BtaINT0129310 @ bosTau6
Intron Retention
Gene
ENSBTAG00000046911 | SCN10A
Description
sodium channel, voltage gated, type X alpha subunit [Source:HGNC Symbol;Acc:HGNC:10582]
Coordinates
chr22:12227627-12232109:-
Coord C1 exon
chr22:12231991-12232109
Coord A exon
chr22:12227708-12231990
Coord C2 exon
chr22:12227627-12227707
Length
4283 bp
Sequences
Splice sites
5' ss Seq
CTCATATCC
5' ss Score
-13.36
3' ss Seq
CCTTAACACGACCCTCTCAGGTG
3' ss Score
3.13
Exon sequences
Seq C1 exon
ACATTTATGGTGCTGAACAAAGGGAGGACCATTTCCCGGTTTAGCGCCACTCGGGCCCTGTGGTTATTCAGTCCTTTCAACCCGATCAGAAGAATAGCCATCAAAGTGTCCGTCCACTC
Seq A exon
ATATCCTTTGCACGGTTGCTTCTTCCACATGTTAGAATCAGATGCTGCCAACTGTGTCCTGTACCTTCTTCAGGGGTTAACAACGGGGCCTTCCTTCAACTGAATCCTAAAACAATAGGATCATTAAATTGAAAACAATGTTTGTGGTTTTAATGTGTTCAACACCTGAAAGCCGTCCCAAGACAGAGGAGGTATTCATGTAACCCACAGGTGGGTTGGGGTGCATGTAGACCAGTCTGGGTCCACCTGTGGGCATACAACTTGTAAAGGGCACCCAGGCACATTCTCACCATATGTGGCCTGCTCTTCCACAACATAGTAACCAGGAAGGCTTTATGGTTTGGGCAGATGAGACAGGGGTACGTTAGTTCTCTGTGGTCTAACCATGCTGGACAGTGACTGCTTATTTGGCAAAAAAGCAGCCCTTCCTAGTGGGTGAAGAGAACAGCCTGTAATGGGCAGAGTGAAGATTGTCTCACTGGGATCCCACTGGTCATGAGGCACTGTCTAGAGCATTAGTTACCGCCCAAACTACCAGCAGGTTAAAAATGTCAATAGTCTGAGGTTCATGCCATTGGGGAATGCAGTAGTGATTAGAAACACACTGCTCAAATGTCTGTAATATATTAATTGCTTTAGGTAGCTTCAGAACTGTCTCCAGCTTTTGTTTTCTTTTTTTTTTTTTCAAGGCAAGCCAAACTAGGACAAACAAGAGACTTTGGCTTGGTTTCTAAGGATCTTCCCTGGTGACTGTCCAAATTGGAAGTTCCTAATAAGGAATTCAGCTGTGGCTTCTAGGAGGTTGATTTGCAAGAACATCCTTGCCTTGACTGGCCTGGCAGATGGCAGCCAGCCTCCTCTGAGTTGAGGGAGGACAGTAAAAGAGCTCTCATCTCATCCTCTGGGACAGCTTGTTGGATTGCTGGGTGGCATTCAGTGAGCTGGTAGCTCACTACATTACATTTAGCCTTTACATGTTTTGCCTTTATGGCCAACCTGTGGGAATGACTTTCTTAATTCAGTCTTGTTGTTGTTTAGTTGCTAAGTCATGTCCAACTCTTTGTGACCCCATGGACCGTAGCCCGCCAGGCTCCTCTGTCCATGGGATTTCCCAGGCAAGGATATTGTATTGGGTTGCCATGCCCTCCTCCAGGGGATCTTCCCAACCTGAGGACCGAACCTGCATCTCCTGCACTGGCAGGTGATTCTTTACTACTGAGCCACTAGGGAAACCCAATTCATTCTTAACTTTCCTAATACTACGGAAGGGCTTCCCAGGTGGTGCTAGTGGTAAAGAACCTGCCTGCCAATGCAGTAGACATGAGACACGGGTTCAATCTCTGGGTTGGGAAAATCCCCTAGAGGAGGGCACAGCAACCCATTCCAGTGTTCTTGCCTGGAGAATTCCATGAATAGAGGAGCCTGGCGGGCTACAGTCCATGGGGGTTGCAGAGTTGGACATGACTGAAGCAACTTAGCACAGCACAGCACACAATGCTATGAAAGAGTCTTTACTGATAATAACAGCCTCCCACTGCTAAATGCTTGCTAAGCATGAACACTGTCATAGGTACAAGAACCCTTGAAGAAGGGATTAGCATCTCCGTCTTATATATGATGAAACTGATACTGGGGCGTTAAATTAATTGTGCAAGGCCATATAGCAAGTTAAAAAATCCGGACTACATCCTGCATAGAGTAGTGTCAGCAATAAGGAAGTAGGAAGTTAATGGAAATGAATTACAGTAATTTTTTCTCTAAGTATGTCATCTCTATATAGGTGTTTTTAAAAATATAAATTACATAAAAATTACAAATAAAAACAGAAAATATGCAAACTCCTTTTCATCCATTCTGGTTGATTTACATCTATTTAAGTAGGCAATGGCACCCCACCCCAGTGCTCTTGCCTGGAGAATCCCATGGATGGAGGAGCCTGGTGGACTGCAGTCCATGGGGTCACTAAGAGTTGGACACGACCGAGCGACTTCACTTTCACTTTTCACTTTCATGCATTGGAGAAGGAAATGGCAACCCACTGCAGTGTTCTTGCCTGGAGAATCCCAGGGACGGCGGAGCCTGATGGGCTGCCATCTATGGGGTCGCACAGAGTCGGACATGACTGAAGCGACTTAGCAGCAGCAGCAGCAGCAAGTAAGAAACAGCTATTTAGAAGTAAAATCCCATTAAGGAACCAAAGTGTACTAGTAAATATTCTTTTTATCTTGAGATTTGATGAATTGCTGGGTGGAGTCACAGCTGGACAGAAAAGCTGTTAAGGATCTCTTTCTCACTAAAGACCGCATTGATATATTTAAATCTCATGAACTTGGTAGCTCCAGCCCCCAGAATATTCTTCCAGATATGGAATTCTCAATCTCCTATTATTAATATTTCACCAAAATTATAATTCTAATCAAATTTTCTGTGAACATTTTCACAAGTAATATTATCAGAATATATCATCATTCTTTTAAAGGTTTGTGGAGTTGGAGATATAATTTTAATTTAATCCTTGGGTTAACATTTTCCCCCCACATGAACACATTTCTTAATTTAATTGCAAGTCAACAGGAAAATGTGGTTTAATTAGTAGAATTTCCTTTTTCAAAATAGATGGGTTCCTAAGTAACTGTAAAACAGAGTACATTAAAAGCATTTACAGAAAACTAAAATAGTTATAGATATTTCTGCTCAAATTGAAATTATGGAAGAAAAGTGATTCTCTCACTCTCTGTAGGTCAAGCTTCTCTTCAGGTGTTGTTTGTCTTTAGGAAGTAACTGTTAGGAACCCCGCTAGTCCCCAGAAAAACGTCCAATGGGAGATATTTATCTTTGGACTTTGCCACCAATATTTCTGCCCCATCTATTTACCCTTGTCCACTCACCTTCCTATTCAGTATCTCTGTCCCCTTCTTGCAATTTATTTGCCCCTTTAATATTCTTTAAAGGGACAAAGATATTTTCTTTGCCTTTAATATTCTTCCCTCTTACTCACCAGAGTTCTCCTTGACAGCCTAATCCTGTTTGGAATCTTCTCCTTAAGCAAACATTTTACCCACCTGTGCCTGCCTCCACCATTCCTAACCAGATGTCCACTTCCTCAGTGTGACTGACCTCAGCTAAGTTAGAAACACAATCTGACTACCCTAATTCCCATGAAAGCATGTGGCCCTCCCCTTATCTCTAACTTCCTCGGAATACAGTTGTCTCCCCTGCCCCTGATCCATAGGACATACATTCCAAGACCCGCAGTGGGTGCCTGAAGCCACAGATAGTACTGAACCCTCTGTGTTTTTTCCTATACATACCTACCTATGATAAAGTTTGATTTATAAATTAGGCACAGTAAGAGTAACGACAGTAATAAAGTAGGAAAATTATGACAAAGTACTGTAATAAAAGTTAGGTGAATGTGCTCTCTCTCTAAAAATATCTTATTGTGCTGTACTCATCCTTCTTGTGATGGTGTGAGATTGAACACCTACAATGATGACATAAAGTGAGGCAAATGATGTAGCCCTTGGGACATAGCATTAGGCTACTATTGACCTCCTGATGATAAGTCAGAGGGAGGCACCGTCTGCTTTGGGTGACCCTGGATCATGGAGCCATAATGATGTCAATGGTTGGGTGTCGGAAGCAGACAGTGTTGATGGTTGGGGATCCCAGGCAGGATGAAGTTAGAAGGCTGAGATGTCACCACGCTAACTGAGAATGGTGGGTAATTTCACGCGTATTTTCAGACTGCCATTGACCACACGTAACTGAAACTGCAGAAAATGAAACCATGGTTAATGGAGGGTAGGGGTGGGGGCTACTGCATTCTCTTTGTCTTTTAGGGAAAACGAGACATTTGCAGGATGAAATTTCAAGCCATACTCTATAGTTAAATGCAAGTGTCAGGGAAGAAGGACATTTTGGAGAAGGGATTCTGTTTCATCTTGCTCAGTTCTGTTTTCAGACAATTTGAGGACACATCTCAGCACCATCATTGACTAACTGTATGACTTTGGAAAAATATTTAAGCTTTGTCAGCCCATTTTCTTAGCTCCAATGTATAGATAATAATATCCACCTATAGGTTAGTTGTATTAGAAATAATGTGGACAAAGTATTCAGCGAGAGTAGGCATTCAGTGTTAGCTGTTATTATGTGACAAGACCATAAAGTTGATCCTAGTGAAAGAGTTATTAATTTAATCAATTCAGTGTCAAGGTGATCAGCGGTGACCTCAGGAAGACATGGTGACTTTCAGCTTCTCCTTAACACGACCCTCTCAG
Seq C2 exon
GTGGTTCAGTTTATTTATAACCATCACTATTTTGGTCAATTGTGTGGGCATGACCCGAACAGAACTTCCGGAGAGAATGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000046911:ENSBTAT00000065485:2
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:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(0.8=7.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
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]