DreINT0131428 @ danRer10
Intron Retention
Gene
ENSDARG00000086819 | scn1a
Description
sodium channel, voltage-gated, type I, alpha [Source:ZFIN;Acc:ZDB-GENE-040426-751]
Coordinates
chr9:50212605-50215765:-
Coord C1 exon
chr9:50215661-50215765
Coord A exon
chr9:50212876-50215660
Coord C2 exon
chr9:50212605-50212875
Length
2785 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGC
5' ss Score
7.31
3' ss Seq
CATTTCCTCATTCATTTCAGAAC
3' ss Score
8.89
Exon sequences
Seq C1 exon
TTTGGGGGTCAGGATATTTTCATGACAGAAGAACAGAAGAAATATTACAACGCCATGAAGAAACTAGGCTCAAAGAAACCCCAAAAACCCATTCCAAGACCAAAA
Seq A exon
GTAAGCAAAAATATCTTTATTTTCATCATGTCACTCCAGAACTGTTTATTGTCTTTTGGATCTGAAATGTCCGAGCTGCTCTTTTTATTTCCCTTTCTTTTAGCTTTCACTTTTATTCCACTAAAGTGATTTTTCTGTGCATGTGGACTATAAAGCACTTCTGCATTAAAGAGATAGTTCACCCAAACATAAAAACCTGTAACCATTGACATCCATAGTTGGAAAAACAAATACCAGGGTTCGTACGATTCCGGAAAACCTGGAAAGCTCATGGAATTTTCCAGGCCAAATAAGCCCAAAATGTTTTGGGAAAGTCATGGAGATTGAGGTTTGAAGATTGAAAAAAGTTGACATAAGGTGCTTTTTTCCAACAAAAGTGTCAGTCACATACTGTAAACACAATTTCGCTACTGAATGAGTCCATCAAGATAATGCTGTTAATAACGCACAGTCTATCGCTGTATAGTAGCAGACTGATATAGTCTGTGAATAATATGCCCTGAAAACTAACTGCAGAATAACCAGCTAACGTAAAGTATATGATCCTGGCCAGTTCTCCTAATCTTTCAGAGTAGCATGTGCAGAAAAAATTGGTCAGAAAAAATGCAGCCTGTGTATAGGCACAGTATTGATATATGAGACATGTTTCATTTGCAAAGTGGCTAAAATAAACGGAAATCTTTATTAAACTATCCCTTTATCAGTTAATAACCTTTTTTATTTCTTAAAAACCGAACCTTTTTGCAGTTATTTGCCTGAATTTCTATTTATTACGAGGTGTAAATATTGCGTTTAAGTGACATTTTAAGAGCTAATTTTTGCTGGATTATCTTGTCGGATGGTTATCATATCCTCAGATTTTTGATGTACCAAAAAATATTTCCAGCTATTTTGTCAAATCGCTTACCATACTATTTTAAGTGTGCATTTAATATAATAATAACATTCAACGTTCCGTAGTCAGAAGTTGACCACTTAAATAATATAAAGAAAAAAGAAATAATGAGAATCAGCACCTCCGAGTCCGAGGCCATGGTGCTCCACTGGAATAAGGTGGTTTGCCATCTTCTGGTTGGAGGAAAGTCTTTACCCCAGGTGGAGGAGTTCAAGTATCTCGGGGTTTTGTTCACGAGTGAGGGAAGGATAGAACGTGAGATTGACAGGCGGATTGGTGCAGCGGCAGCAGTAATGTGGTCAATGTACCGGTCCGTTGTGGTGAAGAAGTACCTGAGCTGAAAGGTAAAGCTCTCAATTTACCGGTCAATCTGTGTTCCTACTCTCACCTATGGTCATGAGCTTTGGGTCATGACCGAAAGGACAAGATCTCCGATACAAGCAGCCGAAATGAGTTTTGCTCGAAGGGTGGCAGGGCACACCCTTATAGACAGGATGAGGAGCTCTGACACCCGAAAGGAGCTAGAGCCGCTGCTCCTCCACATCGAGAGAAGTCAGCTGAGGTGGCTCGGGCATCTGTTTTAGATGCCTCCTGGACGCCTACCTAGGGAGGTGTTCCAGGCATGTCCCACCGGGAGGAGGCCTCTGGGAAGACCCAGGACACGCTGGAGGGACTATGTCTCTCGGCTGGCCTGGGAACGCCTCGTGAACCCCCCGGAGGAGCTGGAGGAAGTGTCTGGGGAGAGGGAAGTCTGTGGTTCTCTCCTAAGACTGCTGCCCCCGCGACCCGGCCGGAAAAGCGGCAGAAAATGAATGAATAATAATAATCCATTTTTGGTCTTTTGAACCACCTGAAGCCCCCTTGTCTACAGGCCTAAAACTTAATAATTTGTACAAAGAGAGGATTAATTATTAACGTATTTTTATAGCAGTTAAAAAATAATACCAACGTGTGTGTGTGTGTGTATATAAATATATTGTTTGATTCACCCATCTGCAGCAATGTCAAGTGCAAGCCTACGCCCTTGGATTATTAACTCTATATTAAACTATAATCCCAGCATTGCATATCCTGTGATGTGAGTATTGCGGGATGCACACATTGTGATATCGATGGTGAAACGATATATAGTGCAGCCCTAACTTGAATATAGGTTAGTTGACTTCTTTTCTGTCCTTGGCCCAAAACTTGCTCTCACATTGTTAGTGCTGTGTGAGCATTATTAAAATCAGTTCTACATAGATATAAGATATATTTTCTATATTTTCTTATTATTTACCATGCATATGTAAAGATTACATGAAACATTGCGTCATGAAAATGTACTTAAAAGTTCTGGAAAAGTCTCTGAAAAGTTGCTGAATTTTAATATTAAAAATGTTTATGTACCCTGTTAGTAAATGATGACAGAATTTTCATTTTGGGTGAACTATCCCTTTAAATAGAGCTTAAATGTATGATATTGCTTCCTTTAAAGGCGCAGTCTGTAATTTTTGCCACTAGAGGGTGTGTATTTGCAACAAACAAAAGCATTGTCTGATGACTCTGTGACTAAGTGTTGTATCATGGGAATTGTGGTCTTCATTACATCCTACTATATGAGACTGCAGAAATCATGTTGATGGATGATCTAAACCCTGCAGAACATTTATCTGTCCTTAAAATAGCTGAAGTGGATTCAGACATAACCTTAATGCTTTTGCGCCATGCACTTTAAAATAGAGCCCTTAGACTTTAAATGACCCCAGAGTGGGTGAAATCCCCATCTCCAACAGCACACAAAAGTTAAATAAACAAATAATGCATATTGTGCCTTTAAAGCATTCTTTTCTTGTTTGCAAATGTCTTCTGTATAAGTGAACGGCTCTTACATTTCCTCATTCATTTCAG
Seq C2 exon
AACAAGATTCAAGGACTCATCTTTGACCTCGTAACCAAACAGGCCTTTGACATTTTCATTATGGTCCTGATCTGGCTCAACATGGTCACTATGATGCTGGAGACGGAGGATCAGTCGATTGAAATGACCCGTGCGCTGTACTGGATCAATGTCATTTTCATTGTGCTCTTCACCACCGAATGCGTCCTGAAGATGATCGCTCTGCGCCATTACTTCTTCACCGTTGGCTGGAATGTGTTTGACTTTATCGTGGTCATCCTGTCTATAGTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000086819:ENSDART00000161648:18
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(19.9=46.2)
Main Inclusion Isoform:
NA
Other Inclusion 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]