BtaINT0129385 @ bosTau6
Intron Retention
Gene
ENSBTAG00000038180 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr2:31024907-31027973:-
Coord C1 exon
chr2:31027735-31027973
Coord A exon
chr2:31025081-31027734
Coord C2 exon
chr2:31024907-31025080
Length
2654 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGG
5' ss Score
9.68
3' ss Seq
AATAAACATTTCTCACTTAGGTC
3' ss Score
6.94
Exon sequences
Seq C1 exon
AACTTGAAGAATCCAGACAGAAATGCCCACCGTGCTGGTATAAATTTGCTAACATGTGTTTGATTTGGGACTGCTGTAAGCCATGGTTAAAGGTGAAACATGTTGTCAACCTGGTTGTGATGGACCCTTTTGTTGACCTGGCCATCACCATCTGCATTGTCTTAAACACCCTCTTCATGGCCATGGAGCACTATCCCATGACGGAGCAGTTTAGCAGTGTGCTGTCAGTTGGGAACCTG
Seq A exon
GTAAGGCTCACTGAGGATTACTCTGCTCATTGAAAGAGTTTATGGTTACTTTAATGAATTTCACATATCACTCTCAAATTAAATATGAATTAACTGGCCATATTTACTTGGGCAACAAAAGTTCAGCATTACTTTTTTATAACAAATTATATTGCTTCATTTAAGCAGTAGAAAAGAGTCAAAGATTTTATTTATAGTTTGACTTAGAATTAAATATAAATTGCCCATTCATTAAAAAGATCATTATGAATTACAGGGGACATAGATCTATGGTAAAATGCTGATGTGTTCCTCAGGTATTTAGAATAGACTCTTTCAGACATGTTTACATTTGTCAAACATATTAAGTCAGATAATTTTGAAATATCTGTTCATACCTGAAAATGGATTTTTAAAGGAAGAAACATCATATAGAGGTTATTATTTCTGTTTGAATTTGTCCTATACATTTTAGGAACTTATAAATGATTCAGTTCAGTTCAGTTCAGTTCAGTCACTCAGTCGTGTCCAACTCTTTGTGACCCCATGAATCGCAGCACGCCAGGCCTCCCTGGTCCATCACCATCTCCCTGAGTTCACTCAAACTCACGTCCATCCAGTCGGGGATGCCATCCGGCCATCTCATCCTCTGTCATCCCCTTCTCCTCCTGCCCCCAATCCCTCCCAGCATCAGAGTCTTTTCCAATGAGTCAACTCTTCGCATGAGGTGGCCAAAGTACTGGAGTTTCAGCTTTAGCATCATTCCTTCCAAAGAACACCCAGGGCTGATCTCCTTCAGAATGGACTGGTTGGATCTCCTTGCAGTCCAAGGGACTCTCAAGGGTCTTCTCCAACACCACAGTTCAAAAGCATCAATTCTTCAGTGCTCAGCTTTCTTCACAGTCCAACTCTCGCATCCATACATGACCACTGGAAAAACCATAGCCTTGACTAGACGGACCTTTGTTAGCAAAGTAATGCCTCTGCTTTTGAATATGCTATCTAGGTTGGTCATAACTTTTCTTCCAAAGAGTAAGTGTCTTTTAATTTCATGGCTGCAGTCACCATCTCTAGTGATTTTGGAGCCCCCAAAAAATAAAGTCTGATACTGTTTCCCCATCTATTTCCCATGAAGTGATGGGACCAGATGCCATGATCTTTGTTTTCTGAATGTTGAGCTTTAAGCCAACTTTTTAACTCTCCTCTTTCACTTTCATCAAGAAGCTCTTTAGTGCCTCTTTACTTTTTGCCATAAGGGTGGTGTCATCTGCATATCTGAGGTTATTAAGTTTTGCATATTTTTTAATCTAAAATTCTATACTAACATTCATGGCTACATGGTAGAGTGATAGAAATGAAAGTCAAAATGAATAAATTCAGGTAACAAAAATATATTGATATCAATGTAAGAGGTTTATTAAGTTCTCATGAACTTCCCACCTTGATAAATGAATATATAGACAGGTTCTATATAGATAGTAAATGATATATTCTGAAGGATGATACACAATATTTTTAGACTCTGAAGTAACCATTATTGTTCTGTTATAACCAGATAGGTCTTAACCGATAAAGTTACAATATATATGCTGACCTCTTGTTTTGTACCAGGCATTGTGCTAAATGGTTTACATAAAATCCCTCTTTCTAGGTACCCACAAAGTCAGTCCTCAGGTAGATACTATGAATGTCTGCATTTTACAGTGAGGGGATCTATACCCATGAGAAATTGACAGAGCAATGAAAGCTCTAAATACTGTAACAGAGACTCTAAAAGATATTTCAGAGACTGTTTTAGGCTGTGCCCCAAAATCACAGAACTTTAGGAAAGGACAATAATGGTACCTAGTCCAAATTTTTTCACATATGTAGGAATCACCTCAACATTATCTATAAAAAAGTGAGCAAGGGATAAAATAAGCTTTATGGAGATGAGTATTAGGAAACAGCTCAAATGAGCTTAAGCAAAAATAAGCAAAATAAATTTAAAAAAATAATTCATTACTTCAAGTAACTAAAGTCCATTTGGGCATAGCTCCAGGTTTTAATCTGTCTAGATTCAAATTCCCAATCAATGTCATTGGGAGTTAGCTTCTTGCCAGACTTTTCCCAGTATGTTTCTTTCATCTCTGGCTGGATATTCTTTTGAGGGTAGTGTTCTACCAACTTCTATCCTACTGACACCGCTCATTGAGCAGAAGGAGTATGCCTCTTAACCAGTATTTCTAACACAACAAGCCCAAGTATTGAATACCATCAGCCTGGTTGGAGTTACAGAACCATTTCTAAGCCAGTCAATCTGGTTCTAGGGTTAGAATGCCCTAATAGGTAATCATTTGGTGAGTTTTTGGAAAGCTAGGGAGATCAGAGGAAAAGTCAGGGTGTTGACTGCAATGAGTAACCTGAACCTTTCACTTAAGAATATAAAAGTGAGAATATTAGTTTTACTGTCTGTCTTAATTCTTATATTCTTCATCACTTGATAAACCTTGACTATAGTAAAAAATTAAATATCAACTTGAATACAAACCATTTGAGGATACTAATTTCCTGGGTCTAAATCAATTTTTAAAACTCAAAACTAAATTGTGATTTGTTGGGATTAAATTAAATTGCTTAATAGTTATTTATGCTTTCAAGAGTCATCACTCATGTAATAAACATTTCTCACTTAG
Seq C2 exon
GTCTTCACTGGGATCTTCACAGCAGAAATGTTTCTCAAGATAATTGCCATGGATCCATATTATTACTTTCAAGAAGGCTGGAATATTTTTGATGGTTTAATTGTGAGCCTTAGTTTAATGGAACTTGGTTTGGCAAATGTGGAAGGACTGTCAGTTCTCCGATCATTTCGACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038180:ENSBTAT00000061380:14
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=PU(1.6=3.8)
A:
NA
C2:
PF0052026=Ion_trans=FE(30.0=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]