BtaINT0129560 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002425 | SCN9A
Description
sodium channel, voltage gated, type IX alpha subunit [Source:HGNC Symbol;Acc:HGNC:10597]
Coordinates
chr2:30180085-30184706:+
Coord C1 exon
chr2:30180085-30180355
Coord A exon
chr2:30180356-30183236
Coord C2 exon
chr2:30183237-30184706
Length
2881 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGA
5' ss Score
9.14
3' ss Seq
ACTCCTCCACTCTTCACCAGGTA
3' ss Score
8.75
Exon sequences
Seq C1 exon
AACAAATTCCAAGGATGTATCTTTGACCTAGTAACAAACCAAGCTTTTGATATAGCCATCATGGTTCTGATCTGCCTCAACATGGTAACCATGATGGTGGAAAAAGAGGGACAAAGTGACTACGTGACTGAAGTTTTAAATTGGATCAATGTGGTTTTTATTATCCTGTTCTCTGGAGAATGCGTGCTGAAACTGATCTCCCTCAGATGCTACTACTTCACTGTAGGCTGGAACATCTTTGATTTTGTGGTTGTAATTCTCTCCATTGTAG
Seq A exon
GTAAGACCATTTATTAATCAGATTTTAATTCTGAGTCAAACTAAACATCACACGTATTCAGAGAAGTTTCTGAATTCATGACTATAAACCTACTTTTGAGTAACACTGAAAAAAAATGAAGTAACCTTTAAAGCAAAACTAAACAAAAACATCTGCGTCAGAATTCCTAGGTTCACGTTATGAACCTGAAGGATACATTTTCTATTTGTTGGAAGCACATAATACCCCTTGATGTTTGACTTCCAGGATACCCTTCACAAACGTAGCAAGTGTGCCAGTAGATAGATGTGTCTTAGACCAATGTAAACTGGCAATGTAAATCTAAATGTAGAATCTGAAATCATTTCTAGTTTTTGCATATATGAGAACTATCCCTTGATTAGTGATAATATAACTAGCCAGAATATTGGTGATTGAAAATTCTCCCTGAAATCAAAGTGAAGTTAAGGTATGAAGAAATGCCAGCTTCATTTCTTACAGCTTCATACTTGTCAAGTCTGTAATCATTTTCAGCCAACCACAGTCATGTCTGTGAATCACAATATTTGATTTTATACTTCCTCTTGTTTCATTCCCATAGCTGTTTTCCTGTCATCTTGTTTTTCATTATTTGTACATGCCTTTCCCAGTAGTTTAGGTTTGAATTTATTTGTATAATTATAAATTTTAGACAGAAGAGATTGTGGAGATTATTTAATACAAACTCACTTAGAGATGCTGAAACAAGGAGACTCAGAAAGGTTGAAAGTACTATAATCTAAAACTGCCATATTGAGTACTGCAACTTAGAATAGGCATTCAAAATCAATTTTTGAAAAAAATAAAAGAAAAATTAAAATTTAGGTAGGAATCACACATTAACAGCAAGCAGAAGAGAGGAAGCATTCCACTTAACTTAGGAAGAAGAAAGGAATATCCCTCTATCACTTCGCTTTGTAACAGTGTTGGCTGATCCAATTAGATCAGAAAACGGAGAGGTACATATATTTAAACAATGGAGCAAATGATCAGTTTCACATCTTACTGTGGTACTCTAAAAATGCAAGAGAATCAACCAATAAAATGGATTCAATTAAAGTTCAGAAGGTACAGATTTTAAATTGCATGAACCATGAACCAATGTTAATAATTGTTTATGTGGACCAAAAGATTAGAAAATATATCTAAGGAAATCTGATTCATGATTCCAATAAAAATAAAGGAAAATACCTAGAAATAACTGTAATAAGAAATGTATAAGACTTCTATGAGGAAAACTAACAGAAACAAAAGAAAGTTTAAATACTAAATCCAGTGTTACCCCAATGAGAATATGAGTGGGATAATAAATTGGCAACATAAATCTAAATGATTCTAAAATTCATCTGGAAGAAAAATTAGAGTAATGAGGGGTGACTTACATTGCCAGATATTAAAGATATTTTACGTTGATGAAGTAATAGATTCAAATAAATAATCCTAATTTAAGCTTCAATATATGGAGAATTACTAAGTTACTCAGTTAAAAGATCTCATGGATCAAGATTAATGGATGTGTAAAATTGTATTCTAGTAGAAATAGATTTATAACCATGAGCTTAAATAGCCCTTTCTATTCATGACAAACAACTCCCTTGAGACAAAATAATAGATATGACCACATAAAAATCAAAATATTTATTCTATGGAGGAAAAATCACTACCGCCACCAAATTAAAAGAAAAAATAGTTGAAAAACATGTTAAAAACAAGGAAATTGTTAATGTAACATTTATGGCTAACAAAGGATTAGTACTTGTGAACACGTGTATACCCGTGGCAGATTCATGTTGATGTATGGCAAAACCAATACAATATTGTAAAGTAATTAGCCTCCATTTAAAATAAATAAATTTAAATTAAAAAAAAAAAAACCACACACACAAAAAATACTCCTCATAAATCAATAAGAAGTAAATCTCCCAACAGAAAAATATTCAAAGAACTAGACTAGGCCAAAAGGAGAAAGTTGAAAATAGTCAACAAGCATACAAAATGTCCAATAAATTAAGAAAATGTGGATTATTTTTCCCCCCAAAAATGCCACAATACTGAGATGTTTCAAACATCACAGGGATATTTTTGGTAAAATTATGAAGAAGAAAACAGCACCGGTGAGCATGTGAAGTGGGAGCACTTTCATAGACTATCATTAGGAAAGTTAGTTTCCACAAACTTTTTGGAGGTAGATTTGCAATATATAACAAAGATTTAAATCACTGTTTCACCTACCTTCTATTATTATCAAAAAATGCTCATGCAAAAAATACACCTGCTTAGATATTCATTTCAGTCAAAACAATTGGAAACAGCATAAAATTCTTCAATATATGGTGACTTTGACAGAACATTATACAACTATAGGGAATTGTTCTGTTGTCATTTATATGGAAATACCTCCATAACATATGATGAAATAACTAAAACAGATGACCAAAAAACCCTTCTATTATCACGCTTACATTTGTATATGTTTGTGTGCTTGCATAGAAAAATGGAGTGATCCTAAACAAAATACTAACAGCAGTTAATGGTTGGTTGATATTTCAGGTGATTTATATTTTCTTTTTAGCATTTTACTATGTGACTTTAATTTTTCTACCCTTACAAATTAAAAAACTGTGCATGAAAAAATATAAGGTTCACAAACCTACTAAAGTAGAAAAAAAAGTCATAGTGGTTAAGGCTAGCCATTTTACTGTGGGATTGCTCAGTCCTTGGATTGTTATAATATTGTCTTCAATATAAAATGAAAATCCTGAAATCACAAGAGATAAAATGGCACATAAAACTATTTAGAGTCATAATTTTCTGTAGCATAGATATTTAAATATTTACCATTTACTCCTCCACTCTTCACCAG
Seq C2 exon
GTATGTTTCTGGCAGATTTGATAGAAAGGTATTTTGTGTCCCCTACCCTATTCCGAGTGATCCGTCTTGCCAGGATTGGCCGAATCCTGCGTCTGATCAAAGGGGCCAAGGGGATCCGCACGCTGCTCTTTGCTTTGATGATGTCCCTTCCTGCGCTGTTTAACATCGGCCTCCTGCTCTTCCTGGTCATGTTCATCTATGCCATCTTTGGAATGTCCAATTTTGCCTATGTTAAAAAGGAAGCTGGAATTAATGACATGTTCAACTTTGAGACCTTCGCCAACAGCATGATCTGCCTGTTCCAGATTACCACCTCTGCTGGCTGGGATGGATTGCTGGCACCTATCCTCAATAGTAAACCACCGGACTGTGACCCCAAAAAAGTTCATCCTGGAAGCTCAGTTGAAGGAGACTGTGGGAACCCATCTGTCGGGATATTCTATTTTGTCAGTTACATCATCATATCATTTCTGGTCGTGGTGAACATGTACATTGCTGTCATCCTGGAGAACTTCAGTGTTGCTACTGAAGAAAGTACTGAGCCCCTGAGTGAGGACGATTTTGAGATGTTCTATGAGGTTTGGGAGAAGTTTGATCCAGACGCGACCCAATTTATAGAATATAGCAAACTCTCTGATTTTGCAGCTGCCCTGGATCCTCCTCTTCTCATAGCAAAACCGAACAAAGTCCAGCTCATTGCCATGGACCTGCCCATGGTCAGTGGGGACAGGATCCACTGCCTCGACATCTTATTTGCTTTTACAAAGCGTGTTTTGGGGGAAGGTGGAGAGATGGACTCTCTTCGTTCACAGATGGAAGAAAGGTTCATGTCTGCAAATCCCTCTAAGGTGTCTTATGAGCCCATCACAACTACACTAAAAAGAAAGCAAGAGGATGTGTCTGCTACAGTCATTCAGCGTGCTTACAGACGTTACCGCCTACGGCAAAATGTCAAAAATATATCAAGTATATACATCAAAGATGGTGACAGAGATGATGATTTGCCCAATAAAGAAGATATGGTTTTTGATAATGTTAATGAGAACTCAAGTCCAGAAAAAACAGGTGCAACTCCATCCACTGTCTCTCCACCTTCTTATGATAGTGTAACAAAACCAGACAGAGAGAAATATGAAAAAGACAAAACAGAAAAGGAAGACAAAGGGAAAGATGGCAAGGAAGGCAAAAAATAGAGCTCATTTTTGATATATTGTTTACAGCCTGTGAAGGTGATATATTTGTGTTAATAAGACTCTTTTGAGGAGGTCTATGCCAAATCTCTTTTTATCAATTTATTCTCAAAGTCAGTGCATTTGCTAGCTCTGATTCTCTGACATAGGTGGGCAGCATTAGCAGATGGCTATTTTTACATTGGTAAATGTATCTCTAAGAATTGTTAAGAGTGAGTGTACAGGAATTATTGATTACAGCAAACAGAGGTGATTTAATTTTATTTACTTTTAATAAATC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002425:ENSBTAT00000003146:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.249
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.4=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.1=42.0),PF0061222=IQ=WD(100=5.0)
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]