BtaINT0129535 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021339 | SCN8A
Description
sodium channel, voltage gated, type VIII alpha subunit [Source:HGNC Symbol;Acc:HGNC:10596]
Coordinates
chr5:28211640-28216900:-
Coord C1 exon
chr5:28216630-28216900
Coord A exon
chr5:28213346-28216629
Coord C2 exon
chr5:28211640-28213345
Length
3284 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
TCTCCCGTTCCCCTTCTTAGGAA
3' ss Score
11.07
Exon sequences
Seq C1 exon
AACAAAATCCAAGGGATCGTCTTTGATTTTGTCACTCAACAAGCCTTCGACATTGTTATCATGATGCTCATTTGCCTTAACATGGTGACGATGATGGTGGAGACAGATACTCAGAGCAAGCAGATGGAGAACATCCTCTACTGGATCAACCTGGTCTTCGTCATCTTCTTCACCTGTGAGTGTGTGCTCAAAATGTTTGCCTTGCGGCACTACTACTTCACCATTGGCTGGAACATCTTCGACTTCGTGGTGGTCATCCTCTCCATTGTGG
Seq A exon
GTGAGTGGGGCAGGAGGGGCAGGGGAGGGGACCCGGCTGACCCTGAGGATGGGATTCCTGGGAGTGCAGCGAATGACATGCGGCCGAGGGGCCCGCAGGGTTACCCCCACGGTGCCCTCAGTCATCTTGTGGGGCTGCCCACAGCGCTGACATGGATCAGCGAGTGTCTGTGAATGTTCACGGTAGTCTTGGATTCCAAATTCTGTGGTTGAAGAGGGGGAAACGATTAGATTTGGTTCTTGCTTTCAAAGAGTTTACATTCTAACAGGGAAAAAAAAAATTGTATTTTAAAATCTATCAGTAGCAGTGTAACGTGAAAAAAGCCCTGGTAAGAGATTGTTACATTGGATGTTAATGAGAATTCTGGTGATGGTGGCTGTGTCAACACTTCGGCTGTTGCCAACACTCATTTACTACAATTTTATGGTGCTGAGTAGTTTGAGAGTTTCTTCACTTGTGTTATCTCATTATGACAGCCCAGGAATCAAGGTATTTTATTATCTTTGCTGTGAAGATGTCCAGAGTCACTCAACTCAGAGGTGGCAGAGACAGAATTCAAAAGTTGGTTTTTAACAGTGACTTTGTGGCATTTGTTTTAACCAACAAAGGGCCTGGAAGGGCTGGTGTCCTGGCAGGCAGTGGAAATGCTGTCCTATTGACCACCCTCCTCAAAATTTCCCTGCCTTCCTCACAGGCTTCTCAAATGATGCCACACTGCCTTGGTCCCAGGTGGGTGTAACTCGAGCCAGAGTGCCCGAGACAGGGAACCGGTCCCAGAGCTGAGGTGGTGACTGTGGCCACCAGAAGGCAACTGTCCTCCCACTGTCTAGTCCTGTCCTCCAGAGCACCATGTCCAAAAATGTGTTGTGTAATCTCATGTATTTCTCCTTAAGCAAAGAATCCCATAATGAAACTACTTTGGGCAACACTGTACGTTGCATTTCCCTTCAGAGGGTCACAGGGCACATTAGCCCACAGGAGGCGCTTGGAAGTCTTGGGGTAAAGAATTCTATTTAAAACGCCATCCCACCTTTATCCAATCACAACACCCTGTTTTCAAGTAATAATAATGTTTCTCAGACTTCAATGGAATATACTCTGTGCCAGTCATCATTCTAAGCGCTTTACATGTTTTAATTCATGCAGTCATCAAACAGCCCTGTAAATATCCTAAGGAGCCAAGGCACAGAGCAGTTACTGAGACACGCAGCTGATGAGCAAGCAAGCCCGGCCCTGGCCTCAGCTCCACACCCGAAACCTCCCACCAAACACACTTTGGATGATGCTGCCCTTGACCACTGTTCTTGAACTTTTTCTGCCCGCCCATCACTGAGTGGGATGGAAAACCCACAGATCAAACCATGCCCCCTATTTTCAGATGGTACTTGAAAAGAAGTAGGAAGAAGTATTTCTCTTGATGCTTGGGATTTTTTTTTAATATCATTAATTTGTTCAGAAACAAAAGTGTAGGAAAAAATCTTTTTAAATTAAGAGGCGTTGGGGTAAAACTTACCCTGGCACCCCCTAGAAAGTGAAAAATGAAAGTTTTAGTCACTCAATTGTGTCCGACTCTTTGCGACCCATTGTAGCCTACCAGGCTCCTCTGTCCATGGGATTCTCCAGGCAGGAATACTGGAGTGGGTAGCCATCCCGTTCTCCAGGGGATCTTCCCGACCCAGGGATTGAACCAGGTCTCCTGTGTTGCAGGCAGACTCTTTACCGTCTGATCCACCAGGGAAGCCCAGCACTGGGTCTTGTAGGCACCTCCTAGAGAACCTCTTAAAAGTTGACTCCACTGCCTCGATAGCTGCCTGCCTATCTCTCCCCACTTTTCTCTGGCACAATAAAACATTGGTCCTACAAAACCTTACTCAGGCATCGTCTTCTCTCTGAAGCCTCCTCTCCATCATATATGGAACACAGACATCACCTGCATTATGCTGGTTATGACTTAATTGAGAGGTAAACAGAGGAGAGCTGAGAAAGTCCTCTTGGGTGCCAGCTGAGGTAGATTTTCTTGAAAGTTCAAATGCCTCCCGAGATTCTAGCTCCAGACAAGACCCCAGCACGTTGTCTGCCTAGTCTGCACTTCCAGCACCTTGTCCCTTCTGAGAGTTAAGACTCTTTCCTAGCATAAAACCTTCAACTAACTCTTCTGCAGTTCCCTGCCCCCGTGTTTATGAGTCCCCAGGATTGGGGGATATTTCTTTCTTTAAATGAAGCTCACACTATCCCATGGGGGGGCTCTAAAGCAGGAGAGGACACTGGAGGAAGAGCACATGGTGTCACTGCCGCCCTTCTTTGTCACTTCCCAGCCGTTTCATTGCCTCTTCCTTCCACGACCCTCCCATTTTCGCTTTGTAGTTTTAAAGGCAAGTGGTCTGGTGGAGGTGGGCCCCTGGAGGAATGTGAACAGAAACAGGCCCTTTGATATGTGTGTTTTGCCCCCTACTTTCATATCCTATTAATGCCTTGACATTTTTATCTGCTGATACTGGTTTCTGATTTATGACTTTAAACACAAAATCTAGAAGCTGTGCGTTAAAAACCACTCCTGAGAAGTCCCTTTAGTTTGCAGGCTAGTTTGGTGGGATAGGGACATGGGGCCATGAGAAACCAAAAATGTCTTTCTAGAGCCAGGAAGAAAATGCCCTGAGAATTGGTGACCTTAGCAGACTAAGATTTTGCAACCACAGGGTGGAGCCAGGACTTCTCATTCACTGTTTGTGAATGTGGCAATTTGACAGCATTTTGGAGAAGAATCCATAACATCTCAGGAAGTTATGCACAGACAAATCTGAAAAAAAAAAACAAAACCCAAATTTAATACCAAAGATCAATCTCAGAAACATAATATTAGGTTTCAAAAGCAAATTAGAGATCTAGAAGAAAAAAAAATTTAAGGGAAATTAGAGATCTAGAAAGATAGATACAGTATAATTCCTTAAACCTTGTAGGCTGCTACCTATATTTTTCATACATAGCAAAATTATGAAGACACTGAGATGATGCATGCCATCTACAGGATAGTGGGTGCTTCTGGAGGTGATGAGTGGAAGCAGATGTGGTCTCTGGGTGCTGTTGTTTTCTCTGCTTTTCTATATGTTTGAAACATGTGATTTTCTTTTGAGAAAATTTTTTTTATTATGAGAGTTCAGATTGACTAGTAAGGCACTCACTCTATAAAGTCCTTTGAAGTTAAGGGTTCCATAGTGCCAGATGACATAAGTAAAGAGAAAGGGCATTTCCAATCTCAGTAACCTATCTCCCGTTCCCCTTCTTAG
Seq C2 exon
