BtaINT0129393 @ bosTau6
Intron Retention
Gene
ENSBTAG00000038180 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr2:30996146-30997745:-
Coord C1 exon
chr2:30997623-30997745
Coord A exon
chr2:30996428-30997622
Coord C2 exon
chr2:30996146-30996427
Length
1195 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGA
5' ss Score
9.21
3' ss Seq
CCATCTCACTGCTGTGCCAGGTC
3' ss Score
6.46
Exon sequences
Seq C1 exon
GTCTCATTGGTTAGCTTAACTGCAAATGCTTTGGGATACTCAGAACTTGGTGCCATCAAATCCCTCAGAACACTAAGAGCTCTGAGGCCGCTGAGAGCCTTATCCCGGTTTGAAGGAATGAGG
Seq A exon
GTAAGACCAAATGCTTTAGTATTTGTTGGAATTATAATTGAAAACAGGGTTTCCCTGATGGGTGAGGTGGTAAAGAATCTGCCTGCAATATGGGAGACCCAAGTTCCATCCCTGGGTCAGGAACATCCCTTGGAAAAGGGAATGGCTACCCACTCCAGTATTCTTGCCTGGAGAACTCCATGGACAGAGGAGCCTGGCGGGCTGCAGTCTATGGAGTCGCGAAGAGTCAGACACGACTAACACTTTCAGTATAAACTGCTGTTTTGAACCTTAGACGTGACACATCCAGGTTAAATTTGTCTTCTACATTCATATTCATGTAACCAATCAATCAGTAATATTTGTCAGACATCCATAAATGACACTGTTGGAGGCACTCACACAACATAATCCCTGAATGATGACTTCTAATTAGAAGCAATGAGATTGCTTCTACCTAGACTTTTTTACTCTGTGGGAAATTTCTAGCATGTTGTGTAGACTTCTGATGTGAGTCAACATTAGTTATGTTCATTCCAGTTTATAAATGTGAAGGAAATCCCACTCACTGTAATTTGAAACCACCAAATCATTCCTCATCGTTTTTCTTCCCTGCTCCATATGATGTCTTCTGAGCCTTTTAAAGTCCAACCCTGGCCTTTTTGCTCTCAAACAAAGGCTGAGCTAGCTAAAAAGTAGATCAGCTGTGGAAATCTAACACTCATTTAGAAAGGTGGTACAAAGGAACCGGGAGGCATTTGTACTGCCAGTTGTCATCCCCTGAGGCATAAAACCTGAGACTACATACCCTCAGCACTGAGGAAATTATGATGCCCTGTCCAGGTAGGTTTGGCCATTCAAAAAGGAACTTTTAGGTGTTTTGTGATGTTTTAAAATAGTTACTTAGGATTTTCTTTGAATGTTGCAGACACAACCAGAAATGGATGATATATGGAGGTATATGTGCTTCTGTATTTGTGTGTGTATGGTATCATAGAAAGGAATGGCTAGCTATTAAATTCTTTTCAGCTTACCAATTTAAAAACCTGTTTTACAGTAGCTATCTTAATTTTTTAAAAAGAGAATCAAGCTTTCAGTACTAGAATGATTTTTATATTTTCTCTGTTGAGTTTTCATGTATAATGACCTACATTTCTAGTTCTTCCATAGATCTGACTCTCTTTTCACTTCTTTCCCCATCTCACTGCTGTGCCAG
Seq C2 exon
GTCGTTGTCAATGCTCTTTTAGGAGCCATTCCATCCATAATGAATGTACTTCTGGTTTGCCTGATCTTTTGGTTGATATTCAGTATCATGGGAGTGAATCTTTTTGCTGGCAAGTTTTACCACTGTATTAACTACACCACTGGAGAAATGTTTGATGTCAGCGTGGTCAACAATTACAGCGAATGTAAGGCCCTCATAGATAGCAACCAAACTGCCCGGTGGAAGAACGTGAAAGTCAACTTTGATAATGTGGGACTTGGGTATCTTTCTCTGCTTCAAGTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038180:ENSBTAT00000061380:21
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(40.6=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:
AGCTTAACTGCAAATGCTTTGGG
R:
ACTTTCACGTTCTTCCACCGG
Band lengths:
347-1542
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]