BtaINT0129383 @ bosTau6
Intron Retention
Gene
ENSBTAG00000038180 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr2:31032200-31036440:-
Coord C1 exon
chr2:31036093-31036440
Coord A exon
chr2:31032333-31036092
Coord C2 exon
chr2:31032200-31032332
Length
3760 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
ATATGAAATTTTTTTTTTAGGGC
3' ss Score
9.43
Exon sequences
Seq C1 exon
TCTTTACTGAGCATCCGTGGCTCCCTGTTCTCTCCAAGACGCAACAGTAGGGCGAGCCTTTTCAGCTTCAGAGGCCGAGCCAAGGATATTGGCTCTGAGAATGATTTTGCGGATGATGAGCACAGCACCTTTGAGGACAATGACAGCAGAAGAGACTCTCTGTTTGTGCCGCACAGACATGGGGAGCGGCGCCACAGCAACGTCAGCCAGGCCAGCCGTGCCTCCAGGGTGCTCCCCATTCTGCCCATGAACGGGAAGATGCACAGCGCTGTGGACTGCAACGGAGTGGTCTCCCTGGTTGGGGGCCCTTCTGCCCTCACATCTCCTGCTGGGCAGCTCCTACCAGAG
Seq A exon
GTGAGACCAGTGAAACCTGCAGCTGTTGGGAAGGGAGGTGTGGCTGGCGCAGGCAGGAATGGTTTTCTATTTCCACCTTTATGAGTTTTAGTGAGTCTACTCTTCAAAGGCCAAGGGTCAGTTCAGTCAAATTATGAACTTACTTTGTCAAATTGTTCCTTTCAGACTTTTCTACAAATGAATTAAAAAATAGGTTGAATCTCATCGACTATAATGAGAAGTCCTCCATCATTATTATCACAGTATCAAACTTGCCAAAAATATAGCAACAATTTATCATGCATTATTTGTAATTAATATAAGCAAAATAAATGCAAGAAATGATATAAATACCCATCTTAAGCATCTTGTTATTTCTAATCCTTTAAAAGAAGAACTTGATACTTATACTTGAAGTAGATAGTATTACTAAATGTATCTAAATTCTGCAATGCAACGTTCTTCCTCTTGGCAGGTCAAGGTGCTATAACATTTTAGCACCCAATCAAATGACCATCGTACATTTATATGGTAAAGGAGCCACTCGAAGTGCCTGGTAAAGTCATGTGTTATAACTGTTAGAGCAGATTTCAATTTTTATATTACTGTCCTGAGTTTTTTAATAAACATAATGGCCAGAAATCATGCATACGGAACTTAGTGGAATTTAGTTTCATTAAATACAAGACACTGGGATATATTATTGACAAAAAAGTATAAAAAATTCTAGCAATTTGGTTGTACTTTATAGTTTACCAAATCATATTAAGTCTTCTTTGTATGATTTTTTTTTTTTTTGCAAAATTTTACTCATTATAGGTGGATAAGCTCTGTCAGTCACATTAAAATCATATGGAGTCAGCTTTCAGTCACCTAATAGAAGAACTTCTTACCTTGGATTATAGAAACAGCCATTGATCATCTTTACTTTTTTTGCCTGGCCTCTCCCCACCACTTCTCCCAGAGAAATATTCAAGTATCCTAGAATCAGATCAAATCATGAATAAAAATAGAACTTTATTGTGAAAAAATCTGGAAAAATACAAAAGGAATATCAACTTCTCTTAAAAAATAATCATGCCTAACTATGTACCAGACAGTGTCCAGAACACTTTACTTGTATTAATTCATTTAGTCCTCGCAATAATGCTTTATCATAGTTATTAATATTACCTCCATTTTACAGAGAGGAAACTGAAGCCTGTGCATGATGGAGCTAGGATTTGACCCTATATATGCTGGCTACTGAACCTACATTCTATCCATATTGCAATATTACCTCCCATTAATTTTCTTTAAATTTTCTTAAATGGAAAAGAAGAGATGATTAAGGAAACAAACATTTTCATTTTTACCCAATGTTTCTCAAAATATATTTCGTCATCAGACTACTTGCCTCAGAATTCCCTGGGATACTTCTTAAAATGGAGATTCTTCATTTCCCCCTCCCTCCACCCCTGGCAGCCACCATTCCCCTCTGCTTCTCTGAGTTTGATAACCAAAGGGTCCAGCGTTTCAGTTATGCAAGATAAATAAGTTCTGGAGATCTACTGTATGGCATAGTACCTAGAGCTACGAATACTAAATTGTAAACTTAAAATTTGCTAAGAAGATAGATCTTATGCTGTCTTCTCAACCCAAATAGCAACAGCAACAATGATAAAGCAGTGAAAGAAAACTGGAAGGTGATGGAAATGTTTATGAACTGATAATGCTGATGGTTCACAGGTATATACTTATCCTTAAACTCATCAAGTTGTGAGCGTGAAGTATACATAGCTTTTTACATGTTGATAATACTTCACAAAAGTGGTTTAAAGAAAGAAATGAAGACTTTTGGGCCCACTCAGATTTACTCAGACCCAGACCAAAAGAAGAAATCAGTGATTTCTTCTTTCTTGACAAGCATCCCACATGGCTCTTATACATAATGAAGTATGAGTATTTCTGATCTTGATAAATGCTAATTGGGAACACAAAAATAAATCTACAACTTCTTTACATAAATGCAAGAGAATTTCAGTCCATCAGAAAATATTTAGTGTTTATCAGTAATTATCACTCCTGTCCTATCACAGAGGGTGGAATAAATCTCTGAAGGTAAATTCAGGCAGTTTAAACAAAGCCTAGTTTAGTATCTGTTTCCTGCTGTCTGGTGTCCATCATTCAGTGTTGCAATCAAGTGCTGTGAGGCAGGGCACCGCAGCATGGTATAGCAGGAGCTGCAGAGGCAGACCAAAGCTGTGGCTTTGCAAGACTGCAGAGAGAAACAACAGAAAATAAACAGCTGTGGGCAAATGCTACCTTCCAGACCACACAATATCCTGCATTTTCACATTAATTCAATTGAAGCAATTTAATTTAAGAAATAATTTCCTTGGTAATATCATTACAGAGTTTGAAATCTAGCACTAAAAATTAGACAAATATCGGATAACATACATGATTTTGTATAGAGCAGAAGGGACCAGATGGCCTTTAAGTGACCCCATTTTTTTCCTCCAAACTTTGAATTTCTCTGATGAGGCAAAATATTTTCAGTTCTGATGCAACATTAATAGGATGTTGCATTCTTAATAATTAACTAAATAATAATTAAACTAAATTTTATAACTTTATCTTACACTTAAAAGAGAACCCATCCTTGGCATTGAAACTCTAATTTAAGGCAAGACATAATAATGGGGGATCTTTGATTTTTAGCAATGATATAATGATTTGATTCTTTTCTATTCCAAAAAAAAAACTCACCAGAATTTCAATATGGGCAGAAATTTATTCCTACTTCAAGAGTTCAAACAATGAAGTTAGTGATCACAGGAGAAAAACGGGGCAAGACTCAAGCATTTCTAATGCAAGTCTGAGTGCTAATAATAAAGAAGTCACTTTTATTCCTCTGAGGATTTTCCTTATTTATATAGCAATATGAGTACTGCTCACCTACTTTGTTGTGCTATCAGTAATTAACATTATTTTATTAACCTTTTTACCTCTAATACATACATAGTCAAAAGCAGAATTTCCACTCCATTAATAGGACTGTCATTAATGAGGATGAACATTCATTTAGGTCACCCTAAAATTAATTTTACCATGAAAGAAAAGTAAAATTCATGAGAAAAAAGTAACTCCTCTCTGAAAAAAAGCTTTTTAAATAAAAAAAGTTGTCTCTTAGAATTGAAAATATTTAGCCTCATCAGGGAAAGGCAAAATGTGAAGGTAAAAAAGTGGGGGTGCTTAAAGGTCATCTCATCCCATCTGCTCTATACAAAATCATATGTGCAGCCCTGTATCTGTACCTGTCCATAATGAACAGAAGCATTTTAACATGGAATTCACACTTTCGGAGAGCTACTACTGATGCATATTAGGGAAACCTGTAAAGTTCTTTTCGTTCATTAAACCACATGAATATATATAAGGATCTAATAACATGTGAGTAAATCAAGGAGTAATATGTTTCAGTTTGAAGCTCTAGATAGGATTGACTAAAATGCTAAAATGTTCTATCCTGAAGCAGGATCCCTCCAGCCCAAAGCCCCAAGATGGAGGAATTAGAAAAGTCCATCTTGATCACAAACCCAGGCATCCCTGAATTCTGAGAATATGATGGGCTTTCAAACCCTTCCCAAGAACAATGATTCTAGCAATGCCTTAGTGAGCTGTTTACATCTGACAAAGCACAGTGAATATTTAGCTAAATAACACCTATTGTGGGAACACTTTGGGTTTTGCTGCCCTTTAAAAATAATAGTTATTTCATATGAAATTTTTTTTTTAG
Seq C2 exon
GGCACAACTACTGAAACAGAAATAAGAAAGAGACGGTCCAGTTCTTATCATGTTTCCATGGATCTTTTGGAAGATCCTACAGCAAGGCAAAGAGCAATGAGTATGGCTAGTATTTTGACCAACACCATGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038180:ENSBTAT00000061380:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.560 A=NA C2=0.244
Domain overlap (PFAM):
C1:
PF119333=DUF3451=FE(51.3=100)
A:
NA
C2:
PF119333=DUF3451=PD(16.5=82.2)
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:
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]