BtaINT0129387 @ bosTau6
Intron Retention
Gene
ENSBTAG00000038180 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr2:31016869-31022972:-
Coord C1 exon
chr2:31022616-31022972
Coord A exon
chr2:31017349-31022615
Coord C2 exon
chr2:31016869-31017348
Length
5267 bp
Sequences
Splice sites
5' ss Seq
GTGGTATGT
5' ss Score
7.64
3' ss Seq
GCTTTCCTATTGTGTTTTAGGTT
3' ss Score
12.68
Exon sequences
Seq C1 exon
CTTAGAGTTTTCAAGTTGGCAAAATCCTGGCCCACCCTGAATATGCTAATTAAAATCATCGGCAATTCTGTAGGGGCTCTGGGTAACCTCACCCTGGTGTTGGCCATCATCGTCTTCATTTTTGCCGTGGTCGGCATGCAGCTCTTTGGTAAGAGCTACAAAGAATGTGTCTGCAAGATTTCCAATGATTGTGAACTCCCTCGCTGGCACATGCATGACTTCTTCCACTCCTTCCTGATTGTGTTCCGGGTGCTGTGTGGAGAGTGGATAGAGACCATGTGGGACTGCATGGAGGTCGCCGGTCAAACCATGTGCCTTACTGTCTTCATGATGGTCATGGTCATTGGAAACCTGGTG
Seq A exon
GTATGTGGTAAAACATTTTTCTCATTTTCAGTAAAAGATAATGTAACCATCAGGAATGTTTTGCATATTTTTTTAAATCAAGTGTCAATTCTTCATGATGGCAGGAGTCAGTTATAGATCAGACTATAGAAATCTACATGAACTCTTTTTAATATCTGCTTACATTATTTAAATTTTTTCCCTTTATATTGAACTGTAATTGACATGTAACACAAGCTCTTAAAATATCTTTTGAACCAAAGTTGTTCTTCATCTCTGTACCTCTTACTGTTCCATGGAGAGGGCCATTTTTGGCTTTTATCTTTCCGTTCTTATGCTAAAGCATGGCAGTGCTATTAGACAGTCATTCATTTTATTTATAAATACTAACAATATTGTCACTTGAAAATGTTTCACATTTGGGATCTCTGCAAGTTGGAGTTAAAAAAAATAGTGATCATCTCAGTCCATTAAAAGCACATCAGTATTTGTTGCATAGAAATGACAGTATGAACAAGTAACACTGACTCAAGAATCATTTGTTATCATTTCTGTGTAAAATGAACTATGCCCAACACACCTCTACTGAGTCCTGGAGGCCTGGGAACGATGGTAGGATGATAAATATGGCATAGTGATAGGACATTTACTCAAACAGGAATAAAAAGAGTAAGTGAAAAAAATGTGCAAGCAAAGTGTTGTATGTAAAGTTCACAAGATGGAAATGTTGCTTCGCGATGGCAAGGATCATCACAGAAGGCTTTGTCAAAGAGTTCAGACCTGAAAATATCTTTAATTGAGATCTGAGAAGAAAGTAGACCATCCCAAGCCAGGAAATAGTGGACCCAGTGGTTGGGGAAGAAAGGACAATAGATTTATTTGAGAGGGATCAGACTCTCACATGTTAAATTTATTATACTAAGTTGCTTGATCAGGCCCCAACTCAATGGAATAGAACAAGGACTATCATAACCAATATTTTAAAGTCTGCAATTTATAGACTTCATTTTCTTTCATACTAAAAGTAACCTCCAATCCCCCAGTCAGTTCACTTCAGTGGCTCAGTCGTGTCCAACTGTTTGCACCTCCATGGACTACAGCACACCAGGCTTCCCTGTCCATCACCAACTCCCAGAGCTTACTCAAACTCATGTCCATTGAGTCGGTGATGCCATCCAACCATCTCATCCTCTGTCATCCCCTTCTCCTCCTGCCTTCAGTCTTTCCCAGCATCAGGATCTTTTCAAATGAGTCAATTCTTCGCATCAGGTGGCCAAATTACTGGAGTTTCAGCTTCAGTATCAGTCCTTCCAATAAATATTCAGGTCTGATTTCCTTTAGAGTGGACTGACTGGCTCAGCCCCCAGAGGAAGAGAAAAGGGAAAGGGAAAAAAACAAAGAATTATTAATTTTTTCTATTTTTTGCAATATTTCAGTCTTCTCAGTATCCTGTTTTTAATTCTGACCTGTTCTTAAAATAACAAGAAACATGAATAGTGTACAATCCAGAAATGTGAACAGTGGCTTATAACAATACACATTTATTAATTATCTCATAATTTCTATAGGTTAGTTAAAAGATTTCTATCAAGATGTTGATGGGAGACAGTTATCTTGACTAAGATTGAAGAATTGACTTTTAATAAGGCTCACTCTCGTGGCTTTTGCTGAGAGGTCCCAGTTCAGCCTTACTGGATGTTGGTAGAAGGCTTCAGTTTCTCTCCACATGGATCTTGCCTTGGAGTTGATTATCTTCATGACATGGCAGTTGGCTTTTTCTTCCAGAGCACAAGACACAAAGCAAAGGGCAAGGAGAAAGCTCTTTTTATGTTCTAATCTTGAAGTTGCATTCTGTCACTTCTGCAATATTCTATTGACTAGTCATTAAAAAGAGCTCACATTTAAGAAAAAGGGATTAGACTTTAACTTTTGAAGGGATGAGTATCAAATAATTTTAAAACCACTACAATTCCAGATATAACTTGCTTGATTTCAGAAGATGCAGGAATGCATGGAACAGGAAGAAACAATCACAGGGCTACATAGAAGAAAAACAGAGAAAATGTCGTTGGTTTGTATTTTAGATTTGGTTTGATTTCACTTATATATCTGGCATACATTGGAAGAAGAGAATAGAAGGCAGAGAACAGAATCCAACAACAATGAGTGAGAAGACTGGATGCAAGCAATGAAAATTCATAGTGGGGTAGCAGAAAGTGTTTGAGGCCAGACTGTGTAGAGTTTAATTTATGAAAAGACTGATTATGCATTACCGAATTGAATATTTTTTCCTGTAGACAGTTGAACGCTACAGATGTCTTTTTATCAGGAAAGTGGCAATGAGCAGGTGGAATTTGGGTAGAATTTATGGAGCCAGAAAACATAGTGAATTTAAAGAAACTCAACATACCACATATGATCTTTAGTTTACTGAAATAGGACACATTTCTCTAACTGTACAAAGGATTTCAAGTTGAGAAGAGAATTTCAGGAAGTATTCATACCTATGGGTGTCATTTGTGTTAATTTGGATTGCTACATATACATAAAATGGTATAACAGATAAAATAATAATTTCCATCTATTGGCATTTATTTAAATTCTGTACTTTTTTTTAAAAAATTGAAGAATCTCCTTATTTACTATAAGTTAAAAAGTATCCCTCCTTTTGTGATATCTTGTATATTTTTTCTAGAGTAACTAAGGTGGTAAAAATATCTGTCATGTTTATCACTATTAAGGAAATATGTTCATATCACATTTCCTTAAATAAGGTTGACTGAACCCACTGCACTGCTTCTTACAATTCTTCCTTCTCATCCTCACCAAAAAGGTTAATGTCCCCCAAAGACAAGCTGACATAACCTCCTGTAAGCACACATAAACTGCCATGTAATGCTCGACCACAAGAGGTGTAAGTAATCACTGCCTAGTCCACAGACAAGACAGAGGTGGGGCTATAGATTGCTTTTCCCAGGCTATCATCTTGGTTTGCTAACACTATGGCCAGAAATCCTCTTACAGGTTTAAGACAGGTGCTGCAGAAAAAGAATACATTTTTTTTTAAGATTATCACATTTAGAAGTAGCAACCTCTAAGTGGGGCATTAGCACACAAGATGGAGAAGGCGATGGCACCCCACTCCAGTACTCTTGCCTGGAAAATCCCATGGATGGAGGAGCCTGGTGGGCTGCAGTCCATGGGGTCGCTAAGAGTTGGACACGACTGAGCGACTTCACTTTCACTTTTCACTTTCATGCATTGCAGAAGGAAATGGCAACCCACTCCAGTGTTCTTGCCTGGAGAATCCCAGGGACGGGGGAGCCTGGTGGGCTGCCGTCTATGGGGTCGCACAGAATGGGACACGACTGAAGTGACTTAGCAGCACACAAGAGGGATGTGAAAATGAGTTTTTCTCACCAATTAAAAATCAGGCTAGAAAAAGTACTGCTACTGACAATATGTTTCAACCTTGAATCCCAAATGGAAATCATTATTCCAAGAGAATAATTTGGAGTCTGTCCATGACCATGTGTGAAACAGGATCCCAGGTTTCAGTTCCTGAGTAAGCTTGTTGAACTGTATTTCTTTAAATTGCCTTTGGTCACACCCACCACCTTGGTCAGCTGTTACACTGATCAATACCCTTTGGTAATAAAGGAGGTCTAGAAAAAGAGATTAGATTGAAAACAAAAACAGGTAAATTGAAAGATAGTATAACAGAGAGTAGGTTGGATCATAGTAACAGTGATATAACAACTAAACTTTCTCAAGTGTTTACCATGTGCCAGTAGCTTTGTGAGGGCCACATGGATCCCTTAACTGAATCCTTACAACAATCTTGTAAGCTTAGCACTGAGAAAATAAACTTGATTCTTACCCAATGCTTTAATTCTAATGTGAAAAGGGAATGGACTTATCATAAGATATAACAGTAAAAGACATAATAGATACCTGCTCCAAAGCTTTGAGAGTTGGATCTCACTCTGGGAAGGTTGACTGATATTTGTCAAGAAAAAGTTCCTAATAGAAAAAGTTCATTAATGAACCTTAATCAAATCTAGAAAAAATTATGGTACCAAAATTCAGTTTGATTAGGGATAAAACCCAAAATGTAGCATTTAACTTTTTCTCTTTCATCTATTTTTATCCAAAAAATACATTCAAGGCAAATCACCATAAAATATAACTTCATTGGTAAATTCCAGATGTGAAGGATCAGTCTTAGTACGAGTACTAGCAACCATGGTGTAGCAACTGAAAGATGTCAGTATAGACTCACAGAATTATGTGCAGTCCTTGTTGGATCTTATAGGTTTTTGCCTTTCTTAACACCATTAGTTAGACTGACTCATAACTGGTTAAACAAAGGAACTCTGAGGCTCATTAGCCTATTAGAAAGATAGGAATACAGCAAGAATGCAGCATCCTTTTCGTTGGCGTTCTACTGAAAACCTTTCCTAGAATTCCTCTTCTGTATTATTTACTTTTTGTCTTTGGACCCCTTCAGGGCCATATCCTTTTCAGTCATTGTTCTGTCTGTCTGAATGATCAAGGACTCATATACTTGGTCTTGTGTCCATGAGAGTGTTCTATTTCTTAGTAAATTACCTCTTTTTGAGTGTACATAGCAGATTTATGGTCACTAATCTTTTTGCTAACCCATATCAGTGGGTCCTATTTTTGGAGACTCAAGTTGTTAATCAGTGGTCTGTAACCATTTCCTAATACTATTTGCAACTACTATATAAATCTAGTGGCCATGATTTTCTGAACCAAAAACTGAGATTTTTGATCTAGTGGTAGGTATATATTTTTTTCTAAACTGATGTTATCTAAAGTGCAAGAATACATACAAACATAAAAATAAAATAATATTTAAATATAGTGGAATCATCTTTGGTTCAGGAATAAAAGTATAATAAATTATCAGTGTCCTGAAAAACCCAGGTTACATGGGGAAAATACTTAACATCCCAAACAAAACTTTTCTTTCCCTTTTTCATTGTATAGTTATATAGATAGCAAAAATTTTTCATTTGGAAATGAACTTAATATAGAAGTTTTACATAGCAGTGGTTTTAGTAATTTTGCAATGACTAAAATGTAAATAGTGTTAATGTAGTATTATTGGCTGGGTATTTTTTTTTCCAGGATAGTTTATCATAAATTAGAAAGAATATCTATTAGCAAAAAGTGAGGTGTAAGAACAACTTTGGAAAATTTGTAGTTCGGAGCAATAGAAACAATGGAATGTTTTGATCACCAGCTTTCCTATTGTGTTTTAG
Seq C2 exon
GTTCTGAACCTCTTCCTAGCCTTACTCTTGAGTTCATTCAGTTCTGACAATCTTGCCGCCACTGATGATGATAATGAAATGAATAATCTCCAGATTGCTGTGGGAAGGATGCAAAAAGGAATCGATTTTGTTAAAAGAAAAATACGTGAATTTATTCAGAAAGCCTTTGTTAGAAAGCAGAAAGCTTTAGATGAAATTAAACCTCTGGAAGATCTAAATAACAAAAAAGACAGCTGTATTTCCAACCATACCACGATAGAAATAGGCAAAGACCTCAATTATCTCAAAGATGGCAATGGAACTACCAGTGGCATCGGCAGCAGTGTAGAAAAGTATGTCGTGGATGAAAGTGATTACATGTCCTTCATAAACAACCCCAGCCTCACTGTGACTGTACCAATTGCTGTCGGAGAGTCTGACTTTGAAAATTTAAATACTGAAGAATTCAGCAGCGAGTCAGATATGGAAGAAAGCAAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038180:ENSBTAT00000061380:16
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=0.119
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(62.1=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(4.2=5.0),PF065128=Na_trans_assoc=PU(61.3=85.0)
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]