAGTAATAATAATAGCAGACACGTTAGTATTTATAGCAGCCCTAGGAGGTGATATATTACTATCCCTTTTATACACCTGGGGAAACTGAGTCACGGGGAAATGAAACAATTTGTTCAAAGTCACTCAGCCAATAAATGGTAGTCCTGAAATTCATAAAGAGGCCCTCTGTTTCTGAGCTTGTGGTTTTAACCACCACACTTTCTCTCCAGGATGTGGTAAACTTCTTAGGAATAGTTTAGAGTAACTGTGATTTTCCCCCACACATAAATGAAACACACTGTTATCATTAAAAGAAATACCAAAATTCTTTCATCTGAAATCTGTGAATAAAAACATAATATCCAAAATACATACGTAAATGCAAACATATACATATAAGATAAAAATAAAACACCTTTCCAAAACAACAATTTCAAGAGTTCGGGAGTCATTGAGTGGTATGAGAAAAGGGTGTGATGAAGCCTGAAAGTGAGATCTTTCTGGTTTTAGAGTTTCTTGGTTATGTGTTAAGGTCACTCACCATGTTACATTGTGTTGCTTGATATTGGAAAGGCTTTGACTAACTTAACAAGCTCTGAACTTGTGCCACCTATTCATAAATCATATTTGCAGACAATGAAGTATTTTAAGTGAGAATGAAGTTCCATCAAAGCCATGGCCACGCATGCATTTTCGTTTGAATGCATGCATATGCTTTTAGGTCATATGTGACCTCTGTGCTTGCATGATACAGCTTCAGCCCTCTGTCAAGGTGTTTTTCTTATCAAACAAGCATGTTAAATTTCCATGGAATCATATCTTTGCTGTGTTTTGCTTTTCAATAATGTGTATTACCTATAAAAGATTATATAATGTATATCAGATTTAGAGATTATTTCCTATTTTTAAATGAAATGTTTCACTTAATACTTTGTTTTACCACAGAAAAATCATTATCACTCTAAATTCTAAGACTAAAACTACAGAGCTGGAGTAATTAGTGGATACTTTATAATTCAATAGAAATAAATGCAAAACATAATAGCGTGAAATAATGTACAGTTTAGATGAAAAAATTGCATGAGAAATAATATAACTTTGAGACCTGAGACATGTCTACATGGAGAAAAAAATGCTTTATCAACACAGCTATTTGTTTGACTTGGGGAAAAAAGAAATCACTGCTTCCAGAAAGTCAGTAAATTAGAGAGTATTTCAGCTAAAACATGGTTATAGACAGATCTCCGTAAGAAGCCACCTGCAAATATGTGTGTGTGTATCCTCACACATATATGGACATGCATGCATATAAACACACGTACATCTATTTATGCCTGTTTGTCTACGTTTTAATATACAAGCATATATAACTGTATCTAAACAACTATACTTTACAACTCTAAATCTGTATATCTATGTATATGTTTGTAGAATGGTGTGTGTGTGTATACATATATATATATATACATACCACATATTGTGACCCCATGAACTGTAGCCTACCAGGCTCCTCCATCCATGGGATTTTCCAGGCAAGAATACTGGAGTGGGGTGCCATTGCCTTCTCCATAAAGTTGTCTGAAGTCTATATGTATATATGTGTATGTGTGTGTGTATTGTTGGCCTGCACTGAACTGGCACAGTGTTTTAACTCTGAATTAGCTGCCGAGATTTAGAAATAAGACATCTTTACATAAATATGGTATACCTGGTAAAATTGAGCTCATATTCCTGCATGGCAGCAATCCTTTGAAGCCTCTTTTAGATGGAGCTTACATTCTCTATTTTGATACAGTGTCCATCAGTCTTAATCATTGTTTTTCTACTGAGTCATTCATCTTGATAGAGCAGTTCATGAGATCTGCTTTGGCAAGAGAAACAGTCATGACCATTGCCCTGTTATTGCCCCAACAAAGAATAATTACAGAAGTTTACCAGAGAACACTGAAGTTCTTCCTTTACACACACACACATACACCATTGCAAAACTTATTTAGCTGTTTTCATGTTAGGACTCTTACATAGTAAAGCTATCTGAATAAATTGGAGACCCAGAAAGATAGATAATGATAGTGATTATAACAATGAAAGCAGCTCATTTTAGTTTTTATTTCCTTAGTGTTAAGCCATTTAATCCTCATAACAAGATTATGAGGCAAGTACTATGATTATTTCCATTTCACCAGTGATGAAATGGAGACAGGTTAAGTAACTCTCCTATGGTACACAGCCAGTAAATGGCAGAGCCATGACTCAAATCAACAGTCTAGGCTCTAATTACTCACTACAACTTTGTGGCAAGATTTTATTTTCTACCTATAATTTATTGAAATTCCATTCTTAAACTGTAATTAATCATCTTTTTTTTTTTCAG
Seq C2 exon
GGTACAACCAATCAAATACACAAGAAAAGACGTCACAGTTCTTACCTCCTTTCTGAGGATATGTTGAATGACCCCAATCTCAGACAAAGGGCAATGAGTAGGGCAAGCATATTAACAAACACTGTAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002425:ENSBTAT00000003146:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.581 A=NA C2=0.136
Domain overlap (PFAM):
C1:
PF119333=DUF3451=FE(52.8=100)
A:
NA
C2:
PF119333=DUF3451=PD(15.5=81.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]