BtaINT0129389 @ bosTau6
Intron Retention
Gene
ENSBTAG00000038180 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr2:31002518-31006733:-
Coord C1 exon
chr2:31006613-31006733
Coord A exon
chr2:31002673-31006612
Coord C2 exon
chr2:31002518-31002672
Length
3940 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
TTTGCTTTGACATATTTTAGACT
3' ss Score
6.68
Exon sequences
Seq C1 exon
AAGCTAAATGCAACTAGTTCATCTGAAGGCAGCACAGTTGATATAGGAGCTCCCGCTGAGGGGGAACAACCTGAAGCTGAGCCTGAAGAATCTCTGGAGCCTGAAGCCTGTTTTACGGAAG
Seq A exon
GTGAGGAACAGAGCACGTACGCTCCTTAGACCTCTCTGATCTAGCTGTCTCTTCCCTCCCTCCCTGGCTCGTTCTAACCCTCTATAGGTATCCAGCAACTGTACATTTACTTGTTTGTTTGTTGCTTTTTCTATATCAAAGCATAGATGATTTTTGAAAAATGAAGATTTAATTTATGGCATCAGATCCAGTTTTCTATTTTTGTGAATCCTGTTCTACTCTAAGAAATGCTGCTAACTATCTGGGTTTTTTGGTGGCCTTGTAGATAGAGTCTTTGATAGGCAAGAAAACCCAATCATACATATTTCTCTCTGCCTTTAAAAAAATAAAAGAAAAAAATTTAAGTTGAAGGAGTAGTTTATTGTTTACTGTTTTGTCAGGTTATAATGGTACGAATTGATTAATTTACATTTAAAGTGTCCATGAACACTTTGCCATTTGATACTGGAACACATTCTTAAATAAATGTGGTTATGTTATTAAAAAGGAACTGTCCATGAATAACAATTACCTGTATCTGTCAAGGTCAAATATATATTATTAGTTCTGAATGATACTAGATAATCAATAATGAAATATCAAAATATACTGAGTGATACAGTATGGGGCACCACGTCACTGGAGTAATACTAAGAGGATTTTGTGAAGAAAGCTAAAATTATGTTATTTGAGGTGTGGATCAGTTGTCTCTGCAACAATAATGTGTACCAAACCACTCAAAACTTATCATGTAACAAAAATCGTATCTTTGCTCACAAGCCCATGGCTGGCAAGATGATTTTGCTGATCTTGGTTGGGATTAGTCCTAGAGCTGAGGTCTTAGATGAGACAATTGCCTGACTCAGCTCCATCCACACTCTGGCCCAGGCTTGTTCTCATGGTGAAAGCAAAGGAGTGAGAGAGGAAGCCTAAATGCCAAGCACTTGTCAATCCTCCACTTACATCAGGTTTTCTCAGTCCTGTTCACCAAAGCAAAAGTGCAATCCAGATTCAATGTGGGAGTGTACTACAAACAAAGAGGCATAAATATTAGTACAATAGCACAGACCATGACAAATCTCTATTGTAGGTACAGAACTGTTTCTCTAAAACCCTAGGAATCACTTCATCCTTAACTCATTTTTTTGGTTAATATCTATTTAATAATTCATCCTATGTCTTAGCCCCAAATTCAATATCATATAATAAATGCTTAAACAAAAGTTTATTTTAATAATGATGATAGTAATGCTATTTAATTACAACTAATTCTAGAAGTGTTCCCTTCATTTTCATTTCATTTAAGAACATTAAAGCTGTTTAATTTGAACTTTAAGCTAATTTTAAAAATATGTGATTATGCAAGTGTCAAAATTGATGTCAATAGATTTAAGAGTTTTGCAGATGAGTACATTACATACACCTATTGCTTTTGGACTTGAATGCATTAGAGAAAACAAATATTTATGTATTCATTGTCAATTTTTAAATTATTTCAGAGGAAGAGATATTTTTTCAGCATGTTATGAGGGAAGCCACTTTTTTCTACTCTTTCTTCCAAAATTCTGCACATATATCAGTGAAGTTAGTTGATTTTGAAAAAAAATTATGACTTCACAAAACATTCAAGAGGTTAGATATATCACAAAAATAATTTATGTAGTATTAGTTGTTATTCTTTCCCAGACAATTAGCTTATTTTTAGGGTTACAATATATTAATAATAATATTTATGGTAATATCAACATTTGTTTTTTGTGAAGTTAAAAAACATTTCAATATGAAGTATAACCAACCATAACATTATAGAACACAATAATAAAAAATATGTAGACACTCACCAACCAACGAGAAGGCAATGGCAACCCACTCCAGTGTTCTTGCCTGGAGAATCCCAGGGACGGGGGAGCCTGGTGGGCTGCCGTCTTTGGGGTCGCACAGAGTCGGACACGACTGAAGCGACTTAGCAGCAGCAGCACCACCAACAACCAACTTTAGCAGTTTGAATATTTTTGTTTTATTTGCTTCAGGTTTTTTGTTTAAGAATAAATCAGATACAGATTTGACCCCCTTTGGACCCTTTCCTTATCCCATCCTTTGCTTCCCTCTCAGAAATGAACCAGTGTCCCAAATTTAGCATTTATCCTTCCTGCTAACATTGATCTTTTTATATTGAACAGTATTTTTTCATCTCATATCCTCTTTAGGGGAAAAAAAAATAATAATTTCAGTTCCACCTAGTTCATTACAAATATTTTCAAGGCATGTTACTCTTCTTAATCCTTTGGGAGACAGAAATGTGAAAAAGATCACCCTCAAAGAAACAAGAAATATATGCTATTTATTTATTACTTGAAACACTAATAATATTTAAGAGGACTTCATTAAATTTTCATGAAACAAATTATATGATCTGGCTGACATTATAAAGTAGCATCTGATAAATATCTGTGCATTAAAATATTATGCTTCTTCAAAATGAGGTTTCTACTTTTCTATTCCTTGAACAAGAGGTCTCTGTCAGAGTCAAACCTCTATGTCAGGAATCTTCTCTTTCTCACACCCCAGCGCCCCCATATACATGTGCTGCCAGGTCCTGTTACTTAGTAGACTCTTTTGCCCCTGACCATTGTCACCACCATCACCCTTGTTTTCACTTTCTTTCATGTTACATTGACTGAATCTTCTAGACTCTTGACTATCTGTCCATCTTTTGTCTTCTAGCCATCTGATGCCTTGTACAGGCATAGATCATTCTAAATCAATATTCTTATCAGGTAAATCTTCATAACTCCCAAATAAACCCTTTAGTGTTGTCCCCGTTAGATAGCACACAAAATCTAAGTTCTCTAACTGAATCTTTCAGGTCCTTTTCAGATTGGCTCTAGCTGTCTTTTCTGGTGGTAATTCCCAATTTTCTGCTTCATACAATTTCCAAATTTCCCTGCCACCAGACTTTATTTATTTCATTGCTTCTCCATTCCTTTGCAGCTCTATGTATTAGAGCTGATTCTAACACATCCTTCAAAGTTTAACCCCCAATCCACTTCTGTACAGCTCAGTATTAGGAGTTAACCTGCTGGTAAACTCTAACAAGAGTTTTCTTTCTATAACTATGATATCTATGGACAAATCTTCCCTACTTGAAATGCATACTGTGTTTAGAGACACACTGCGTTTTGCATATTCTAGTATTATAATTGTCCAGTATAATTCCTTGAATAAACAAGTATGCAATAAATATTTGTTGAGAAGCCTTTGATCTAGTAAACCACAAAAGTGTTTGTTACCTTATTGCTGATAATGGCTGGAGTTGCAGAAACATACATATTCAATAATAGTAGGATCTTTATATCAATTCTTGTTTATCTCTGGTTATCTTATTTAGAGAAGTATTATGAAACTTTCCAAAATTCTATTTAGTGAAGTCGCTCAGTCGTGTCTGACCCTTTGCGATCCCATGGACTGTAGCCTACCAGGCTCCTCCATCCATGGAATTTTCCAGGCAAGAGTACTAGAGTGGGCTGCCATTTCCTTCTCCAGGGAAAATTTTATTTACTTGTGACTAAAAGGGAAATGTTTACATTGTATCATTAAGTGAACTAATTAGAAATCACATATAAAGTTCAAATATGAGTGGAATTATAGGATAGGGATAGGATGGAAATACTAACCTTTGGTGATTTCTTTCTTTCTCTTGTTCTGTACTGAGGTTTTATAATGTAATACATTATACTATATTATTAGACCATTATAATAGCCCCATAAGCACTAAAAAATAGTTTTTGGATGAATGATTTTAAAATGTGTAGATGATTTCTATGTCTACAAGTGAAAGCCATCTTAAAAAATAAAGTTATTTATAATGTATCAGGTAATAATGTAGGTGAATCTCCCACCCACACAAATATGCACAATCAAAGAGTGATATTTTTTCTTCATTTGCTTTGACATATTTTAG
Seq C2 exon
ACTGTGTGCGGAAGTTTAAGTGTTGTCAGATAAGCATAGAAGAAGGCAAAGGGAAACTCTGGTGGAACTTGAGAAAAACTTGCTATAAGATAGTGGAGCATAACTGGTTTGAAACCTTCATTGTCTTCATGATTCTGGTCAGCAGTGGGGCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038180:ENSBTAT00000061380:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.780 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=FE(18.0=100)
A:
NA
C2:
PF065128=Na_trans_assoc=PD(19.8=84.6)
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]