DreINT0131532 @ danRer10
Intron Retention
Gene
ENSDARG00000005775 | scn8aa
Description
sodium channel, voltage gated, type VIII, alpha subunit a [Source:ZFIN;Acc:ZDB-GENE-000828-1]
Coordinates
chr23:27367992-27370485:-
Coord C1 exon
chr23:27370279-27370485
Coord A exon
chr23:27368277-27370278
Coord C2 exon
chr23:27367992-27368276
Length
2002 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGG
5' ss Score
7.2
3' ss Seq
TCTAAATGATGTAATGGCAGGCA
3' ss Score
1.27
Exon sequences
Seq C1 exon
ACACTGAGAGCAGCAGGGAAGACCTACATGATTTTCTTTGTGCTGGTCATCTTTGTGGGCTCCTTCTATCTTGTGAATCTGATTCTGGCTGTGGTGGCCATGGCATATGAGGAGCAGAACCAGGCCACCATGGAGGAGGCGGAGCGAAAGGAGGCGGAGTTTAAAGCCATGCTGGAACAGCTGAAGAAACAGCAGGAGGACGCACAG
Seq A exon
GTCAGGCAGTGCTTTAATGCCGATAATAAGGGTGATAATAATTAGTATATCATGTTTGCTTTCTGTATTGGATGGTTGGATTGTGTTTTATTATTGAGTAATGACCAATTCTGGTTTATAATTGTCGACTTTAAGGCAAGATGCTGCAGGTGAAGCGAGTAAAAGAACATAGTATATTGTTTTAATTAGTATATTGTAGTACATTTAGTATAAATAATAATATTTTCACCATATTTCCCACTTTTTATAAATACAGACCACAATAAATCTTTTTTGTATTACATGTTTACTAAAACCTTATATTTAAATATGCAGATGAAGCATTATTTCATAATATGTGCACTAATGTGCATACATTTTTAGCACAAAAATCAGGTCTGGTTCAGAATTTCTAAACTCTTGTTTCTTTTTTCATTTTCTTTTCTTTTTTTTCCTTTTTTTACATGTTAGAGTCAGAGAATTTAATTGACGAAATTTAGGGAATGACTATTTATCACTCCCAAAACATTACATGCAGAAGTTTTGTAGAAAAAAAAAAATTGTATATAATTAGGCAAATTACAAATGAACTTATTCCTCAGTAAAACCTGCAGAAAACAGATCTTAAACAAGGCTGCAAGCATCGATGAAAGAGACCTCACACCTGGGCTCACTGCCGCCTGGTGACCTTAGGATGAAAGAGAACAATGGACAATAATAATTTAAGCAGATGTTAAAAAAAACCTAAGAAACTCACAGATTTCTGCCAAACTTCCTTCTATCGGCAAGTGGCACTATGGCTATAACTTAATATTCGAATTTAGATGTCTTGAGGAAGGGAATCTTATAAAACATTTTGGGCAGATCGGACATTGTGTGTCTAAGTACTTCCTCTTCCATGGCAAAACACTGAACTTTGTCAGTCCGCCATAGACATGCCCTTCATCAAAAACTCTAGATCTTCACAATTTAACATCGCACAGGCCTTTGGATTAGACAAATGGAACTGATTCATAATGATAACATTTTTAGGAGTTTGTTACACTGTAAAACATGTCATTTGCCAGCAGGTGGTGCTGTAACTGTAACTGGATATTGACATGGAAACTTGTTTAGGTCAGGATTGTTATTAAACGTGTGGACAACAACTTTCTGTTTCGTGGCAAAACATCAAAGTTTGTGAGGACGCCACGAACACGCCCTTTGATGAAAACTCTAGATCTTCGCAATTTCACATTGCCAATTGAATTTAAATGAGAATACCCAAATTTGGTGTTGATCTGTTAAAATCCCTAGAAGGACTTTGATAAAATACAATGCCTGGAAAAACTGCACTTTTTTTGGCAAAGAAAGTTAAAAATATCTGACTTCCTGTTGGGTTTGAGACTTTTTTGTAGGTATTGGCATGTTTATGTGTGTGCCAATATTTGTATGTGGGCATGAAACGTAGTTTAGGGGCTTCACCGCCAAATGTGCATAGGAGGCAAATTTTTGTGCGTTTTTGAGCATGTTTAGACCCTCAAAAATGCAAGTCATTCTAGAGAAGAAGATAAAGAAGGAGAAGAATAAACTGAGCAATTCCAATTGGGCCTATGCACCGTAGGTGCTCGGTCCCTAATAAAACTGTGAAGTTTGGTATTTGAAAATGGACTTTGAAAATACGTATTTTAATTGAAATCTAGACACCAATATTAACAATGTAATAAAAGAAATCATGTATTTTGGATGTTTTCTTAACATTATACTTAAAATATTACATGCTTAAAAACTTTATAATTTTAAGCAAAAAAGCCCAACAAATTTCTTAAATTAAACTGATACATTTTGCACCTTAATGCTGATAATAAGAGTGATGATAATAATTACAATATCATGTTTGTCTGCCTATTTAGAGGGTTGGTTTGTATTTTATTATTCACTCTTGACAGAGTCTGGATTATAATATTAGACTAAATAATTTCTCATTTTGTGACTTTAAAAGGATCAGAAGTGAAATGTATTAATCTAAATGATGTAATGGCAG
Seq C2 exon
GCAAATGCAATGGCGACGTCAGCGGGAACAGTGTCTGAGGACGTGGTGGAGGATGATGGAGATGGAGAAGGGAATTTGTCCTGCAGCTCGTCTGAGATGTCTAAACTGAGCTCCAAGAGTGCCAAAGAGAGACGCAACCGCAAGAAGAAGTGGCGGCAGAAAGAGCAGGACAAAGAGAAAGGGGACAGCGAGAAGTTTGTCAAATCCGAATCAGACGATGGAAGCAGAAGGAGATTTCGTTTCCCTGATAACCGTTTGGGCCGAAGGAGTTCCATAATGAACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000005775:ENSDART00000022042:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.145 A=NA C2=0.958
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(12.3=44.9),PF0043013=ATP-synt_B=PU(76.5=89.9)
A:
NA
C2:
PF0043013=ATP-synt_B=PD(21.0=17.9),PF119333=DUF3451=PU(33.0=67.4)
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]