DreINT0131577 @ danRer10
Intron Retention
Gene
ENSDARG00000018032 | scn8ab
Description
sodium channel, voltage gated, type VIII, alpha subunit b [Source:ZFIN;Acc:ZDB-GENE-060906-2]
Coordinates
chr6:39460678-39461882:-
Coord C1 exon
chr6:39461795-39461882
Coord A exon
chr6:39460807-39461794
Coord C2 exon
chr6:39460678-39460806
Length
988 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
ATTTTATCGCTCTATGTCAGGTA
3' ss Score
7.31
Exon sequences
Seq C1 exon
TTTTCAGCATGATCATCATGTGTACAATTTTGACAAATTGTGTCTTCATGACATTCAGCAATCCTCCAGAATGGTCCAAACAAGTAGA
Seq A exon
GTAAGTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTGGTGTATATTTGACTCTTATTGCTTATGAGAGACAATAAGTATTACCGTTCATAATTTTCAGAGGTTTATTTATATTGGTAGTACATTCTTAAAAAATACTCAATATTGATGGAACAGTTCCATTGCACTGATCCTTCTTCAGATTTCAGTATTTAGAACAACACAAACAAAACAATACATATGGTTCTTTTATTAATTGTAAGTTCTGCAAGGAATCACAAAAAAGCTTCTTCTATGGCAGATTTTAGTTTCACACTGAACAAAAAGAAAAACTGCTGTAAAAAGAACCAACTTTTTTGCATGCTCACAACATAGAAACCGAATGACTTCTGTAAATGGAATTAAGGGTGTGTTTACACCTTTAGGTTGGATCTCCTAGTGCAATCTATTTCAACAACGTTCCTGGAGGACCACCAGCTCTGCACATTTTCCATAGCTGTGTCACAAATCGCTTACTTATGCACTATTCTACGCCATTTTCTAGTATAAATAGAGTCAGTAGTGCGTTCACACTGAAAGCTCTAAAAATATAGATTTTTTTATGATTTTTTTTTCACTATATCTTCCTTTCTGTTAAGCAGAAGAAAGAAACTCAAACAGGTTTGATTAAATAGTGGCAAAATTTGGATGTATGGGCGAACTATCCCTTTAATATGTCTGCCCAGTAAGATGCTAGAATAAAATTGTAAGGTAACATCATACTGTATATGTTGTCTTTGCTGTATCCAGTACCACAATACATTTTGACTTTTAGTAAAAAAGGTGGATGAAGCAGAAGAACTATTTAGAATAAACTAGCATTCAATTTAATACAAAAAGTATCTACAAAATATTATAAAATGCACATTACCTGCATGTTTGAACTCATTTTATCGCTCTATGTCAG
Seq C2 exon
GTACACCTTCACAGGAATCTACACTTTCGAGTCTCTCACAAAGATTGTGGCTCGAGGTTTCTGTATAGACGACTTCACCTTCCTCAGAGACCCCTGGAACTGGCTGGATTTCATGGTCATCTCTATGGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000018032:ENSDART00000151299:4
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=PU(0.8=6.7)
A:
NA
C2:
PF0052026=Ion_trans=FE(17.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGATCATCATGTGTACAATTTTGACA
R:
GCCATAGAGATGACCATGAAATCCA
Band lengths:
208-1196
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]