BtaINT0129533 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021339 | SCN8A
Description
sodium channel, voltage gated, type VIII alpha subunit [Source:HGNC Symbol;Acc:HGNC:10596]
Coordinates
chr5:28219468-28220735:-
Coord C1 exon
chr5:28220598-28220735
Coord A exon
chr5:28219573-28220597
Coord C2 exon
chr5:28219468-28219572
Length
1025 bp
Sequences
Splice sites
5' ss Seq
AAGATAGGT
5' ss Score
2.1
3' ss Seq
CCTCTTTTTCCCTCCTTTACTTT
3' ss Score
2.47
Exon sequences
Seq C1 exon
CCTGATGAGCAGCCTAAGTATGAGGACAACATCTACATGTACATCTACTTTGTCATCTTCATCATCTTCGGCTCCTTCTTCACCCTGAACCTGTTCATTGGTGTCATCATTGATAACTTCAATCAACAAAAGAAAAAG
Seq A exon
ATAGGTCTCCTCCCCGCATTGCCAGTGGCCAGAGGTCAACCCAGACGAGAGGCACTTCTGTCCCTCTGTCTGGAGAAAAAGGCCTCTCTTTCTTTAGAATCCACATCACGACGTCACTGTGGCACAGCCTCACAGTACTGTAGGCCCAGCCAGCTCGTTGTCTTCTGCTGGATTTTGCAGTGTGAGGTTTTCCACACTTATTAGACCAAACCAGCAATTTACTGGTACCAAATTTACTAGCAGTTCTTGAGGCTCTTTACTGGGTTTGACCTCCCACCAGAGGGAGGTTGGGTCCCAGAGGGTCTAGCAACAGCTGAGAAGGAAAGCAGCAGATGAACAGCTTAAGTTAGAAGTAGAAACTGTCTCGTTTTGGCATTATCTTTGTTCCTCCCTGGACCACCAGCACTTTGGGATTTGAGAGATCAACCTTGGAAAGCTCCTTCCTCACTTGTCCCAGATGGTTACTTTTTCTAAAGCAAATTGAAAAGATTACTCTTGTCATTCATTTTCTAAATCAAGTCTGTCCCAACAGACTCCAAGGAACTTCTCAAATTGCTCCCACCAAGATTTCTAAATTTTTAATATTGTCGGAAATGGGCCACTAGCTAGAACTTGAAAATCCTTTCATTTTATTTATTTTTTTTCCTTTCATTTTAAAATGTCTTTTTTAAGAATTGTATTAGGAAGCAGGCCCCCCAAAATTTATGAAGATGCGTTTAGAATCATAGCTCTCAAATTTACCCTTCCCTGAGGGTCTGTCAGTCTATTCTCTTCCTTCCTTCCTTCCCATCTCCTAGCAGGTCTCAGAAATCCCAACCTGAAAACAAAGACAGGTATATTTTTGAATTAGAATAGTTGTCAGGTCTTCCTCACTCTGGGACAGCCGTTAGCTAAACTGACCTCTGGCTTAAGAGGGTGACCCCTGGTTTACAGTGAAGGGCGTAAGGCCTTCTGGGTTCCCAGGGCTGCACCTACAGCATGTAAGAGCCAGTTGTAATTGCGCATCCTCTTTTTCCCTCCTTTAC
Seq C2 exon
TTTGGAGGTCAGGACATCTTCATGACCGAAGAACAGAAGAAGTACTACAATGCCATGAAAAAGCTGGGCTCAAAGAAACCACAGAAGCCCATCCCCCGCCCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021339:ENSBTAT00000061543:23
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=PD(15.2=76.1)
A:
NA
C2:
NO
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:
TGATGAGCAGCCTAAGTATGAGGA
R:
GGGATGGGCTTCTGTGGTTTC
Band lengths:
231-1256
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]