BtaINT0129447 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004770 | SCN4A
Description
sodium channel, voltage gated, type IV alpha subunit [Source:HGNC Symbol;Acc:HGNC:10591]
Coordinates
chr19:48798842-48800674:-
Coord C1 exon
chr19:48800552-48800674
Coord A exon
chr19:48799121-48800551
Coord C2 exon
chr19:48798842-48799120
Length
1431 bp
Sequences
Splice sites
5' ss Seq
AGGGTGGGT
5' ss Score
5.37
3' ss Seq
TCCCCACCCCCGGCCCCCAGGTG
3' ss Score
9.73
Exon sequences
Seq C1 exon
GTCTCCATCATCAGCCTGGTGGCCAACTGGCTGGGCTACTCGGAGCTGGGACCCATCAAATCCCTGCGGACGCTGCGGGCCCTGCGCCCCCTGAGGGCACTGTCTCGATTCGAGGGCATGAGG
Seq A exon
GTGGGTGTCGAGGGGGACTGTGAGTAGGGCTAAGGATTGGGGGAGCAGCCACAGCTTGGAAGGGGGCTGGGGGCGTGTCTGTACTCTGGCCACCACCGGGAGTCAAGGTTTGGGGGTCCCCCAGGCAACTGATAGCAAAAGGAGAAGCAGGTGGCAGAGGATGAGATGGTTAGATAGCATCACTGACTCAATGGACATGAATTTGAGCCAACTCCGGGAAGACAGACGAGCCTGGTGGGCTACCGTGCATGCGGTCGCAAAGAGTCGGACACGACTGAGTGATTGAGCGACAACAACAACAAAAGGCACCCCCACACACCAGCCCAGGTGCCCGTTCCTGCCCGCAGCCCCCTCCTTCACTCCTCTCTGCCACCACTAGGGGGCAGCAGAGGCCGCAACCACTCCCAGGAAGGGCCTGAGGGCACCCAGGCAGGAGAGGAAGGAAAGGTCTGTGGGTTTATAGGTGACTCTCCCCAGCCTCAGACTGGGGCCCCCCAGGGCTCCGAGCCTGCCCATCCTTCCCTCAGGCCGCTGAGGGCGGAAGTGACAGGTAAATACAGGGTTCAGGCAAGACCAAGGGGACTTCCCCGGCTAAGGCTGGAAGTAGGGGTTCTGTTAAGAGCAAGGCCTACTCTGGCGGGGACAGACTTCCATGAAGCAGATGATTGCAGATCAGCAGGGCACTCAGCCTGGGGTCTCCCATACAAGAGCCCGGCCCAGCCAGGGACCCCTCCCCACTGGGGGAAAATGACCTGGCCATGGCCACACAGCTGGTTGATGCCCCAGCCAGGAATAGAATTGCCCTGGGCATCACCGGGCTTACACCACTCACTTTGTCTGGAGGTCATGAAACCACTTCTCCTTGAAAACAGATTAATTCTCAGATTCAGCTCAGCCGGAAACAATGAGGTTGGCCTGTGTGGCCAGGGCTGGCTGGGCACAGAGCTCCAGTCCCCAAGGTTCCTGCTGCTTCACAGGCTCCGTTCTTTTCTGGGTCTTTGTCTCTAATCCTGTGAGCAGATGAGCCGGGGGCCAGGTCACGGGGACTGAGTTTCCTATGGGGGCCGAGGAAAGAGTGTTTGTCTCCTGCCTGGTGACCCATGGCCGGGCTGCTTCCAGAGAAGCCCAGCTCCCCACCCTGGGCTGTTGGCTCCAGCGAAGCAGAGAGCCCTCTTCAGCCAGCAGGCCGGCAACCCCCTACCCCTGCTCCCTGCTCCCACCATCCCCCACCCCCACAAAAAGCCCAGTAGACTTCTCCTGCAGGCCTGGGTTCATTCAGATCAGCCCTCCTCCAGGAAGCCTTCCCTGCCTGGTCCCTTGGTTGGTGTGGGTGGGGAGTCCTCTCCCAGAGGAGTCTGGGTGATGCCCCCTACCCTGCTGCCTGGGAGGGGATCTGGCTGTGACTCCCTCCTCCCCACCCCCGGCCCCCAG
Seq C2 exon
GTGGTGGTGAATGCCCTCCTGGGAGCCATCCCCTCCATCATGAACGTGCTGCTCGTCTGCCTCATCTTCTGGCTCATCTTCAGCATCATGGGTGTCAACCTGTTTGCCGGCAAGTTCTACTACTGCATCAACACCACCACCTCCGAGAGATTCGACATCACCGAGGTCAACAACAAGTCCGAGTGCGAGAGCCTGATGCACACGGGCCAGGTCCGCTGGCTCAACGTCAAGGTCAACTACGACAACGTGGGCCTCGGCTACCTCTCGCTCTTGCAGGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004770:ENSBTAT00000006265:18
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:
PF0052026=Ion_trans=FE(17.5=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(40.4=100)
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:
TCTCCATCATCAGCCTGGTGG
R:
TTGACCTTGACGTTGAGCCAG
Band lengths:
358-1789
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]