BtaINT0129392 @ bosTau6
Intron Retention
Gene
ENSBTAG00000038180 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr2:30997623-31001365:-
Coord C1 exon
chr2:31001192-31001365
Coord A exon
chr2:30997746-31001191
Coord C2 exon
chr2:30997623-30997745
Length
3446 bp
Sequences
Splice sites
5' ss Seq
GATGTGAGT
5' ss Score
7.77
3' ss Seq
TGTTGCTTTTTTCTGTATAGGTC
3' ss Score
11.06
Exon sequences
Seq C1 exon
GCCTTTGAAGATATATATATTGAACAGCGAAAAACCATTAAGACCATGTTAGAATATGCTGACAAAGTTTTCACTTATATATTCATCCTGGAAATGCTTCTCAAGTGGGTTGCATATGGCTTTCAAGTGTATTTTACCAATGCCTGGTGCTGGTTAGATTTCCTGATCGTCGAT
Seq A exon
GTGAGTATTCTGCATGTTATTGTTTCATTTCACTGGCATGTGAATGGTAACTTCTAGTCCTTGCTTGGTGTCTGGCACACAGTAGGCACTCAGTACAACTGCAGGACCCCAAATATAAATGATGGGTCCCATCTTCCCAATAAGAAAATGTCCCAAAGCGTTTTTTGCCAGAGTTTCACAGACAAAATAGTTAAATTAATATTTAAAATCCCAAGTTACACAAAGGAATATATAAATGTAGAAGTTTTGCTTTATCACTCTCACATATAACTGTATTTAAATTCTTCACGGGCATCTTTGATGTTCACATTTTTGTCGTCTCCAGAACCTGTTGCAAAGTGTGTCCTGTAGGTGTATTAGTAATCACAAAGGAATATGAAAGTCCAAGTAGCAAGAGACATTTCTTGATTTATATGATTATAGAAACAGATTAGCTATGAGCCAATTACTTAAGAGTTTTATGAAACTATATTGGTGTTGAAAATAATATATTAATAAGATGCAGTGCCAGAAAGTAAGAGGCTTTAAAAATATGAATATGAGTTTATTCCCTTACTTTTGAGGGAAATTTTTGAAGAAGATCTTAACCAGACAAAATTTTAAAAATCAATTTTATTTAATTTTGAAGATATGCTTCTTAAATGCCTTTAAATTAATAGTTAATTTTGTCTAGAAATTTAAGGCCTTTTGTCTAGGAAAAAACTAGGAGAGCCAGAGGGAACAAGGGCCAGGAAACCTGGAGGGAGGGAATAGAATGATACTCAGATTAATTAAGAAGAAAGACACTGAAATTTTTAGGAAAGAAAAATGTGTGTTTTAAGTACTGAACTTTAAGATAATATTCTGTTGATTATAATAACTCCTTGGCAATTAAAGAAATATTATGATATATAAAATTTACATATACCAGAAAAAGAGAAAAATGGACTCTTTCACGGAGAAAGTTAGTTTTTATAGTTGTAGGTGAAAAAAATTCAACTTAATTTAGTAGGAGCTTTCTAGTCACCAAACAATTAAATTTATAAGAAATAAAGAGATTTCTTTGAATTTAAGAGACTAAAATATCTTTTCCTTTTGCTGAATCTGCATAAAGCAAGCCTATTATTTATATTAACATATAAAGCCACATGCAGAATTATATCAAAAGTTTACTGGTGATAAAATGACAATAATACTTTAAATCACATGTGTTTGAGCACTACGAGCAAAAGAAAAACATACCATGACAATACCAGTTCTTTTATTTGTATAATGAGATTATGGATGATACTTTATTTTCTGTCTGTGGTTATGATACACTGTAAATTTTTAATAAACATATCTTATGTTTACTATATCCATGTAATAATAAAGGCATTAAGTCAACACTACCTAAATATAAAGAAAATCTTAAGAGAAATGTGTGAGCTGCTGTTCATGTTACCTAGTGTATTCTGATGTTTACCTTCTTGGATTTAAGAAAATTATTATGATAATACATTAAGCTAATTAATGCCTTGATTTATATCAAACATGTTTATCAATCATCTATTTTGTATGGAAGAGGCAAATATGTATGCCATTTTCTGGGCCTATGGGAGCTTACAGGCAAGTAGTGAGGATAGATATGTATACAATGAGAAGATGACATCTCTATTAGAAGTTTCATCTGCTTCGCTGAGGAAGAAGCACAGGCTTCATGAGGGCAGTGCAGTGTGAACTGGCATTTGAAGGATGTCAGTGTCAGCAGGTACAGATGAAGCAAGGGCATCAAAGCCTTGAAGACACTGCTACATGCCAAGCAGGGCTTGTTCAACCACCAAGTAGTCCTATAGGATAAGTTCTGTGCCACAGGGTGAGGAAGAGTAATTGGTTGATACTTTGTAATTGGTTGATAAGAAACTTAAGTTGGAGAAGAGATTGAAGGACCTGAGATGCCATTCAAAGAGATTTATTAATAGATCTATGATTTAGTGATTGAATAAAGAAGCTATTGAAGAGTTCTCGAAGATACTCTTCTGTTCAAAAGTATCTATGGAAAGTGAAAAGAAAAGCTCACCCAAGAAATTTGCTGGAGATGTCAGTGATGGAATGGAAGAAAATTACTATTTAGAGGCCAAAAAAAGAAGACCAGAAAGAGAAGATCTACATGTATCTCCTTTTCATATTTAGCAACACAAGACACATAAAATTGAATGTTTACTACTTCTTTAGCCAATAAATACTGTCCCTGTTCACAATTTTTTTCTTATGTCTAACTTTTATTTTTCATTCTTTAATTTATACCTATCTCTTTTTCATTCTGTCTTCAGAGAAGATAAGGTACTATAAGTCCTCATGTTTTATACCTAGAAAATCTTCACAATAAATGATAATTCAGTAACTTTATCTTTCATTTGTCTTTGAAGAGATTTGCAAAGCCTAAAAATTTAGATTTTAGGAAAAATATAGAACCTCCTTAAGACAATTTTATAGATTAAATTTTTCCAAATTAATGGTTTTTCTATTTCATATTACATGTGCAAAATTAGTTTGAATAAGTCAAGTTGTGTTGTAAAATATTTTTATGTGCCTCATTTACTTCTCTTAAAAAATGTAATACCACTAACACCATATTCTTAAAAGCTATATTACACATCTGTTCTCATTTTCCTGCTTTTGAAATTCAGGTGCACTTTAGGAGAAAATATCTTTTCTTTAGCTTATATAGTTTCAATGGGTTTTCTATGTATTTTCAAAGGAAATTAGACATTTCTGTGCCACCTGTGGCAGTTATTCTTTTCCTTTTTCGCTGTAATGTTACAACTTATATCAACTACATTAGCCATCAGTATAAATAAGAAAACATTGTTCTGACAATTTCTAATTAGTTATACTAAAATCTCAACTTTTAAACTTAATGATTTCAATTTTCCCTAATGAATGATCTTAGGCCTTCACACTGACATTTACAAGACTAAAGCACTTTTAGAAATCTAGATCTTTCTGAGTGTGTTTATATTCAGCGTCAACTGTGTCTTGCATACTTTTCTTGCATACTTGTACTAGGTTTTCTTTTCTCTTTCAGGTCTGCTAAATAATATGAGAAATGATAAAGTTTTATAAATCTATAGATGAAAATTTCATTTTGGTGTCATTCTTTTTCTTTCTTTACATTTAACTCTTTTAAATTTTCTTGTCAAGAATCTTGATAAAAAGAGCATATATTGCTGCTGCTTTTTCATTAAGTTTATAGCAATGGTTCTCAAAGTGTGGTTCACTGGCCAGTATCATTAAGCTTAAGTGGGAACTTAAGGAAATGCAAATTCTCAGGTCTCATCCGAACCTTGGCCAGCCATCTGTGTTTGCAACAAGTGATTTTGATGCTCACTAAGGTTTTGGAACTGGTTTATTGCATACAGCAAGGCTGAGTTGTGTAAGCTTTTTTGCCTATAAATAAGACAATTGTGTTGCTTTTTTCTGTATAG
Seq C2 exon
GTCTCATTGGTTAGCTTAACTGCAAATGCTTTGGGATACTCAGAACTTGGTGCCATCAAATCCCTCAGAACACTAAGAGCTCTGAGGCCGCTGAGAGCCTTATCCCGGTTTGAAGGAATGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038180:ENSBTAT00000061380:20
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(17.0=67.2)
A:
NA
C2:
PF0052026=Ion_trans=FE(17.5=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]