BtaINT0129524 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021339 | SCN8A
Description
sodium channel, voltage gated, type VIII alpha subunit [Source:HGNC Symbol;Acc:HGNC:10596]
Coordinates
chr5:28237144-28240811:-
Coord C1 exon
chr5:28240455-28240811
Coord A exon
chr5:28237615-28240454
Coord C2 exon
chr5:28237144-28237614
Length
2840 bp
Sequences
Splice sites
5' ss Seq
GTGGTTAGT
5' ss Score
4.94
3' ss Seq
TCCTAATGCTCCTGGTGCAGGTA
3' ss Score
7.02
Exon sequences
Seq C1 exon
CTCCGAGTCTTCAAATTGGCCAAATCCTGGCCCACCCTGAACATGCTGATCAAGATTATTGGAAATTCAGTGGGTGCCCTGGGCAACCTGACCCTTGTGCTGGCCATTATTGTCTTCATCTTTGCTGTGGTGGGGATGCAGCTCTTTGGAAAGAGCTACAAAGAATGTGTCTGCAAGATCAACCAGGACTGTGAACTCCCTCGCTGGCACATGCATGACTTTTTCCATTCTTTCCTCATTGTCTTTCGAGTGTTGTGCGGGGAATGGATCGAGACCATGTGGGACTGCATGGAGGTGGCTGGCCAGGCTATGTGCCTCATTGTCTTCATGATGGTCATGGTTATTGGCAACTTGGTG
Seq A exon
GTTAGTACTAACTTGTACATCTTTTTGTTCTGTGCTCTGAGCATTTGACCCTTGACCCAGAAGCCCAGTCTACTTAGTCCTTCCATGTCTCTGTTGGTCTTTATTCTTTCTTGGCCCAAGAACCCTAAGGTACAAAGGAAAAGAGACTGCTGTTTTCAGAGGCCTAGTGGGTCATGAGCCTCACAACCTGTCAACCTTTTCATAACTGTGGAAACAAAATTCAGCAGTTAAGGCACTTTTCCAAAGTCCCGCAGCTAATAAACGTCAGGGCTTGTATTAGATCCTTGACTTCAAAGTCTGTGGTCTTTCTACTATTAAAAAAACCTCAGAACTTCTCAGCCTGATCTTTTGGGCTGGATAATTGTTTGTTGTGGAACTGTCCTGTGTATTGTAAGGTGTTTGCAGTATCCCTGGCATCTGCTCTTTACTGGCCAGTAGTGACCCCCAGCCCAAGTTGTAAAAACCAAAGATGTCTCCAGACATTACCGACTGTCCTCAGGGGGCAAAATTGCCCTTCTTTGAGAACCATGGATCTAAGCCATCCTAGGATTTTATCTGATGTTTATAAATTTCAAATCACTTCCTTACTTCACTCTGTCCACCTGCTGTCACTTGCCTCTGGAAATAGAATGTTCACCAACAGAAATTAACACCTTGTTTCTCAAAGTGTCATCCGAGAACTAGCAGCAGTGAGAACGTTCAAGGGTGTACTAGAGAGTCAGAATCCTAGGCCACTCCCCACAATCAGTACCTGCAATTTTTTTTTTTTTTTTTTAGTATCTGCATTTTTAACATGATTCCCAGGTGATCCACATACACATTATAGTTTGAGAAGCACTCATCTTTCAAATCAGGCCAGAGCCCGCCTGCAAGTGTACAAGAAGGAGGGTTGGAAGAAGACACACTCAGATGACCCCTTATAAGCTCACCGAGAGTGGTTTTCTTCCTTTTTCTGCCATAGAGAAGCATATGCCAGTAGGGCATTCCTACTCATCAACCTCTGAACCAGCCTTGCCCACCCTAGTCTCTCATTGGACCTATAAAAACAGGCAATGTAATGTTTCTTAGTCACTCCCATTCTCCACTCCCAGCCATCTCCCCTCAGTCCTGATCCCTCCAGTCTTCCCACTCCTTCAGTGGAGACAGCTGCTGCCTGCAGCTCCTATCCATTGTAGAGTCAACATCACCAGCCCTGACCTCCCATTGCTCTAGTCTCCTGTCCTCGGTAGTCTCAGGGACATCTTCCCATGACTGGCTACAGACACCTGAGCACATAACAAAATCCACTATTATTTCTGCCTGTGATGACACTGTTCCCAGTTCCCCCTTGGCTCAGTCCTTCTGCCCATGTCATCTCTAGGAATCTGTCAGTCTCTTCTGACTTTTCTCTCCATTCCAGGTAAATATCTGATGTCTCTCATATCTTTCTTCTTAGCATTTCTATATATGCATCTTTCTTTGTAGTATTTCTGAGATCTGCCCCTTCCTTTCCATTTCTACAACCCATCTGGTATTTCTAAAAGTCCAAGGAAGACCATCTTCGTTACAGTCACCTTGAGTTTCACTCATTAAAAAAGGCCAAGTCCCAGGACCTACACCAGACCTACTGAATCAGAATCTTTCTGGTGAGACCAAGGAGATGCTCGTTTTTAACAAGCATCCCACTCCAGGAGATTCTTCTGCTTGCTAAGGTTTGAGGTTCCTATAGCCTGATCCAGACCCTTATCAACTCATGCAAGGAACAGCTTCCTAACTCCCAACCCCTCCTCCCAGCCTACCACATGTGTACCTAGAAGGAATGACTTTCTCAAGTCTCTGTCATCATCTGTGACTCCTTTACTCAAGGACCAATAGTGGATCCAATTAACATTCAAATATTTCAGCCTGGCCTTCAAAGCCCTCATCAGCTGACCCCCGCTTAACTGACTGTATTCCTCTGTAATGCTGAAAATGGCCAAGGTAACCCAGATACGTAGAGTTCATATATTGTTTCTGTTTCCCCCACCTTGTACATATGATTATTTCCACCTAAAATGTAAGCCTTACTCTTCTTCAGAAGTATGACAAAGTAAGGGCCAAGTGTAAATCAAGAAGTGAACATCTCTCCCACTTTTCAAAAGTAAGTCTTAATAAAAATAAATTAATCTTAATGCCCAGTGTGGTTAAGAAAAGAAAAATAAATGAACTTGTTTCTAATGGCCTGACACTTAGATATAGAACCCCAAAGTCACCATCACCCTCTTGCTAGAGCTACTTAATTTTGATAAATGTTAGGAAAACAAAGAAAATCAATTCTTAAAATAGGATAACATGGAATATATTTCAGTTCCACCTTCGAGATTTGTTACATGAAAGTCTGGTTCTCCAAGCCTAGTTTTTTTCTAACCTGGGTCCTCCAGGACACCTGCTGCTGAAGAACACGTGGCGTCTAGGCATTCTTTGATCCTTCTCAATAATCCATGCCCACCTTTTTGTATTTTTTGTATTTTTGTATTTGTTTGTATTTTTGGAGAATTTTCTCCCAAAATGGGTACAACCTTTGCTTGTTCTGATTATAAGAAAAGCAATATGTTTTGAAGTACATATATATGTGAATAGCACTATAAAAGAACCAAAAAAAGGAGTACTAAACTCCTTGTATTACAACCAAAACCAAACAAAATGTCCACATAGTGACACGAGCACTTAAAACACTATGTGAGTCAAACAGAACACAGTAGAAACTCTGGAGTCTTTTACGTAAGCCTGTGAGCTTGCAGTTTACAGCCCTAGTTGAGTGGATAACTGTACCCAACACCATTCTCCATTCACTCGCCATTTTCCTAATGCTCCTGGTGCAG
Seq C2 exon
GTACTGAACCTGTTTCTGGCCTTGCTTCTGAGCTCCTTCAGTGCTGACAACCTGGCAGCCACAGACGATGATGGAGAAATGAACAACCTGCAAATCTCCGTGATCCGGATCAAGAAGGGCGTGGCGTGGATCAAACTGAAAGTGCACGCCTTCATGCAGGCCCATTTCAAGCAGCGCGAGGCCGACGAAGTGAAACCTCTGGACGAGCTGTACGAGAAGAAAGCCAACTGCATCGCCAACCACACCGGCGCCGACATCCACCGGAACGGTGACTTCCAGAAGAATGGCAATGGCACCACCAGCGGCATCGGCAGCAGCGTGGAGAAGTACATCATCGACGAGGACCACATGTCCTTCATCAACAATCCCAACCTGACTGTGCGAGTGCCCATCGCCGTCGGCGAGTCCGATTTTGAGAACCTAAACACCGAGGATGTCAGCAGCGAGTCGGATCCTGAAGGCAGCAAAGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021339:ENSBTAT00000061543:15
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=0.210
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(62.1=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(4.2=5.1),PF065128=Na_trans_assoc=PU(61.0=84.7)
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]