BtaINT0129529 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021339 | SCN8A
Description
sodium channel, voltage gated, type VIII alpha subunit [Source:HGNC Symbol;Acc:HGNC:10596]
Coordinates
chr5:28300338-28302819:-
Coord C1 exon
chr5:28302701-28302819
Coord A exon
chr5:28300428-28302700
Coord C2 exon
chr5:28300338-28300427
Length
2273 bp
Sequences
Splice sites
5' ss Seq
TTCATATCC
5' ss Score
-14.87
3' ss Seq
CTCCCTTGACTCTTTTCTACAGT
3' ss Score
-0.32
Exon sequences
Seq C1 exon
ACCTTTGTAGTATTAAACAGAGGGAAAACTCTCTTCAGATTTAGTGCCACGCCTGCCTTGTACATTTTAAGTCCTTTTAACCTGATAAGAAGAATAGCTATTAAAATTTTGATACATTC
Seq A exon
ATATCCTTTTCTGCAAATGTGGAGTGAGTGCAGCCGTCCTGTGGTCCCTGGTATGTTTCTGAATGTCCACCACCTAATTGTATATTAACTATTTTATCAGTGGTGTAGCTGACTATTCCTCCAGTCAGAACTTCTGCTAAAGCCTTAGCTGAGCTTCAGCAGATTCTTTTTTCTTAGGATGATATCACGGGAATCTGGAATTTTGTGGGTATCATTAAGAGGGACAAGTTAAGATGGTAGCTTTGCTGCTGCTGCTAAGTTACTTTAGTCGTGTCCGACTCTGTGCAACCCCATAGACGGCAGCCTACCAGGCTCCCCCGTCCCTGGGATTCTCCAGGCAAGAACACTGGAGTGGGTTGCCATTTCCTTCTCCAATTCGTGGAAGTGAAGTCGCTCAGTCATGTCCGACTCTTCGCGACCCCATGGACTGCAGTCTACCAGGCTCCTCCGTCCATGGGATTTTCCAGGCAAGAGTACTGGAGTGGGGTGCCATCCGCCAAGATGGTAGCTTTACTGACGTCTTAATTTTTAGAGCACTCAGGCTTTAGTAATTTCATAACAAGTTATATTATTCAGCTTTTTTACATATTAAAGCCCAATTAGAATTTTTGAAATGCTACTATAAATAATTGAGCGAGTGTTTTAGAGATCTTCTTTGATTTCTTAACCACAAGTTTAGAAAGTAAGATAATCTCTCAGATTAAATGGCCTCTTTGGAGCACAGGTTTAGATCTAGATTGCAGGATTGATATGAATTTTTTATATATATTTTTTCTCCCCTTAAAAGAAAATGCCAATTTACTCCTGCAGCTTGACTTTGTATCTCATTAATATAGGAGAGCATATGACAGATGAAAAATTACGTGATGGGTTTAGCAACTTCACTTAGTAACTTTAAACCTTCATGGTTGGTATTTAATTGGACAGTACTTAGTCCCATGCTTCAGAGTTTTGTATCCTCCAAGTAGGATGAAGAAACCAGCAGTTGCTGCTTCATAAACAGGTTTGTTAAGCTTTTGTACCTTTTATTTTTGTTAAGAATTTAGCAGCCTGATCTGGAATTTGTGAGTTTTGCAAGCAACATAGTTCTGAAACCTAAAGGTTTATAAGAAAATAAATAATTCACAATGGACTCTTTCCTTTCTTGTTGGATCAGAGGATGATGTTTTTTTCTATTCTAACCAGAACATGTGATTATTCCCTGAAGAAAAATCCAGCTGTAGGAAGAAAAAAATCCAGCTGTAAGAAGTGTTCTTCCTTTTTAAAACTCCACTAATAGAATGAAGGTAGTGAATGTCACTAGCAAGAGAGAGTGAATTAGTAACAAATGAGATGTGACTTCTGTGCAGTTTTAAGTAACTCGTATTGATTAAAGCAGTTTAATTCTTCTCAGTAGACAAGAACATGGAGAAGGAAATGGCAACCCACTCCAGTGGGTTGCCTGGAAAATCCCATGGACAGAGGAGCCTGGCGGGCTACAGTCCATGGGGTCGCAAGAGTCAGACACAACTTAATGACTAAGCCAGACAAGAACAAGAAGGGCTGAGCGAGATCTTGGATAGAAATGAAATGGCAGCAAAATGATTTGCTACGCATAAACATTCCTGGACACTCTCAGAAAGATCAGATGGATTTGCCTTGTTACCTAATTCTTAGGAGTACGGTGGTACAGATGTCCTTAAAATCCTTACTCAGTCCTTACCACAACTGGTTTCTCAAATTTGACAGATTCAGCAGACATTAACTGTTGCCTTGCCCTGCAAGGACACAGCCCTTTGAAGGGCTATGGAAAAAAAGTAAAGTGTTAAATACATGAACATTTCCAATAATTGGTAATACAAGATAATTAACAATAAATGACTTCTCAATAACATAGATAAGATTTAATTTGTTTTTCTCATCTGATGACTTTGGCATCTGACAGACTGCAAGATTTCTGGTTATTGGGCAGAAAGGTGTTTAGAGGCATAAATGGTAAGAAGGAAAAATGTTTATCCAAAAGGAGAACGGTGACAACCCTTTTGAAAAAAAGAGCGGCCACCCTGCCATGTCCACTCACATTCTCTGGCCGGGTGTGGATACATATGGTGGCGCTCATATGGTTCATGGTGGTGGCCACAGTTTTCATTATCACCTTGCCTTTTCCTCCTCTGTGCTTTGTCTCCTTTCAGGTTACTGATTTTAATTATCATGATACTTAATGTGAAATGTATTTGCTTCCTGAGGATAAAAGCAGGCCAGAGTTTGTGTATTCTCCCTTGACTCTTTTCTAC
Seq C2 exon
AGTATTTAGCATGATCATTATGTGCACTATTTTGACCAACTGTGTATTCATGACTTTTAGTAACCCTCCTGACTGGTCGAAGAATGTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021339:ENSBTAT00000061543:2
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(0.8=6.5)
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]