BtaINT0129558 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002425 | SCN9A
Description
sodium channel, voltage gated, type IX alpha subunit [Source:HGNC Symbol;Acc:HGNC:10597]
Coordinates
chr2:30170331-30178733:+
Coord C1 exon
chr2:30170331-30170464
Coord A exon
chr2:30170465-30178628
Coord C2 exon
chr2:30178629-30178733
Length
8164 bp
Sequences
Splice sites
5' ss Seq
AAGATAAGT
5' ss Score
2.82
3' ss Seq
ATTTATTTTTATTTCTTTACCTT
3' ss Score
-0.36
Exon sequences
Seq C1 exon
ACAAGCAGCCCATTTATGAATACAGCCTCTACATGTATATTTATTTTGTCATCTTCATCATCTTTGGGTCATTCTTCACTTTGAACTTGTTCATTGGTGTCATCATAGATAATTTCAACCAACAGAAAAAGAAG
Seq A exon
ATAAGTATTTCAAGTTTTTGTCATTGCCCTGAAAGACATGAACATTATTTTTCCAAAAAATATAATGTGAAATTTAATGTCAATTACTTCATTAGAATTTCATTAATTTTCCAAGTAGTTTTTAGTATCCAGTGATGGATATGTTTAATCTCATTCATCTCTGCACAGAAAATAATCACCCTGCGATACATGAGACCTGGGTTCAATTCCTAAGTCAAGAAGATCCCCTGGAGATGGAAATGGCAACCGACTCCAATATTCTTGCCTGGAGAATCCCATGGACAGAGGACCCTGACAGGCTATACTCCATGGGGTCACAAGAGCTAGACACAACTTAGTAACTAAATGACCACAAAGTCCTAATTATTTTTAAGCAATACATCAACTATTCAGGTTTTTTCCCCCCAGTGTTCCCTGTAGAGACTTGATTAAGAAAACTCAGTGCACTAATTATTTATTCAAAATGCTTTTCATAAATAGTTCCTATATTCTGTTCTGAGCCGTAAGAGGGATTATTGTTATAGACTTTGTCTTATAAACGAGAAAAGGCACAGAGATTTTGTGTAATTTACCAAAATTATGCACCTGGTAAGTGATAGGGTTTTAATAGTCAGTAGTTGATCTTATCAGAGAAGGCAATGGCACCCTACTCCAGTACTTCTGCCTGGAAAATCTCATGGACAGAGGAGCCTGGTAGGCTGCAGTCCATGAGGTCGCTGAGGGTCGGACCCGACTGAGCGACTTCACCTTCACTTTTCACTTTCATGCATTGGAGAAGGAAATGGCAACCCACTCCAGTGTTCTTGCCTGGGAATCCCAGGGACGGGGGAGCCTGGTGGGCTGCTGTCTATGGGGTCACACAGAGTCGGACACAACTGAAGTGACTTAGCAGCAGCAGCAGCAGCAGTTGATCTTATATACTTTGTATATTATTTAGGCCCCTTTCTACCCCCCAAATACTTTAACATGATATAGTTATAAATGCAATAAGAAGTTAACAAGAAATGTAAATAGGCAGTTAGAAGAAAGCTAGATACAGCTAAAACATTTTTATGATGTATGTGACAATTGAGCAGGCCTTGGAAGATGGATGAAGAAACACATAGCAACGGGGAGGCAAAAGGATAAGTAGTCCACAGCGGGTCAGAGATATGTCTGAGAACACGCACAGTGATGATAAAGGAGGCAGCAATCCAGGCAAAATACCAGTCCATTCAGTTGGGATGTAGTTTTGAGAAAAGAAATAGCAAGAGGTCTTGATTTGCTTGAGCACAGATCTGAAAAGCCATATTAGATATTTTTCAATAGGAGCTGATGTCATTGAAGTATTAAGGAAGAACATACAAGCAGGACATACACATTTATTAAGATTTGATGACATGTCTGATCCTGTGTAAAGTACTTTACACAGTAATCTTCATCACATTCTGTAAGTGTAGAGGGCATAGTATCCGCATTTCACCTCTCAGAGGGGTTATGTGCCTTGCACATGATTGGATAGCTCAGAAGTAGCTGCATCGTAGATCCAACTCTGAGGTCTTTTTTCCCAGAATTTATGGAAATCCAGCTTTAATTTAAAAAATTAATCTATCAGTGATGCAGAGAATGACTGTAGGAGCCCAAAGACTAGGTTAGGCTCTCCTTTACCTGCTGCCTAGACCACACTTCGGAGAAGGCAATGGCACCCCACTCCAGTACTCTTGCCTGGAAAACCCTATGGATGGAGGAGCCTGGTGGGCTACAGTCCATGGGGTCGCACAGAGTCGGACAAGACTGAGCGACTTCACTTTCACTTTTCACTTTCATGCATTGGAGAAGGAAATGGCAACCCACTCCAGTGTTCTTGCCTGGAGAATCCCAGGGATGGGAGAGCCTCAGAGTCGGACACGACTGAAGTGACTTAGCAGCAGCAGCAGCAGACCACACTTCATTCTCCAAATTAGTCATTTGCAGCACTAGAGAATGTTTGTGTGTGAGTGCTAAGTCGCTTCAGTCATGTCCGACTCTTTGCATCCCTGTGGACCATAGCCACCAGGCTGCACTGTCCATGTGATTCTCCAGGCAAGAGTACTGGAGTGAGTCGCCGTACCCTTCTCCAGGGTATCTTCCCAACCCAGGGGTGGAATCCCATGTCATGTCTCCTGCATTGACAGAAGGGTTCTTTACCACTAGCGCCACCTTGGGAAACCCACTAGAGAATAGGGGATACATTCAATTAAGAGATTTTAGAGGGTAGGATCTACAGTATTGTTTGTGGTTTGCAGGAGAAAAAATTGTCTATGAAGTCTCAGTTTTCTCAAAGTAAACTGGGTTACTGTGGCTGTAGCACCACCCACAGGAAAAGAGACTTTAGAAGGATGAGGTATAGAATAACAAGAGGAAGTGATTTCAGATACTGGCTTAGTATCTAAGAAAAGACAGATGTACTTGCAATGAAATGTCATTCATGATATGATTGACTGTTCATGGGTGAAAGAAAATGTAGTAAATATTGTGTTGTTTATGCTTACATTCTGAATACAGGTGTTTATTTTTCAAAGAATTTTTCAAATTCCTTGTTCCATTCTAACATTTTATATCTGACGGTCAAAGTTAGTATTATCATATATTCATGCCTTTAGGCAGAGAATCTTAAATAAATAATAATCTTGAAAAAAATATAAATTATACCTTCATTTCCAATGTAGTTATTTTTCCTACTTTGGTCATTATATATGTGTACCTGTGATATATAAGCACACATATATAGTTCTGCAGCATTTGCTATAGAGGATGAATTATACATGTATCTAGAAAGAGCAGTATGACCATGACAGGACAGCTACAGCCCTCACTGCTTTAGTCCCCTTGCTTTTAAATATTATTCTTACAACAAGAATTGCCACTGCAGGAAGATGGGATGAATAGACACCATTCCCAGTAGCATCAGGCAAAATTACTAATTTCAAAACCCTGTCAGCTCCTGTTATCCCCTACCATTCTTCCTGTGTTTCATTTGCATTTGAAACATGCTTTTTATCTTCTGCCCCTTTCTGAGTAAGTTTACAGTTTCTTTCCAACCTACTTGGAGAATGAAAGAAGACAGGAACAACCTGTCTTCAGTTAATAACCTACTACGTAGGAGGCCTCCTGTGCTATACAAAGTGTGTATGAATTCATCTAATCCATAGAACAAGCAAATGAAAGTGGTACCTTTATACGTGCGTATAAACCGAGGCCTATAAAGAGTAAACAGCTTGTTTCAAATCAAGAACTAGGTCATTGGCAGTCAGGGTCCAAAGTTCTGTTTGAGTGTAAAGCCCATCCAAAATGAAATGTGGCCTCTTAGTGCTTTTTAACTTCAACACTTTGATCTCGGTTTGGTATGAAAGTGTTAGTTGATCAGTCATGTCCAACTCTTTGCAACCCCACGGACTGTAGCCCACCAGGTTCTTCTGTCTATGGAATTTTCCAGGCAAGAATACTGGAGTGCGTTGCTATTTCCTTCTCCAGGGGATCTTCCCAACTCAGGGATCGAACCTGCTTCTCCCACTTGGCAGGCAGATTCTTTACTGCTGAGCCACCTGGGACGCCCACCATTACCCATACCTCTTTCTAATAGCCAACCCCACTTTACTAGTTTTTCAAACTAGTCTTTGAAACTAGTCCTTAAGTCTTATAAATACTGTTTTTATCTTTAACAAATCTATGTGATAATTGGGTTTTAATAGTTCATCAGAAAATATACTTCTAAAATTTGAACTTAACGTTATTAATGAGTTCAGGTTATAAAAGGGAAATGTATGCAATGTATTTACACAAATGACTAGTACAGACCTTGGTACATGTAAGTAAATTCTAAGTAACATCAACCCTTTTCAGTAACAGTAACCTTATTTGGAACGTTAATAACAACCACGGGAATTATAAATAATTATTGAATGTTTGGAATGCAGTATCTTAATTGATCCTCACAACAAACCAATGAGGTAATTACTCTTGCAGTGTGAGATTATTCAACCTTCAGTTCAGTTCAGTTCAGTTCAATCACTCAGTTGTGTCCGACTCTTTGCGACCCCATGAAACACAGCATGCCAGGCCTGCCTGTCCAACACCAACCCACGGAGCCCACCCAAACTCATGTCCATTGAGTCACTGATGCCATTCACCATCTCAGCCTCTGTCGTCCCCTTCTCCTCCTGCCCTCAATCTGTCCCAGCATTAGGGTCTTTTCAAATGAGTCAGCTCTTCACATCAGGTGGCCAAAGTACTGAAGTTTCAGCTTCAATATCAGTCCTTCCAATGAACACCCAGGGCTGGTCTCCTTTAGGATGGACTGGTTGGATCTCTTTGCAGTCCAAGGGACTCTCAAGAGTCTTTTCCAACACCACAGTTCAAAAGCATCAATTCTGTGCTCAGCTTTCTTTATATTCTAACTCTCACATCCGTATATGACTACTGGAAAAACCATAGCCTTGACTAGACAGACCTTTGTTGGCAAAGTAATGTCTCTGCTTCTTAATATGTGATCTAGGTTGGTCACAACTTTCCTTCCAAGGAGTAAGCGTCTTAATTTCATGGCTGCAGTCACCATCTGCAGTGTTTTTGGAGCCCCCAAAAATAAAGTCTGCCACTGTTTCCACTGTTTCCCCATCTATTTCCCATGAAGTGATGGGACCAGATGCCATGATCTTCATTTTCTGAATGTTGAGCTTTAAGCCAACTTTTTCACTCTCCACTTTCACTTTCATCAAGAGGCTTTTTAGTTCTCCTTCACTTTCTGCGAAAGTGGTGGTGGTATCATTTGCATATCTGAGGTTATTGATATTTCTCCCGGCAATCTTGATTCCAGCTTGTGCTTCTTCCAGCCCAGCGTTTCTCATGATGTACTCTGCATATAAGTTAAATAAGCAGGGTGACAATATACAGCCTTGACACACTCCTTTCCCTATTTGGAACCAGTCTGTTGTTCCATGTCCAATTCTAACTGTTGCTTCCTGACCTGCATACAGGTTTCTCAAGAGGCAGGTCAGGTGGTCTGGTATTCCCATCTCTTTCAGAATTTTCCACAGTTTATTGTGATCCACACAGTCAAAGGCTTTGGCATAGTCAAAGCAGAAATAGATGTTTTTCTGGAACTCTCTTGCTTTTTCGATGATCCAGCAGATGTTGGCAATTTGATCTCTGGTTCCTCTGCCTTTTCTAAAACCAGCTTGAACATCTGGAATTTCACAGTTCATGTATTGCTGAAGCCTGGCTTGGAGAATTTTGAGCATTACTTTACTAGCATGTGAGATGAGTGCAATTGTGCGGTAGTTTGAGCATTCTTTGGCATTGCCTTTCTTTGGGATTGGAATGAAAACTGACCTTTTCCAGTCCTGTGGCCACTGCTGAGTTTTCCAAATTTGAAGACATATTGAGTGCAGTACTTTCACAGCATCATCTTTTAGGATTTGAAATAGCTCAACTGGAATTCCATCACCTCCACTAGCTTTGTTCGTAGTGATGCTTCCTAAGGCCCACTTGACTTCACATTCCAGGATGTCTGACTCTAGGTGAGTGATCACACCATCGTGATTATCTTGGTTGTGAAGATCTTTTTTGTACAGTTCTTCTGTGTACTCTTGCCACTTCTTCTTAATATCTTCTGTTTCTGTTAGGTCCATACCATTTCTGTCCTTTATCAAGCCCATCTGTGCATGAAATGTTCCCTTGGTATCTCTAATTTTCTTGAAGAGATCTCTAGTCTTTCCCATTGTATTGTTTTCCTCTGTTTATGTCATTGATTGCTGAGAACGGCTTTCTTATCTCTCCTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGACATGTAATTATAAGTTATTAATAGGCTACGACATTCAACCCTTGGGCTTCCCAGGTGGCACTAATGGTAAAGAGCTCGCCTGCCAGTGTAGGAGACATAAGATGCATGGGTTTGATCCCTTGGTCAGGAAGATCCCCTGGAGAAGAGGGCATGGCAATCCACTCCAGTATTCTTGCCTGGAGAATCCCATGAAGAGAGGAGCCTGGTGGGCTACAGCACACAGGGTCACAAAGAGTTCGACATGACTGAAGTGACTTAGCATGTACTCACTTTCAACCCTCGTCACCAGACAGTGAAGGGTTTAGATTTCTCTTGACATTATCTTGAAAATTCTTTCTTGTACATCAGTAGATCAAATGAATACCAAAGTTACACAAAGACTGCGTATCAATTAGAGGACATGTAAATTAAAACACATAAGACAGAAAGGGAAGACTGGTTTTCATTAGGTATTTGATAGATAAGAAAATGCAATCCAGGAAAACCAAAGGGAAACCATATCCAAATCACCTTTAACTCCAGGACCCTACAAGTAAAGGAAAGATGTCAGAACTATAAATTTCCCCCCCAATTCCTAATTACATGGATTGTGCTAATTTATGCCATAACTTAAAGTTTATATTTCAGGTCAATGAGGAATGTGCATGAATCTGTATAAATTGTAGATAATTTTAAGAAATCAACAGAGTTTAAAAGAATAGGTAAAGCTTCTAGGTCTCCTGTGTGAGATTTAGACTTCTACAGTGAAGAAAGGATCAAAAACTTTATTTAGATGTTACTTTATTTACTGTTGAATCTTAAATGTTGTATATTCAATTAGAAAGTCCTTCAAGTCAGAAACCCTAGAGTATTGATAATTTTCTCAACATCTAAAACTCTATTATGTATATTGTTTATACCCAATAAAGTGTTTATGTTGAAATTCCTTTATTTGGAATTAAAGAGGTAATGAAAGTTTTTTTTAGTAAATAAGTAAATAAATGTACTATGTGTATACCAAATATATTTGTGTGTGTACACTATTTATCAATGTGTTATCATAACATATATAGTATATTCATTTGTATGCTAAAGGAATATGGTATGATAAAATGAATACAAGTGAATACAAAAATATTATTACTTTTTGCCCCTACTATTTATGAGTCAGTATGGCTAATAAGTAAACATTAGCCAACTTATTATTACTTACTTTTGTTTCTTATCACTCTTCCTGATATATTTGTTATTTAACAATGAAATGCCTGATGAGACAAGTAGCAGATAAAATGAGATACCAGCATATCATTTAAAACAAAACAAGTTAGGCTACTAAAAAATAAGTGAGCCAATTATTATTTCACGTAATCCATATATGTTATATATTATGCATATTACATTACATACAGAGAGTCATGTCCCTATGTGTAGGTAATCCTTTAAGATAGATTTGATTTATAGCTACCTTGCACATAATAAGATACATTTCATTTTATTGAAGTGTAATTAACATATAACAATATATTAGCTTCCCAGGTGGTACTAGTGGTAAAGGACCTGCCTGTTAATGCAGGAGACAACAGATGCTGGTTAGAGCCTGGGTTGGGAAGGTTCCCTGAAAGAGGAAATGGCAACCAACTCCAGTTTTCTTGCATGGAAAATCCCACAGACAGAGAAGCCTGGCAGGCTGCAGTCCATAGGGTTGCACAGAGTCAGACACAACTAAATGACTCAGCACACAGCACGTACAATAGAATCATTCAGTACTTGCATACATTGTGAAATTATTACCATAAGACTTTAGTTACATCTGTCACCATCTGTCACCAGAAGTATGCAATACTTTTCAAGAGCCATACTAATCTCTATATGGTTCCAATTTTAATATATGTGCTGCTAAGTCGCTTCAGTCATGTCCGACTCTGTGCAACCCCATGGACAGCAGCCCACAAGGCTCCCCTGTCCCTGGGATTCTCCAGGCAAGAACACTGGAGTGGGTTGCCATTTCCTTCTCCAATGCATGAAAGTGAAAAGTGAAAGTGAAGTCGCTCAGTCGTGTCTGACTCTTAGCGACCCCATGGACTGCGGCCCACCAGGCTCCTCCGTCCATGGGATTTTCCAGGCAAGAGTGCTGGAGTGGGGTGCCATTGCCTTCTCCAATATATGTGCTACTGAAGTGAAAACACATTTCATTTCTGTATGAATACATTTTTAACCTGAATAATCACCTGAAGGAATATCTGGAAAATGATTCTGGTTTTAACTAGATTTATTTTTATTTCTTTAC
Seq C2 exon
CTTGGAGGTCAAGATATCTTTATGACAGAAGAACAGAAGAAATATTATAATGCAATGAAAAAGCTGGGATCCAAGAAACCACAAAAGCCAATACCTCGGCCAGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002425:ENSBTAT00000003146:24
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=0.057
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(14.8=75.6)
A:
NA
C2:
NO
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]