BtaINT0129540 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021339 | SCN8A
Description
sodium channel, voltage gated, type VIII alpha subunit [Source:HGNC Symbol;Acc:HGNC:10596]
Coordinates
chr5:28283310-28284602:-
Coord C1 exon
chr5:28284539-28284602
Coord A exon
chr5:28283452-28284538
Coord C2 exon
chr5:28283310-28283451
Length
1087 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGT
5' ss Score
10.24
3' ss Seq
GCTTCCTTTTCTTTCCTCAGGCA
3' ss Score
10.34
Exon sequences
Seq C1 exon
CAAATTTCTACATAGTTCCTGGTATGCTGGAACCTTTGCTCTGTGGGAACAGTTCTGATGCTGG
Seq A exon
GTAAGTAGCTCACTTAATTTTATTCTCCTCCCATGAAATAATGTGTCACACAAAAATGAACAATATTTTCACTTTCTTTGTGCTCATGTAGTGGGTCCAATAAATTGGTTGACTCAGATTTTCTTTCTGTTTTATATTTGCCCATCCAAAGTTGACATTTCACTAGTAGGTGAAGGTGGCTATTAGACTTAAGCCAAGATCAAAGTTATAAAAGGCTAAGGGTAGGATCTGTAACACCAGGTATCTTGCCTGTCTCTTGTAGACTCCCCTCATTCTGTCTTAATGCAAAAGTTATCAAGTAAGGGCACTGTTTTCATGATAGATTAGCACCCAAGGTTGACCCCAAATATGCCAGGCCTGACAGCATGTGGGAGGGAAAAGAGTTGCAATGTATTATCCCCCCCGCCCCCGCCTTTTTTTCATTGTGGCAAAATACACATAACATAAAATTTGGTCTCTTAACCATTTTTACATATACAGTGCAGTGATATTAACTAGAAGTCCATTTACTTTCTATACTGAAGTATTGATAGATACTAGAAATTACATTGGAATAAACATCAGGTGAGTCTTAAAGCAGAAGAACTATTATAACCGAGATCACTGAAATCCTAGTGTGATACAGTTTGTCACAGTGAGTGTTAAGAGAATAGAGATGATTAAGAGGAAGGTCTAGGCTTTTGTCATTTAGGTTAGTAGCTAAGTTAAATTTGGTTGAATTGCACATTGATATGAGTCTAGGACAGCGATTCTCAAATTTTGGCATGCGTAAGAATCATCTGACATGCCCCTTAAAAATGCCAATTCATGGATCCCATATGCAGAGTTTTTATTCCTAAGTCTTGTCTAGGACATAGGTATCCGCATTTTTAAGGTGATTCTGATCCTAGACTGTCCCCAGGACATCATTTTTGAAAAATTCACCTGGCTACTTTGTTTCTTTCCTCTTCTTTTTAAAAAATTCCTGTTTGTTGGCATAGTCTCTATGGATGGCTGTTTATCATCTGCAAGGTCATAGAGATGACTTCCAGCTGATGACCGGGTAGGATTACGCTGAAAAGCCCGGTGCTTCCTTTTCTTTCCTCAG
Seq C2 exon
GCAATGTCCAGAGGGATACCAGTGTATGAAGGCAGGAAGGAACCCCAACTATGGTTACACGAGCTTTGACACTTTCAGCTGGGCCTTCTTGGCATTATTTCGCCTTATGACCCAGGACTACTGGGAAAACTTGTATCAATTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021339:ENSBTAT00000061543:7
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(8.4=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(18.7=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:
TTTCTACATAGTTCCTGGTATGCTGG
R:
TGATACAAGTTTTCCCAGTAGTCCTG
Band lengths:
198-1285
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]