BtaINT0129552 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002425 | SCN9A
Description
sodium channel, voltage gated, type IX alpha subunit [Source:HGNC Symbol;Acc:HGNC:10597]
Coordinates
chr2:30150216-30158835:+
Coord C1 exon
chr2:30150216-30150336
Coord A exon
chr2:30150337-30158680
Coord C2 exon
chr2:30158681-30158835
Length
8344 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
ATGCATGTCTTTCTTGCCAGGTT
3' ss Score
8.8
Exon sequences
Seq C1 exon
AGGCTGAACCAATCAAGTTCCTCAGAGTGCAGCACAGTTGATAACCCTGTGCCTGGAGAAGGAGAAGAGGCAGAGGCTGAGCCTGTAAATTCAGATGAGCCAGAGGCCTGTTTTACCGATG
Seq A exon
GTAAGAGAAAAATTGAGACCTCACTTAACATCCATTTGTTAATGTTTTGGCCTCGGTCTTAAAGCCTAATGCTTACTTGGGATTGATGAATAAACTGTCAGAAGACTCCATTCCATGCTGATTTAGTCATGGCTCTTTGACTAGGCTTCTGTTTCCATACTTATGCTACTAATAGTAATTTAGAATGTTTATGTGTGTGTTATGCTGTAAAGCACTGCCATTTTTTGAGAGAAGCAAATAAGTGTGATACCTGATTAATGGAAATTTGTGTTTGCTCAAATTAGTACTATAAGCAAAACACATGGAGTTTCCTTTAGAAGTATCCCTATTAAAGGCATTTAAGGGTCTCATCTGGAGAAGGCAATGGCACCCTACTCCAATACTCTTGCCTGGAAAATCCCATGGACCGAGGAGTCTGGTGGGCTGCAGTCCATAGGGTTGCTAAGAGTTGGACACGACTGAGCGACTTCACTTTCACTTTTGACTTTCATGCATTGGAGACGGAAATGGCAACCCACTCCAGTGTTCTTGCCTGGAGAATCCCAGGGACGGTGGAGCCTGGTGGGCTACCGTTTATGGAGTCGCACAGAGTCAGACATGACTGAAGTGACTTAGCAGCAGCAGCAGCAGCAGCAGCAGCAAACCCTCTGTGGAAAGTATTAATGCTAAACTATTTCAGACTGTAGGTGCTATTTTACTGAGATCAAACTTTACAAAGGCTATTTTAATCCTATAAAATACCAATGAGAATACTTATATAATAACTTAGAAATATTCATAACTTTTCAAATTCACAACTCTAATTTGAGTCTAGTATATAAGAGATATTACAGAAACACATTTTCAATGAATTATAGCCTTCAACACTGAAAACATGCTGTAAACCAAAGTTTCAGTTGTGTAAGATGAATGCATTCTGAAAATATAACAGGCAACAATATGATTATAGTTAGCAATACTTTATGGTATACTTAAATACACAAAAGGGTAGATCTTATATGTTTTTAATTACCCACCCCCCAAAAAAGAAGAAATTGGTAACTATATGAAGAGATGGCAATTTAATTAGCTTGATTGTGGTGATTATTTCACAGTGTAAACATAACATATTTACAAGCTGTATAACTTAAATTTTTAATTGTCAATTATCTCAATAAAGCTGAAAAAAATGGACAGAATAAGAGAAGAATGTTTGCATACAAAGTCACTTTAATCATGTCTGACTCTTTGCAACCCTATGGGCCGTAGCCCACCAGGCTCCTCTGTCCATGGGATTCTCCAGGCAAGAATACTGAAGTGGGATGCCATGCCCTCCTCTAGGGGATCTTTCCGACCCAGGGGTCAAACCCATGTCTCTGGTGTTTCCTGCCTTGGCAGGCAAGTTGTTTACCACTAGCACCACCTGGCAAGCCCAAAAGAAGAATAGGCAAAATCAGTCTACAAAGGCAGAAGTCAGACTCATACTCACCTTTAGGAGGTACAGATTGGGAAAGGGCATGATGGTGATTTCTGGGTGCTTGAAAATGTTATATCATGACCAACATGGCTATTCCATGAGAACATTAATCTATATAGTTAAAATATATATACTATACTGTATGTACGTTCTCCTCAAGAATTTAAATAAATAGATAAATATATTTTTTAATGACCAGAACACCAAAGAAAATCTATGAGCAAACACACATCTCTTAGTTATATCATTTTGAGCAGCTGTGTTCCACTAGAGACTTTATACTCATTGGACCTGCTGGGGTAAGAGGTTCAGCCTGATGAATTAAACAGGGCAACCAATGAACAATGGCAACCTTCAGCTTATCTACTTATTTTATCCAGTCACCAAATAATCATTAAGTACTTTCTGCCAGGCCTAGGCCTGAGCACTAGACAGAGCAGTTGAAAAATAGAAAAAAGTTTCTTACCCAAATGAAATATGTAAGTATGTAGTAGATCAGATAAGCAATATGTGCTCTAGAGAAGTAAAATGAAAATAGGAGTACCAAGGTCAAGGGGTAGAAGCCTACTACAATATAAGTAGAGTGATCAGAGAAGGACTTTCTAAAAAGATAACACTTGATCAGAGACCTAAAGGAAATTGAAGCAGATATATGAAGGAAGACTGTTCCAAGCAGAATAAGGAAGGCATATGCCCTGAAGTGGGGATATGCACATTTGAAAACAAAATCAAGGGGCCAGTATGAGTCGAACAGATTGAGAGGTGGGAAGATTGGTAAAAGATGAGGTTAGGAAAAAAAAAAAAAAAGATGAGGTTAGAGGTGCAACAGAGGCCAGATCATAAGAGTATTGAAAAAACATAAGAATCTTATTTAGAAGTCTCACAACATGCCATCTTATAAGCAGATGGGTGGGTAGCAAGGGCAGAAGTTGGAAAACCTCTGAATGTTCCTGCAGTAATCCAGGTGAGAAGTGATGGGAAATTAAAAACTACTGTGGGAGTATAAGTGTCTGAATATATTTTGAAGTTAAAGCTGAAGGGATTTGCTGATGGATTAGATGTTGGGTGTTAAAGCTTTCTTTTCTTTAGAAGAGTCAAAGATGACTCCAAGCTTGGGGCCTCTGAGAAATACATAGTCTCCACACGAAGGGTTAAAAATGAGCAGGCTTGGTCTCCATGGGAAATCCACAGTTTGTTTATTTATAGTAGAAATGACCATGACCAAGCTGTGATTGGCTGACAGGCGTTGAGCTAGAATCAATGCCAATTTAGAGCAGTATTTGGCCTTCACAGGTTTTTGTTACCTGAATGGCAGCAGAAAAATCAAGGCAAATGTGTGAGTTAAGTCAGAATAATTGTGTTTTGGTGAAGACGAACACTAACAGGATTTTGTTGTTTATAGTCTCGCATGCATTTTTTCAGCTTCATAACTACCACTTTATCAGTTTGCACCTTATTCCTCTTCACCTTTTTCTCCTCCCTCTTCTTGTGTGTCTTTCTTTAGTTCTTTGTCATTAGTGTTATAATTCAAGGCTTCAGGTTCCTGCCCCAGTTCTAGTACCATTCTTTACTATCCTTAATTCTAAATGTCTTTGCAATCTGTATAATTATGAGCATGACATGACTCTGGTTCTGCTTGGTTTTATATTGTACTCCTGTTGGATTAAACAATTAGTAAATCAAAAAATTAGGATTAGGGTGTGAGAAGGATACACTCTTCCTTAAAAGGATGTGTTTTCTATTAATTTGATAGGAGGCACTAACTCAGCTCTGCCCTCAAGTGTTCTGAGTTCAACTTCCTAAAAAATAGCTAATAACTAATCCTAACTTTGATAACACAATAACGAACTCTTTTGTGCCTATTTTGTCTTTTTTTTTTTGAAGGAATATATGGACAAAACATTTGTTTTAAAGGATTTATAATTTTTAAGTGTTTAAAAAAAGACATTTTCTAATCAGTTTTTACATTAATTATACTGATCATGCTGTTACATTTTTATTAATGGATAAACTGTCTTAGAAGAAGTCTGTGGTTTTTTTTTATTTGAAAGCGTTAGTTTAACATGATGAAACCAAGTGGAGATTTGATGTAATGGCTCATAAGAGCAAATAAATGAAACCACCCAAAAGGAATAGCATTTACCCGTGGGGACCCATTAAAATGTTTGAGAGGTTCTCTGTTATGTTTACATTTAATTAATAGTCCTTTTAAAAAAGAAAGTGTGATTCCATTGCTAACCAGCTAGGTTGGAAACATCTTGGGATATACCTTTCTATGATGGTCAGACAGGCAGTGGTCTTACACTCCTGTCTCAAAATAAGAGAGAAACTCTGTGAGGTATGATAAATCCTGAGGAAAATATTTATGCACCTTCATCTCAGATAAAAGGTTTATCTACTTTTCTAATTATAATATATAGTGCCTTTTCCTACCTGAATCATAAGAATAATATTCTCTTCAATCTAAATACTGACAAAAATAAATCCCAAATGGTAAAATCTTCTTGGGGCTTCCTTGATGGCTCAGTGGTAAAGAATCCGCCTGTCAATGCAGGAGATGCCAGAACTTAGAAGTTCCCAGAAAGGACAAGAACACATAAAATATACATGCCAGGGAAAATGTCAGAGACTTGGGGGGAAACATCGCTTGCTGCATTTCTATAAAGCTGAAAATTATTTACTAAGACTTACCTCCTATTAAGAATCAATGAACTAATTTCACTACAGAATCATAAAAGAAGTACAGTACATTGTCCAAAAAATGTATTTCATTAAAATTCTAGCTATGTTGTTTCAGGACATACAGTTTATGATTATATGAAGTTATTACTTGATAGGCTCAATATTTTAATGAAATATATTGCTTGATAGACAAGGAAATTATTTTTAAAGCACCCATGAAATTAAAAGGCACTTACTCCTTGGAAGGAAAGTTATGACCAACCTAGATAGCATATTCAAAAGCAGAGACATTGCTTTGCCAACAAAGGTCCATCTAGTCAAGGCTATGGTTTTTCCAGTGGTCATGTATGGATGTGAGAGTTGGACTGTGAAGAAAGCTGAGCACTGAAGAATTGATGCTTTTGAACTGTGGTGTTGGAGAAGACTCTTGAGAGTCCCTTGGACTGCAAGGAGATCCAACCAGTCCATTCTGAAGGAGATCAGCCCTGGGATTTCTTTGGAAGGAATGATGCTAAAGCTGAAACTCCAATACTTTGGCCACCTCATGCGAAGAGTTGACTCATTGGAAAGACCCTGATGCTGGGAGGGATTGGGGGCAGGAGGGAAAGGGGACAACAGAGGATGAGATGGCTGGATGACATCACCAACTCGAAGGACATGACTTTGGGTGAACTCCGGGAGTTGATAATGGACAGGGAGGCCTGGCGTGCTGAAGTTCATGGGGTCACAAAGAATCGGACACAACTGAGCAACTGAACTGAACTGAAACTTCTGAAACAAGTTTCTGAAAGCACTGTTCATTTTTGCTCTCCCAATTCTACTTTCTTTGCAAATGAGGTTTTATGTCTAAGATTTTTAAGAGAAGAATTAACTATAGTACCTCTTTTTAAATTCTTTCTTTTTTTTTTAAAGTAATTTTGATTGTTTATTCTTAAATCAATTTTAATTTTTAAAATTTTCAATTGTTATTTCTCTAAGCCTCTCTTGGTCATAGCTCTGTTCACAGTCCTTCAGGAAACTTCTTCCTTTCTAACTTTTCTTTTACTTCAGCCTCTTGTACATTTCCCCCACTACCGACTTGTCATTTCCTTCAGGGTTTTCTTTTCTTCCGCCTATCCCAGTGATGTACAGCTAAATGTTTAACAACCAGTTCTCCAAGAAAAAAAAAATGGTATACGTACTGCCATCAGTTGACCATATTCTGTTGATGTAAAGGATATGTGGTACACAATTTACAAATAATAATATAATCAACATCCTTCATTGACTATTCCATATAGCGATTCTCACAGAGTGTGAATTTTGCCAATTTTTAAAATTTATAACAATGATTGCAATTGATAAACAATAATAGTTTTAATCTGAAGGTTGCTTGGTATTTTCATTTACATTAATCAGTAACATGAAACAGACTTCCTGTCAGAACTTGACTCATTCATCAGTGATGTGAACAAATTTTTGCTGAATCAGATAATAGGATTTGAGCAATGAAGGAATATTTCCTCAAGTTTTTCATGCTATTCACAGTGTAAGGGCTGCAAACATACATAACTATTACTGTTTTATTAACATTTTATCCATCACTGTCTTAGTCTACTCTAGAAAATCAGCAAGCCTTGATTTATAGCACTTGATAACTTTTGTAAAGATTCCCACCATGACTCATTTCAAACTACTGGTGTCACTTTGCTGCATGTGGAGTTGAAAAGAGACACACAGTAGCCCAACAGTGTAACATATTTCTACCAACCAGGTAGAATACATAAAGATACTCAAGAGCATTCAGTTCAGTTCAGTCGCTCAGTTGTGTCCGACTCTTTGCAACCCCATGAATCGCAGCATGCCAGGCCTCCCTGTCCATCACCAACTCCCGGAGTTCACTCAGACTCACATCCATCAAGTCAGTGATGCCATCCAGCCATCTCATCCTCTGTTGTCCCCTTCTCCTCCTGCCCCCAATCCCTCCCAGCATCAGGGTCTTTTCCAATGAGTCAACTCTTCGCATGAGGTGGCCAAAGTACTGGAGTTTCAGCTTCAGCATCATTCCTTCCAAAGAAATCCCAGGGCTGATCTCCTTCAGAATGGACTGGTTGGATCTCATTGCAGTCCAAGGGACTCAAGAGTCTTCTCCAACACCACAGTTCAAAAGCATCAATTCTTCAGTGCTCAGCTTTCTTCACAGTTCAACGTTCACATCCATACATGACCACTGGAAAAATCATAGCCTTGACTAGATGGACCTTTGTTGGCAAAGTAATGTCTCTGCTTTTCACCAATTGTAAATTGTAGTAAAATTATTAGAGTAGTATGTTTTTAGTATTTATTACCTTTTCTAAAGTTATACTTTTAGGTTTATACACTTTAATTTTTGATAACAGCTGCATTTAACAACAGGCTAGCAAAATTTTCCTGACAATTTAACAATAAGTTGTCAAGACCAATGTGAGTTAGTTCCAGCATACCTTTGAATTCTCTTAATATAGCTGTTCCAGAATGTTCCAGACTTGCCCCTTTTCTCTCTTACCCTAAATACTTTTTTTGTGTGGCCTTAACAACTATCCTGATCTCAGCTGACACATACATGCTAATTATTCCTTCACATTCTTTTCCAGCCCAGACTTTTCCTTTAAACTTCACAGATTCACACCTTCAAATATCTACAGGACCTCTGTGCTTAGAGATTTCACCGGCATCTCAGACTCATTACCACCCCAAGCAGCTCCTGCTTCTGTGGTCTTCATTCATTGCTGACATCCTCACAATTGTCTGGGCTTCTCCCTTCTTCTTACATCCCATATCCAGTCAGTCAGCAAATCCACTGATTATACCAAATATGTCTTGACTCTGTTACTGCTCTAGTTCCGAACAAAAGCTACCCTAATCTATTTTTCTTGTTGAGGATACTGAACCAGCACCCTAAATGGCTTTCTAGTCTGGGTTTTTCTTTGTACCTTCCCATCCCTCTTTTTTCTTCTCTTCCAACTTATCCTCCACAGTTGTTGGAGATGTCTATTTAAATTATGATCTTCCTATGTAGTTCTCTACCTACAACCCTTCACTTACCCGTCATCAGAATATAGGATATAGACCAAACTGCTTAAGGTGGGGGAAAAGATTTCTATAATCGGACCAATTTCTCTGCCTCATCTCTCATCTGTGCCTCTTGTGTACACTTTGCTTTCATCACAGTTCTGAAATACATCACAGTTCTGAAATAATCTCTGTACACATTTTGCTGTCTCTTGGCTGGAATTCCACCCAAACTCTTCTTGACTAACAATTTGATTTAATACACCTCTTCCAGAAAACCTCCTCTGACCTTACTTTTTTAACAAATTAAGCCAGCTTAGGTGAATGTCTTCCATGCTACCAAAAATAACCCCGGCATATCTGTCCTTTTAGTTGCTTTATCCTATTGTGGCCATTTATTTCTATATCTAGCTGCCTAGCTAAAAGCCAAAAGTAGATTCCATAAGAAGAAGAAACTATGTACACAGCTGAGTAAAATGCTTGCTCAATAAATGTTTGATAAGGATGTGAATGAATAAACCTAAACAACTTTAAAAATTCCTGTTTTTTTTAATAGAAGTATGTTTTACATCTGTAATTCCAAAGTCAAATTGGTTTTTAACCTACATTATTCGAAAGTTTTATCTGCATCTTATAATCAAGATCTCTTTCTTTTGAACTGAATGTATAGGTCCTTCCACTAATTTTTAAAATATTACTTAGAATGCTGTTTCTCAAAAGTGCTTTTTTACAGAGGAGTTGAAGCAGCACCAGATTATAGACTAAATTCACATCAAGAAGGTCATGAAATGCAATATTATCTTGAGATTTATATTGATTCACCAATCATTATTTACTGCTCATTGTGTATCAGGATTAGGATTGTATTAGGGCTGCAGTAATAAATAACAGTATGTGGTTTAAATACTGTAGAAGACGTTGATGAGGAACTAGAGAAATATAGAAAACACAAATATATCCAAGTTAGAAATTACTGACAAATATTAAGAAAACGCCATGGAGATTTAGGAGATAAGAAAAAGCAACACCCAAGTTAAAATTATTTGAAGCTTCAGATGTGCTTGAAATTATTTGGTTGAGGAATTGTCATAGGGAGCACTTTGCATTAAATAATATTTCTTAAGTATTTTATTTATTCTGAATATCCAGATTTTACATGCATGTCTTTCTTGCCAG
Seq C2 exon
GTTGCGTACAGAGGTTCCCATGCTGCCAAGTTAACATAGAATCAGGGAAAGGAAAAATCTGGTGGAACATCAGGAAAACGTGCTTCAGGATAGTTGAGCACAGTTGGTTTGAAAGCTTCATTGTTCTCATGATCTTGCTCAGCAGTGGTGCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002425:ENSBTAT00000003146:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.659 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=FE(18.1=100)
A:
NA
C2:
PF065128=Na_trans_assoc=PD(19.9=84.6)
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]