BtaINT0129397 @ bosTau6
Intron Retention
Gene
ENSBTAG00000038180 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr2:30986397-30991751:-
Coord C1 exon
chr2:30991647-30991751
Coord A exon
chr2:30986668-30991646
Coord C2 exon
chr2:30986397-30986667
Length
4979 bp
Sequences
Splice sites
5' ss Seq
GCTGTAAGA
5' ss Score
4.19
3' ss Seq
TACTCTTTTTTTTTTTGCAGAAC
3' ss Score
10.74
Exon sequences
Seq C1 exon
TTTGGAGGTCAAGACATTTTTATGACAGAAGAACAGAAGAAATACTACAATGCGATGAAAAAATTGGGTTCAAAGAAACCACAAAAACCCATACCTCGACCTGCT
Seq A exon
GTAAGAATAGCATACTTTCATCACTAATAAAAGCTATGTTATCTATCACTTTTATAGCCCAAATTGCTAGATACTAATTTTCGTGTATTTGCAAAACAGTTTTAGTTTGCCTTAGTAATGTGACCAGATAGCCTCAATAGTCTAAGTATTTGGTATTTTTTAGATACATAATATGTAGAAATTATGTAATATATTTTATACACAGACATAAAAATATATAAGTAAAAATGTTCAGGCTTATATACCAATATTATTCCATAGGATTGACATCACTGAGGAGCTTCTAATAATGTAGAAAAGAAAACATATTCATATATACATAGTGTGGAAATATTGAATGTTCTCAGAGTGCAGTGAGGACCAATTGGGATAACTGATACGTCTTGGATATGCCCCATATTCTGTCCAGCTCTGCATATTGAATGGAATCATTAATGAAACAAGTCATAGGTCTTGTTTGTTCCTGGTTTTTAAGAAAAATTTCCTATTTCCTCCAAGCATCTTGCCCTAAATCAGATGACATCCTTCTCTATGGCTTTTTATGGTGATTGTGATTGTATATTTGCCAGTGGCTACTGGTCTGTTTGGTTGCAGCAAGGAATTGTTGTCAGAAGAGTCCCTGAGATCTTTTATGTTTCAGAACTCCTCTCTGAAGGTATACATGGTACAAGGTAATCAAGTGTTCCCCAGGAATCATGATGCTATGATTCCATTAGTGATGATGTAAAACTAGCTAACCTAAAACTGCCCATGCCCCTATTCTGTTTGTAAGATAGCCAAAAGCCCAAAGAAAGTAGATAGTAATATTGGACAAAACATAAGGAATGTAGAATTTGAGCCTACTTTTTGAGAAATAATACAACTTGAATGGATAAAGGAGAAAAGCAGAGTAATGACTTATGTGAAAAAACAAACACTCCAAAGTCATGGAAATAAATATTGCAGTGAAAAATAGCGATATATTTTTGAAATAGTAAGTAGGAAACAAGGTTTTCTGGGTTAAATGAGTCAAGCCCACTATGAATCTGAATAAATCCATCTTAATTTATCCAAGTAAAAATACAATATCAAGTGCACAGCATGGTAATGTGAAGAAAAAGAGATTTTTAGAGACTGGTATGGAGGGGGGGGCAGGAGGAGAAGGGGACGACAGAGGATGAGATGGCTGGATGGCATCACTGACTCGATGGACGTGAGTCTGAGTGAACTCCAGGAGTTGGTGATGTACAGGGAGGCCTGGTGTGCTGCGATTTATGGGGTCGCAAAGAGTCAGACACGACTGAGCGACTGAACTGAACTGATAGGAAAATGTTAGACAAAGTAATGCTGGGCCTTAGACAAGAAGATGAACCCTTACATGCAAGAAGATGAGTCCACAGTATAGGGTCATGCCAATAGGACTGGAGATAAGTGAGCCAACAAGAAGCCTCAGTGGCATGAGGAACCTATAAAATATAGGAAAGGAGGGAGGACATATAGCTAATAAAGAAAGTAAAGCAGTTAATGTTTTGTGAAATTATTGATTCTGTTAATGTAACTGAAAGTCCTGTAAAGGCATTTGGAAAGGTGAGGTCTTATGAATATGGGATAAGGATTTTAGAGTTGTCATTGTCATACATAATTCAGTTGAGCTCTAAAGCATAGGTTCATTTTTGAAAGACAATTATAATATATCAAAAAAAAAGTGGTGAGCATAAAGCCTTGTGTACTTCACCATTATAAAAGAGGTAAATCAGTGAAAGAGTGAGATTTATTAGTAAGGCAGCACATACATATAGATAATGAGAAAAAAATTTTAATGGCTGTTTAATTACGTCAGATAACATGTAGATTTACTTTAGTAGGAGTAGGGATGCACAGGAAATGATTAGTGAATTTAGCTAGAAGATTATTGGCAACAATTTGGCAAATTAATTCAGTCATTCATTTACAATGTATGATGCTAAGCATTTGGAATTAAATACTAAACAGAGAGTCTATTTGGTAATCAAATAGTCACACCAACAAATAGAAATATCCAAGAAGGAAAGAATCCATTTAGCTATGAGAGCTGATAAGAAAGAAGGGGCTGATTAATCAGGGAAGGCTTTACTGAGCATGAGCCTAGGCCTGAAGAAGAATGAGGAAGTTTCTATAGGCCATGTAAGAAGAAAAGAGGGATGTATATGTGAAGGTCTTGAGGTAGGAAGGCCGGTGAGGCTGGAGTACAGAGGCTGGGGGTTCATTTGGGACATGGTGAGAATGAACAGGTTAGGATGGTCCAGACTTTTCTGGGCTTCTTAGGCCACATTAAGGCAAGTCTTTGTCCTTAGAGCAAAGCGAAGCCATTGAGCAGAGCCTGGTCAGTTTGGGTGTTGTGACTGTCACTGAACCAGCATTGACAGAGGCAGTGTGTGCGGTACAGACTCATTGTGGAACTATTTCAGGGGTGATAGGGAGCCTGAACCAGAGTGGTGTGGAGATGAATAAAATGGATTTGTGAGCTATCCTAGGAATGAAATTAAAAGGTTTATTAATTGAATATGAGACGTGAAGAAGGAAGCAACAAAGATGACTCATGAGTTTCTGCCTTACACACTGGAAGAGTGGTGTCACACAGAATAAGAAGTAGGGACATGAATGGAGAAAACAACTGGAGATGCTGGTTTACAGAATTTGAAAATCAAAAGGGGACTCTGAAAGAGAATGAATGTTGAATGAATGTTAGAAGTAGTAGTAAAATTTCTAAAGTAGTAAAGTTTCTAAAGATTGAGAGATTAGTTTCAGAGCAAAGCAGCAATTCTAGAGAGGAAGAGATTGAAGAGAAAGGGAATAAATATAGAATAAAACTGCACAGGATGTGGCCCAAAAACAGTGTAGATTACATTACAGAGGAAAAGGGACTGAGTCCTCCAATGATTTTGGAGTAGTATATAAAAAGATAGGTGTGGACATCAATATAATATAAAATGACAAAGAGGTAGAGGAATTTCTTTATAACAATTGACTTTGGTGTTCTCAAAAAAGAAGTAAGAATACAGGGCAAGAGAATAAGAAATTTCTAAGAAGTTTGAAATTATCCTGGGAGCAAGTGAGGGACAAAGGATTGCTCATCATTATGAAGAGCCAAGACAAAGTGAGAGAACATAAGCCTTAGTGAACATGGCTTCCAAGGCTATACAGCTTCCTCCAGCATATTCTGAAATTTAAATTGGAGACAGTGACTGTGTAGTGGAGTTGTATATTGATCTAACCCACTGGAAAACTAAATGGGCAAAGAATCTTAAGAGATTTTTGGTGAAAATGCTGACATGAACATAAATAGCAAGTTGCTGCTTTTCAGCCATTTTGAATCTGCTTCACTCTAGGTGCTGTATCTGTGGAAGAAAATTGATTTTTTAATTAAATAAAAGCAAACCATTTGCAATAAAATGTCGTACATTTTATGAAACATGTAAGCACAAAATTGTCTGAGATCACAGAGTGCTTAAAACTTAAAACGGAGTTAGGATGCACCAGACTGAGAAGGGGAGTCTAATAATGCCCCTTGACAGAAGCATTATGACAGAGGAGATGGATAAACAAGATAAAGCAGTATGGTACAAGAGTAGTAGCAAGTATCAGAAGGGTAGAAATAAGGGGAACGTAACCAGACTTGGAAAGGTAGACTTCAGTACCCGAGAGCTAAGAACAAGGGGCTGAGAACTGGAATTAGACGCATTTAAGTTGAAGGAGGCCCTCGAAGAACAGATGCAGCTGAAACAACATAAGTCCAGTCCATCGGGCTAAATATGTATTCAGAGAAAATACATGTTTTATTTATGTATTTATTTATGCAAAAATCAAATGTTATTTTTACAAAATATAACAAACCAGTACTATTTGATATCCCAGAATTCCAGTATGGAGTAATGGATGCCTCTACTAGTCGGGCAGGGGCAGAACACTAGCACAGAGAATCCAGACCAATAAAGGCATCCATCTGGAATGCAGACTATGAGCGTAGATGCAGCAGAAGCTCTGTAGTTCTAGTTGAGAAGGTAGAGGACGACCTAGCAGAGGTGAGCCAAGTTCCAAGCTCTAGGATGAGGAATATTGAGCACATAGAGGTGAAACGAAGGAAAAAAACAGGGCCCAGTGAACATAATTGGTTTACAAGATGAGGCCTTAACTTCATAAACAAGACATAAGGCTAGTTAGTGCTTAGAAATTAGGTCCAGATTGAATAGGGCGAAGTTTGAACATCTAAATTTTAAGCTATACTTTTTTAAAAGATGATTTTATTCTTTTTTTTTTTTAAAGATGATTTTATTCTTGTAGCAGTTACCTCATATAAACTTCATTCTGCTTTCCTTTGTCTTAACATCTTACACAACCATAGATGGGTCAGCAAAACGAAGAAATTTACCCTGGTATGATAGTATTAAATAAAATATAGAATTTAACTGGATTTTACCAACTATTCCACCAATGTCCTTTTACTTGAACTATAATTTTAAAAGCATCTTCTCAGCTGAACCTTAAGGTAGAATTTAAGATGCTGTGGCTTTGCTGCGCATAGTGGGTGGGGAATATAAAGGAAGAAACTAGGGTGAAAATGACCCCAAAAAGCTAGAAAAGTATTTATTCATTAGTTCTTCAAAGTTAATTTTGATGCTCACCCCAAACACAGAAGATAACAAAGATTCATTATAGTGACCAATATTTACTGTCTACTGTACACATGGTTATGTTTTAGGCACTGAGAAACTAAAAGGTGGTTCTTAACATAAAGTTAGTTTACAAAATCTGCTATCATAAACAGTATAAATAGAACAAATACCATTTGGAAAGAGCTGGATATTCCAGTATACAAAATTTTCTTCCAAGTGTAAACCAAACATGGAACGTTTTGTAATAAAAGCTGTATTTTCACATTGTTATGTTAAAATCAGATAAGTTGGACTTGATTTGTTTTTCAGTCTCTAAGGGAATTTCACATACTCTTTTTTTTTTTGCAG
Seq C2 exon
AACAAATTCCAAGGGATGGTCTTTGATTTCGTAACCAAACAAGTCTTTGATATCAGCATCATGATCCTTATCTGCCTCAACATGGTCACCATGATGGTGGAGACTGACGACCAGAGTCAAGAAATGACCAACATTCTGTACTGGATTAATCTGGTGTTTATCGTTCTGTTCACTGGAGAATGTGTGCTGAAACTGATCTCTCTTCGTTATTACTATTTCACCATCGGATGGAATATTTTTGATTTTGTGGTGGTTATTCTCTCCATTGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038180:ENSBTAT00000061380:25
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:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(20.4=47.3)
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]