BtaINT0129525 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021339 | SCN8A
Description
sodium channel, voltage gated, type VIII alpha subunit [Source:HGNC Symbol;Acc:HGNC:10596]
Coordinates
chr5:28236301-28237614:-
Coord C1 exon
chr5:28237144-28237614
Coord A exon
chr5:28236419-28237143
Coord C2 exon
chr5:28236301-28236418
Length
725 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGG
5' ss Score
6.35
3' ss Seq
CTTTCTCCTTATGTATCTAGAAA
3' ss Score
7.42
Exon sequences
Seq C1 exon
GTACTGAACCTGTTTCTGGCCTTGCTTCTGAGCTCCTTCAGTGCTGACAACCTGGCAGCCACAGACGATGATGGAGAAATGAACAACCTGCAAATCTCCGTGATCCGGATCAAGAAGGGCGTGGCGTGGATCAAACTGAAAGTGCACGCCTTCATGCAGGCCCATTTCAAGCAGCGCGAGGCCGACGAAGTGAAACCTCTGGACGAGCTGTACGAGAAGAAAGCCAACTGCATCGCCAACCACACCGGCGCCGACATCCACCGGAACGGTGACTTCCAGAAGAATGGCAATGGCACCACCAGCGGCATCGGCAGCAGCGTGGAGAAGTACATCATCGACGAGGACCACATGTCCTTCATCAACAATCCCAACCTGACTGTGCGAGTGCCCATCGCCGTCGGCGAGTCCGATTTTGAGAACCTAAACACCGAGGATGTCAGCAGCGAGTCGGATCCTGAAGGCAGCAAAGAT
Seq A exon
GTAAGGTCCCAGCCGAGAAACCTGTCTTGATCCTGTGTAGGAACAAATGATCAGCCTTGGGACTGGTCCAGCCATGGGCCTGGCAGAGAGATTTTGGAATAGCCAACTCTCAACTTCGAACTTTTGGGCTTCCCTGACGACTCAGTAAAGAATCCGCCTGCAGTGCAGGAGAACTGGATTCAATCCCTGGGTTAGGAAGATCCCCTGGAGAAGGGAATGGCCACCCACTCCAGTATTCTGGCCTGGAGAATTCTGTGGACAGAGGAGCCTGGCAGGCTACAGTCCATGGGGACACAAAGAGTTGGACAAAACTGAGGGACTTTCACTTTACTTTCAACTTTGAGAACCAATTCTACCCACCCCCAGACGAGCTAGATTCCTGAGATGGTCCCTCTTGCTTCTGAGTCATCTGGATCAGGGGCTGGAGGAAACCCTCGAGTACTTCCCTGCCATCAATCTGTCTGAGCTGTACCACTGAGACCAGCTATAGGCACCTTCTACTTAGGGTGGACCCCCGTCATCTGCGAGCAGGCTATGATGTTGTACGCCCTCCTGACAGGTTCTGCGGGCCCTGTGATAATTGTCAGCCCATGGTGAATTGCATGATGATGAGTTTCTAGCCTGAATTGTAGCTGCTGCGTCATCAGTACCAAAGGCAGTGTAGTCAGCATAGAGCAGACGTGCTGCTATAGCAATGCTTCTCTCCTTTCTCCTTATGTATCTAG
Seq C2 exon
AAACTGGACGACACCAGCTCCTCTGAAGGAAGCACCATTGACATCAAACCAGAAGTAGAAGAAGTCCCTGTGGAGCAGCCTGAGGAATACTTGGATCCAGATGCCTGCTTCACGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021339:ENSBTAT00000061543:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.210 A=NA C2=0.575
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.2=5.1),PF065128=Na_trans_assoc=PU(61.0=84.7)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(17.9=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:
CTCTGGACGAGCTGTACGAGA
R:
TGCTCCACAGGGACTTCTTCT
Band lengths:
352-1077
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]