GAATGTTCCTGGCTGATATCATTGAGAAATACTTTGTCTCCCCAACCCTGTTCCGAGTCATCCGATTGGCCCGTATTGGGCGCATCCTGCGTCTGATCAAAGGCGCAAAGGGAATTCGTACCCTGCTCTTTGCCTTAATGATGTCCTTGCCTGCTCTGTTCAACATCGGCCTTCTGCTCTTCCTGGTCATGTTCATCTTCTCCATCTTTGGGATGTCTAATTTTGCATACGTGAAGCACGAGGCTGGCATTGATGACATGTTCAACTTTGAGACCTTCGGCAACAGCATGATCTGCCTCTTTCAGATCACCACGTCGGCTGGTTGGGACGGCCTCCTGCTGCCCATCCTAAACCGCCCCCCTGACTGCAATTTGGATAAGGAACACCCAGGGAGTGGCTTTAAAGGAGACTGCGGGAACCCTTCAGTGGGCATCTTCTTCTTTGTGAGCTACATCATCATCTCCTTCCTGATTGTGGTGAACATGTACATTGCCATCATCTTGGAAAACTTCAGCGTAGCCACAGAGGAAAGCGCAGACCCTCTGAGCGAGGACGACTTTGAGACCTTCTATGAGATCTGGGAGAAGTTCGACCCCGATGCCACCCAGTTCATCGAGTACTGTAAGCTGGCAGACTTTGCAGATGCCCTGGAGCATCCCCTCCGCGTGCCCAAGCCCAACACCATTGAGCTCATCGCCATGGATCTGCCAATGGTCAGCGGGGATCGCATCCACTGCTTGGACATCCTTTTTGCCTTCACCAAGCGGGTCCTAGGAGATAGTGGGGAGTTGGACATCCTTCGGCAACAGATGGAGGAGAGGTTCGTGGCATCCAATCCTTCCAAAGTGTCTTATGAGCCAATCACGACCACGCTGCGGCGCAAGCAGGAGGAGGTATCAGCAGTGGTCCTGCAGCGTGCCTACCGGGGACATTTAGCCAGGCGGGGCTTCATCTGCAAAAAGACAACTTCCAATAAGCTGGAGAATGGAGGCACACACCGGGAGAAAAAAGAGAGCACCCCATCCACAGCCTCCCTCCCCTCCTATGACAGTGTGACTAAACCCGAGAAAGAGAAACAGCAACGGGCGGAGGAAGGACGAAGGGAAAGAGCCAAAAGACAAAAAGAGGTCAGAGAATCCAAGTGTTAGAGGAAAGCAAAAATTCAACATTGTACAGACTTAAAACTTGCAAGTGAAAGATTGTTTACAAACTTCTGAATATTATCAATGCAGAACAGCTGTGGAGACACTTTATCCCGAAGATCTATACCAAACGTAGTCTGCTTACCACGTACCACGGTTGCATCTTGAGCAGTGACCTGCCAAGGGCAAAGGACCCTGCTCCCTGGACTCACAGATTTTCTAATGCTTGGGCAGGTGGTTACTGCATGTTCCACATCAGTCAATGCAACTTAGGACAAAACTAACAGGATACATAAAACAGAGGTCAGGCTGCCGGGACCAGTGTATTTCCGTTGCAGCCAGATGGATTTTTTTTGTTTGTTTTTTATTTTGTTGATTCTCAGAAGCAGAAAGCATCACTTTAAAAGTTTGTTTGTTCATGCAAACTCTATTTGCATTCTTACATTAGTTAAGCTAAGCAGCAAAAAGGAAAAACACACACACTCACATTTAGCCCATGTCATTTACTTGTCAGTTTCTTTGACATAATGCCGCATCTTCTCCACATGGGCTTCACGTGGTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021339:ENSBTAT00000061543:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.175
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.5=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.0=43.3),PF0061222=IQ=WD(100=5.5)
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]