BtaINT0129523 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021339 | SCN8A
Description
sodium channel, voltage gated, type VIII alpha subunit [Source:HGNC Symbol;Acc:HGNC:10596]
Coordinates
chr5:28240455-28242878:-
Coord C1 exon
chr5:28242705-28242878
Coord A exon
chr5:28240812-28242704
Coord C2 exon
chr5:28240455-28240811
Length
1893 bp
Sequences
Splice sites
5' ss Seq
TTGGTATTC
5' ss Score
0.59
3' ss Seq
TTTGGGTTTCTTTTCCGTAGCTC
3' ss Score
8.57
Exon sequences
Seq C1 exon
GTTTTCACTGGAATTTTCACAGCGGAAATGTTCCTGAAGCTCATAGCCATGGATCCCTACTATTATTTCCAAGAAGGTTGGAACATTTTTGATGGATTTATTGTCTCCCTCAGTTTAATGGAACTGAGTCTAGCAGACGTGGAGGGGCTTTCGGTGCTGCGATCTTTCCGATTG
Seq A exon
GTATTCCATATTTCTCCAATTTCTTTTTTACATTTCCTGTCTTGTAGCTAGTAGGAAGAATTTTGTATAAGTTAATCTGATGATTTTACAAAATTCTTAGCTGTATCCTGCTCCCAGTTTCAGTTGACTGTTTATTGGTTTATCAACTAAAATATTGAAAAACTTTTCTGCTGGTTACCTAATCTAGAAAGTAGGTTTTTTTTTAATCAGTCAACAAACATAAATCAATTTTATGAAGTTCCTCAGAAAATAATGGTTAATCTAAAAGATGAAGAAGGATTCACAAGAGCTATTCTGAGGTCTGATTTGAATTTGCTCGTGAGCCCATTTCTTTATCTGAACATCTCCCTGAAATGGCAAATATTTCTCCCTTTTCCAAAGATGGCTCATTTCTTCTATCATGGTGACCCCTTCCAGAAAATGAGAATAAAATAATGTTTTTTTAAGTTATATTGAAATTAGTTGTTGAACACAGATCTTTAGCTCAGAAGGATTTTTTTAATGTATTTGAAGAAATTAGTGTTCAAATTACTAAAATGCCTCTGAATGTATTAATAGTTAACAATATCCTCAGAATAGCTTCCTATGAAGCATAGGCATGAGTGATGTCCTGATTGAGTCCCTTGAGAAGCTGAGTTACCTTGAGGGTATCCCAGTCAGACAGAGCATCAGAGATGGCTTAGATTTGTTTCTCTTATTGGGAAAATACCTAAGCACTGACAACTGAAAGGATTTAAGGATATTCAGCTTATCTAAGAAAGAGAATTGGATTAGAATGAAACTGTTTATAAAACAGAAATCTCATTCAATCCAAGTCACAAATAACATCTGTCACATTTCTGGAACCTCTGCTTACTGGTCTTTGGTTAGGATCCAGCCAACAGTAGACTTTTTGAGAGTAGTTCTTGTTATTTAGAAGATATGAAGAATTAAGTGATAGAAGCATTATCACTAATACTCTGAATAAATTAACAGCCAGTGAGAATGGTGGAAAACTGTGAGAGACCCAGATTACGTACAGAGCATCACCTGGTAAATCTTGAACTCTCAGACAAAACTCAGATTTTCAGTAGGGGAAAAAAAATGTCCAAATCAGCATGGTTGCCTTCTACGAGAATTCCTGTTAACATCCTGTTACACATACTACTACGTGTGTAGTTATTAACTTAAGACATACGATGGTGATCTCTGTTCATGGGCTTTATTATAATTCTCAGCTGGCTAGCCAAGACCTTATAATCATTCATCACAGAATACAGAAATTTTCTGATTAACAGATACCAAAAGTTCTGCCCTCTGAATTAATATCAGTGTAGTCCCTTTTCATAAGGCTTTTGCTATATTAGAACTGCCCCTTCGAAACTGCTTTTCCTCCTAGTTAGTCTAAGCATGTCACAAAGTTTCATATCAACCATTACCTATTTATTGGCAGGCAAAAAGAGAGATATGTGGAATTTTTAAATGCTTGCTTTTTTAAAGAGACAGATGATTTATTCTCACTGTCCTTAACAAGCTGATCTTTCGGTTCACTACAAATCACATTTTCCTTAATATGACTGCTGAGAAGTCAAGGGAGAATCAGTAGGAAAAGGATATGTTCATGTATGGATTTTTAAAAGGTGGATTGACCTAGAGACTAATTTAGGGACTAGAAGCAGTATTCTTGGTTCTTAGTTCTAAGTCTTTCACTTATTTTGCAGTTAATTAGTTTTCCTTTATCTGTTCCTCAGTTTCTCTCAGTTTTAAGATACTGTTAGAAAACCCTGAGAATTTCCCAAGGGTGCTCAGTAAATGTAATGATCTTACTAATTTTGTATGTTTTTATTGTAGCCATGTGATAAGAATAAATTAATTGAATTTCATTTGGGTTTTGTTTGGGTTTCTTTTCCGTAG
Seq C2 exon
CTCCGAGTCTTCAAATTGGCCAAATCCTGGCCCACCCTGAACATGCTGATCAAGATTATTGGAAATTCAGTGGGTGCCCTGGGCAACCTGACCCTTGTGCTGGCCATTATTGTCTTCATCTTTGCTGTGGTGGGGATGCAGCTCTTTGGAAAGAGCTACAAAGAATGTGTCTGCAAGATCAACCAGGACTGTGAACTCCCTCGCTGGCACATGCATGACTTTTTCCATTCTTTCCTCATTGTCTTTCGAGTGTTGTGCGGGGAATGGATCGAGACCATGTGGGACTGCATGGAGGTGGCTGGCCAGGCTATGTGCCTCATTGTCTTCATGATGGTCATGGTTATTGGCAACTTGGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021339:ENSBTAT00000061543:14
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:
PF0052026=Ion_trans=FE(30.0=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(62.1=100)
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:
TCCTGAAGCTCATAGCCATGGA
R:
GAGGGAGTTCACAGTCCTGGT
Band lengths:
345-2238
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]