BtaINT0129390 @ bosTau6
Intron Retention
Gene
ENSBTAG00000038180 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr2:31001192-31002672:-
Coord C1 exon
chr2:31002518-31002672
Coord A exon
chr2:31001366-31002517
Coord C2 exon
chr2:31001192-31001365
Length
1152 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGT
5' ss Score
8.37
3' ss Seq
TGGAGTTTTTTCACTTACAGGCC
3' ss Score
8.54
Exon sequences
Seq C1 exon
ACTGTGTGCGGAAGTTTAAGTGTTGTCAGATAAGCATAGAAGAAGGCAAAGGGAAACTCTGGTGGAACTTGAGAAAAACTTGCTATAAGATAGTGGAGCATAACTGGTTTGAAACCTTCATTGTCTTCATGATTCTGGTCAGCAGTGGGGCACTG
Seq A exon
GTAGGTAACATGATCTGCTCCTTTACTTTTACCTGAAACCCTTTACCTTTCCCCTCAATCAACCTCCTATTGCACAAAAAGGTGTTTTCACAAGAAGGTGTTTGTGAAGATGAGAGACATTGTATGATATTTTTAGCACAGTGTGAGAGGCTCGCTAAGTAGCAACTTTTATTGTTCTGCCATAGGCCTGAGATTGAATCAAATTTAGATCAGTATGATTTTTTGTGAATATTTAAAGTACGACCCTTCTAACTTTTAGTCATCAGAACCAGTTCCTATTAAGAATCAATATGTAGACAGGGTATGGGATTATCAGCTAAGTATCAATCTGCTTAGCATAAGCCCCATTGCTCTGTTCATGCCAGTTCACTAGGGCCATCCACATTGAAGGGTAAATAGATTAAATTACCCACAAGCAGCAAAGTGAGATCATTACAGACTTATTTTATATCTGATTTCACTCAACAGAATGGTCAAAAAACCAACAAAAATAAAAACCAATTTCTCCTTTCTCCTTGATCCAGATCACCAAGTCCTGATAGTTTTTCCTGTAAAAGGATTGAATTATTAATAGACAAATGCTCTTTTCATTCCAGAAGACCCAGGGACTCCTGCAAATGAGTTCCCTTGCCCTTTCCAAAGAGCTCTGCAGAATAGTGGCAAAGGGAGGTTGCCACTAAGGGACAACTATATTCATGCTCAGATTGAGCTAGAGAGATAGAGAAAGCAAAAGACTAATCCCTGCCCCTTCCCCAAGCTAAGGGGACTCTTTGTCTTACATTTTCATCACTAAATGGGTTTAGGGTTACAGTCAAGCAACTCTGCACTGAGCAAAGCATATATGCTCGCAGATGGTTTTGTGCCTCCTATTGTAGACAGAAGCAGCTGGCAGTGTCTCAAAAATTTTAAGCTCTGATGGGATATCCTGATACCAAAATTTAAAGATTATTTGAATTAATTTGTTGGCTGAAATGCCCAGTTAAGAGTCACTTGCATACAGACAACTATAGAGCAAAATGCAGCTCTGGGAAGCATGAAGTCTTCCAGCCTTAGGCGCCTGAAAAGATGCTTGCAAGCATGAGTTTTTCTAATAAAATACCAATTAGAGACAGTTTATGACAATGAAATTCAATGGAGTTTTTTCACTTACAG
Seq C2 exon
GCCTTTGAAGATATATATATTGAACAGCGAAAAACCATTAAGACCATGTTAGAATATGCTGACAAAGTTTTCACTTATATATTCATCCTGGAAATGCTTCTCAAGTGGGTTGCATATGGCTTTCAAGTGTATTTTACCAATGCCTGGTGCTGGTTAGATTTCCTGATCGTCGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038180:ENSBTAT00000061380:19
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:
PF065128=Na_trans_assoc=PD(19.8=84.6)
A:
NA
C2:
PF0052026=Ion_trans=PU(17.0=67.2)
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:
ACTGTGTGCGGAAGTTTAAGTGT
R:
GACGATCAGGAAATCTAACCAGCA
Band lengths:
326-1478
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]