BtaINT0129542 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021339 | SCN8A
Description
sodium channel, voltage gated, type VIII alpha subunit [Source:HGNC Symbol;Acc:HGNC:10596]
Coordinates
chr5:28280036-28281790:-
Coord C1 exon
chr5:28281584-28281790
Coord A exon
chr5:28280330-28281583
Coord C2 exon
chr5:28280036-28280329
Length
1254 bp
Sequences
Splice sites
5' ss Seq
CAGGTTGGT
5' ss Score
8.08
3' ss Seq
GTGAAATTTTACTTTCCTAGGCG
3' ss Score
7.29
Exon sequences
Seq C1 exon
ACCTTACGAGCAGCTGGGAAAACGTACATGATCTTCTTCGTCTTGGTCATCTTTGTGGGTTCTTTCTATCTGGTGAACTTGATCCTGGCTGTGGTGGCCATGGCTTATGAAGAGCAGAATCAGGCAACACTGGAGGAAGCAGAGCAGAAAGAGGCTGAATTCAAAGCAATGTTAGAGCAACTTAAGAAGCAACAGGAAGAAGCACAG
Seq A exon
GTTGGTGATCAACTCTTTGCCGTAGTCCTTCCTGCCAGATCATGGTGACTAAGGCCCCATCTGATTGCCACTCCAGTTGATCTTTTTAGGCACACTGTCTAACAGAAGTCATTGATCTGATTGAAATAACCCAAATAACAACTGCAGATGGTCAGTCCAATTGTTACATTTGTCTTAATGGCCAAATTGTTTGTGAATGTGATCTTCTGTTGAATCTCTCGACCGTTCAGTGCACAACTCCTGTGATAGCTGGAGAGAGGGAAAAAAAAATGACCAGAGCAGTTTATATAATACATCATGTAAGCATAGGTGTTTTTGTTGGGGGAAACATTAGGATCTCCTTCAGAGATTGTCTGTGTTCATAACGAGTCCTGAAAAGAAGATACAAGTAAAATATTGAAGTAAAATTTAAAAAAGAAACTTGTGATTCTACTAATACCCTAACATCTTACTTTTTTAAGAAAAAATTATGAAAGTATGGTGATATTTACAGGAGACTTGGAAAATACCGAACAAAATTACATATAGTTCCACTGTACATTACAATTATTTTTAAATAGATAAATTAAGATTTTTAGTTAGAGTTTCAATATCAAACTTTCAAAAATTAATAGAACAAACAGATAGGAAAGTAGAAAGATACAGTAGACCTGGAAAGCACTATGAACTAATTCAACATAATTAAGGTTTATATAATTTTCACTCAACAACAGGATGCAAATTCTATTCACGTTCCCATGGACTATAAACTGGGAGACATGGGACTGTATCCTGGGTCATAAAACAAAGTGCAAAAATTTCGTGGTATAAAGGTATTGAAATCATACAGAGTCTGTTTTCTTATCACTGATAACACTTTACTTTTTAATTTTTATCCAATTATACATGTATTTTTTACATTGTTGGGGCCATAATATATAGTATTGATTTTCAGAGTTGCCCAAAAAAAGATGATTTGGTATCAAGGTGGCAGCCAAGTTCTTGTCTTATATACTAAACAGAGTAAGTCCCAAAGCTCTCACCATGAAGTTCCGCTCTGATTATGCAGGGCTGTGTGCCACCATACAAATTTAGCTAGGAAATGGAGATACCAGGCCGCCACCACAGTGTCCTCTGACAGACTTGTTTTCCTTCCTCCTTTTTTCCCTGTCTTTGGGAAAGGAAGGAAGTGATCTCCACCACTTGCTTAGCTTTGTGTGGCTCTAGTTAATTGCTTCCGATCTGGTCTGTTGCTGTGAAATTTTACTTTCCTAG
Seq C2 exon
GCGGCAGCGATGGCCACTTCAGCAGGAACTGTCTCAGAAGATGCCATAGAGGAAGAAGGTGAAGACGGGGCAGGCTCTCCCCGGAGCTCATCTGAAATCTCTAAACTGAGTTCCAAGAGTGCCAAGGAGAGACGGAACCGGAGAAAAAAGAGGAAGCAAAAGGAGCTCTCTGAAGGAGAGGAGAAGGGGGATCCTGAGAAGGTGTTCAAGTCAGAATCAGAAGATGGTATGAGGAGGAAGGGCTTTCGGCTCCCAGACAACAGAATAGGGAGGAAGTTTTCCATCATGAATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021339:ENSBTAT00000061543:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.116 A=NA C2=0.908
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(12.4=44.9),PF0310514=SPX=PU(19.6=55.1)
A:
NA
C2:
PF0310514=SPX=FE(50.0=100),PF119333=DUF3451=PU(29.4=68.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTGGAGGAAGCAGAGCAGAA
R:
CTGTTGTCTGGGAGCCGAAAG
Band lengths:
342-1596
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]