DreINT0131424 @ danRer10
Intron Retention
Gene
ENSDARG00000086819 | scn1a
Description
sodium channel, voltage-gated, type I, alpha [Source:ZFIN;Acc:ZDB-GENE-040426-751]
Coordinates
chr9:50220552-50224437:-
Coord C1 exon
chr9:50224315-50224437
Coord A exon
chr9:50220825-50224314
Coord C2 exon
chr9:50220552-50220824
Length
3490 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAAA
5' ss Score
4.51
3' ss Seq
TGATGTTCATATGCCCACAGGTG
3' ss Score
9.28
Exon sequences
Seq C1 exon
GTCTCGCTGATCAGCCTGGTGGCCAACGCCCTCAACTATTCAGAGCTGAGTGCCATCAAATCCCTGCGAACACTCAGAGCCTTCCGGCCGCTTCGGGCTCTCTCACGCTTTGATGGAATGAGG
Seq A exon
GTAAAATCGCTTTTTATGGACTTTTTGTTTTACTGTATATGCATATTTAGAAATAAACATGAATTTTAAACATAGAATTCACATACATACTGAAGCTGAAGTCAAAATCCTTAGCACTCCGGTGACATTTTTATTCTTTTTAAAATATTTCCCAAGTTTAACAGACCAATTAAATTTTATTAAACAAAAATCTTCTGGGAAAAGTCTTATTTTATTTTGGCTGGAATAAAAGAAGTTTTTATTACAATTTTAGGTTAATATTATTAGCAAGAAGAACTCACTGTTGTTCAATGACTTGCATATTTAACCCTCGTGCACTGTTTAAAATTACTACCCCTAAGCATGTGGTTATGATTGAACACGGCTGGTCCTGTATTAACTAACACATGATTCACCATTCAGAAGATCCCTAACTCACTATAAATAACCAGTTTTTTAAGGCTGGCTCACAATGTCTACGTTGACATGGACACCAATAATTCGATTTTAATGCAATTAAGGGTGCTTTCACACCTGTGAATCGATTCAGTTGTTCCGAAACAGAGATTACAAATGTTACATTGTTGCTCTTTGCTCCTAGAGCAGTTTACTTTCACACTGCAAAGTTTCTCATCGGACCAAAAGAGCTTAAACAAGTCACGTGTGAGTAAACTCTCCTTGCATTGGTCAGTGTCAGGGTTTATTTTTAAGAGTCCCGCTCAGCTGTCAGGAGAGGTGGTGGTTTGGTGGTGTTTGACAAGGTGCGCGCGACGTTTCCAAAGAGTGAGGAGTGATGCGGCAGGGGGGGAGAGAAGAGTGCGCGACGTAGCCTATTTGAGGACCGGGAGGGAGACGCGAGATTACCAGGAGATTATCACTTGTTTGCGGGCATCCGGGAGACTCGCGAAACTTCCCGCCCTACTCATAATTCTCTCTTCATATAGCTGTATGCCTATTACGTATCCATAAAACACAGTGATACAACCGCGCTCGGATCCAATCGCTTTCTCTTTTTCTTTTTCTTTTTGCTTTCACTGCAATCAATCCGCTCCAGAGTTCGTTTCAATCGAGCCGAGACCACCTCATTCAAGCGATCTCGGAGCGATGGATTTGGCGCGGATCCGAGAGTGATTGGTGGTTTCACATATGCCAAACGAACCCCGCTAACTGGGCAAACGAGACAGGTTCCGAAACAAAAGTGTAGGTCTGAAAGCACCCTAAGATAATACTCCTATAATTAAGAGTCTACCATGTAAACAGCAATTTTTGATTCATTGAACAAGATTTAGAAAATAATCGAACTAAAGAGAAATCGAATTAAGACATGTGGAGTATGCCGATTTTAGTCGCATTATTGAAGTGCATATTATATATATTTACGCTCCCTATATTGTTTACCTTTACTCTGAATATTCAGTTTGAAATAGCATGTCAGTATGGCTTAGTAATAAGTGTAATTCCTGCACACCGCTGGCCAACCACTAAGCATTCAGTAGTCGCTTTAGGACAAAGCGTGTGAGAGAGTAAGATCTGCAGTCTTTGCATGCATGAAATATTGCACATTATGACAAGTTTTGCTTGCTACACAACTGTAAATATGCTGATATAATACAGTTTCACACTCTGAATTGTAGTATTATTAAGTTCTATAATGTTTTCTAACTGGCGAATGACATGATCTAATGGGTCTCTGTCATCTTTAACATGCACAATCGTGATTTCAGGAGGCGTGGCTTTGAAGCTTGGAGGAGGGACTGTTTTTATAAAGATATGTTATCGGGTAGCATTTAGGCATATCATCTACTGCACTTTAATTCAACTATTATGTTGGATGTATAATATGTATTATGTAAATATAATGCATTAATGTAAATATGCGATGGGTTCATTACTGTGACATGATCCTGTATCTGCTCTTCATTCATGAGTTTCAGTAAGTGGTATTGTAGGAAGAATTGATGTGCAGCTTTATATAATAAGCAAAGGTCGATAGTGCAGCTATTGACCAAACACTTGCCTACGTTTTCCCCATAAATGTGATGTTGCAACGGCGTCCCCTCACGTGGCAAACGCAGATCTCTCCTCTCCACGATTCCTATTTTTTTTTCTGGAAACTTCACTGCTGAGTGTCTTCACGTGTGTTTTTTTTTCTTTTTTCTTTGTGTTTGTTGATTTACAGTAAACCGTAATACTGTGGCTTTACGATGCATCCTAAAGGTCACGCTTTTTCATCCCAATCCGCCAGCGCTGTGCACTATTCATAATTCAATTCAGACGCTTTTAAATGGCAAGTCTGATGGTGGAATATGAGAGCAGTTTGAATCAAAGAAAATCATCAATCAGCTTTATCAGTTTACCTGTTTCTTTCTTTTTCTTCCAGTCTGTCTTTCCTTCCTTCCTTCCTTCCTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTGTCATTCATCTCTTTCTTTCTTGCTTGCTTTTTCTTTTTCTTCCTTTCTTTCTTTCTTTCTTGCTTTTACTTGTTTCTTTCTGTTTCTTTCTTTCTCCTTTGCTTTCTCTGTTTCCTTGTTTTTTTCTTTCTTTCTTTTTCTCTTTTCTCTCTGTCTCTTTTCTTTCTTTCTTCTTTGATTTCTCTGTTCTTTCTTTCTCTCTTTTTTTCTTTTTCTTTTTTTCTTTCATTCTTTCTTTCTTTTCTTCTTATTTCTTTCTTTCTTTTCTTTCTTTTTCTTTTTTCTTCCTCCTTTGCTTTCTCCCGGTCCTTTCTTTCCTTCTTTCTTGTATTTTATGTCTGTTGTTTGTTTGTTTCTGTCTCTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTGTTGTTTTAAAATGCAGTGTGGATAGGGGAAAACGGAGACATCTGAAAGCGGAGGTGTGGCTGCAGACATTCGCCTGTGTGATTGGGCCTTTTTCCTCAATATTAAGTAGCCTACACAAAATTAATTATTAATTTATTATTCATTAAAAATATTTAATTAGTTTCCACTTAATTTGAAAAATCTTCTTTTCTTATTTTCTTTCTTCTAAAAAGTTGATGTAATTTATTTAAGTTGATTTAGTGAGGCTTTTTAGTGTACTGTAAATAAATCCAAATTAAATACAGCTGAATTATTAACCCACCGTGTATATTTTTCCCCATTTTTTGTTTAAAGGAGAGATTATTTTTTCAACACATTTCTAAACATAATAGATTTAATAACTCTCTAATAATTTATTTATTTTGTCTATTCAGCTTGAAGTAACATTTTAAAGGCGTAGTTATATAATAATAAAAAATATTGTAGGAAATACTGTGAAAAATTCCTTGCTCTGTTAAACATCATTTGTGAAATATTTGAATAAGAAATTCACAGGAGGGCTAATAATTTTGACTGTATTTGAGCTGTAAAGCAAAGTGCTTATGTTATAATGGTACGACATTGTAAGTGTGTGATGTTCATATGCCCACAG
Seq C2 exon
GTGGTTGTGAACGCTCTTCTGGGCGCCATTCCCTCCATCATGAACGTCCTGCTCGTCTGCCTCATCTTCTGGCTCATTTTCAGCATTGTGGGTGTCAACTTCTTCGCTGGGAAGTTTTCTGAATGTATAAACATAACCACGGAGCAGCGCCTGCCTGTCTCAGAGGTCTATAACAAGACAGACTGTGAAAGAATGGGGAAAGGAGTCCGCTGGAGAAATGTGATCATTAACTTTGACAATGTTGGGAATGGATACCTGGCCCTGCTGCAAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000086819:ENSDART00000161648:14
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(18.1=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(40.3=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:
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]