DreINT0131555 @ danRer10
Intron Retention
Gene
ENSDARG00000005775 | scn8aa
Description
sodium channel, voltage gated, type VIII, alpha subunit a [Source:ZFIN;Acc:ZDB-GENE-000828-1]
Coordinates
chr23:27375315-27377369:-
Coord C1 exon
chr23:27377306-27377369
Coord A exon
chr23:27375457-27377305
Coord C2 exon
chr23:27375315-27375456
Length
1849 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
GTGCTCTCTTCCTCTCTCAGTCG
3' ss Score
9.26
Exon sequences
Seq C1 exon
CCAATTTCTACTTCCTGCCAGACCAGTTGGATGCACTTTTGTGTGGAAACAGCTCTGATTCAGG
Seq A exon
GTGAGTGTTTGGCCTTCTCTTTCAAAACATATCAATTATATACATTTGGAAAGCACAATGCTTCTTTATTAAATGACCCATGAACTATGAAATCAAAATTCCCATCATTTGTTCTACATTTAAGAGGCTATTTAACTTTTAAGAAGTTTCAAAACTTTCTTGTTAGTCTAAAACAGCTAAAATTGGCAAATTGTGGAAAACACAGCCTTTGTGTTGCCTTTCTACTGATTCAAAAATAAGGTAAAACTCAATAAACAGCATTAGCAATAACTTAGTTCTTTTCTTTGTACCGTGGTTATTTGCCATTCAGTGCATTCAATTATATTTTTCTACACCATGCTCATATGTGCAACAGGTAACAATTTCGCTTTTAAACGTGTAGTAATCAAAAAGCTATTATCAGTCAAACACAGCACAGCCATCACAGTGAAATGGAGAGATTTCAATTGACATATTGCACAAATGGAGTTATCATCTCCCTGCATGTCAGAGTAGGCTATGACAAACATGCAAAATGTCTATTATTATTATTATTATTATTATTATTTTATATTGTATAAAACAAAAGTTATTAAGTAATTATTAGTAGGCTGTAGATAAAGCAAGTTATTCCCTTCATGGCTTTGAAAACGTCCTGCAAGCATAAAAAGAATTGCTGAGGAGAATCACGTCTGTTTTTACAAACATATAAATGTATATTTGTAACCTATCCTATAATAAATAATAATTATTTATAAAGCAAGTTATAAATAATGCAATCAGGTGATGTGCTCCATCGGCTCGATACCTTAAAATTATTTTGTAGTGTGCGCTGTGCCGCAGTTTTCATATCTTGCTGTGTGCCCACGTTTAGGATTTGAGGTAATACCATCGCCATGATGGTCAAAGAAATCGAAACATTCTTTTCACACAAACGCAATTTAATAGGGCACTATAAAGGCTAAACAATTGAATTCTTATATTTGCTTATTTTTTGCAGCCTAGGGCTATACTTCTCACCATGTATTGTATCTTTTCTAAAACATACAGTATAGTGTGAAAGCTTGTTTATTACTAAGAAAACTAAAACAAACAAACAAAATTATATTTTAATTGAACACATCACATAAGGTACTGTACACATACAGCACCATTCTATTGTGAAAAGGCAAAGCTAAAAATCTATGGTTAAATCGCAACCCATAGTACAAAAGCTGCTGGCGCGCAGTAGGTACCTCCGCGGCGGCGTTAACAATGGCGGCAGACCGACCGTTTTGAAATGGTGACGTCTGTAGATTTGTTAACAAACCAAAAAACTACAATTTGACGCAGGATTTTTATAAAGACTGAATGTAAGACAATGCTATGCCGATCATATTGGACGTGTCGGTAATGTTGCTCTACGCAAGTGTGAGTCATTGTGTTCAGTTACATGTAGGCTGACAATGCAGAAATTTACATTGGTCCTTTCAAACATTCAAAAATGTATTATTATGCAAGCTGTCAGCCAATCATTTCAGCGGGTATTTACTTCAGAGTACAATCTGTCACGCATATGTCGGTGTGTTCTGATAAGCAGGGTTAAAAAAGACAGAAAAATAGCCAACTATGTCTCAATTCTGATGTTTTTATGTAAAAAATATTGATAACTTTTAAAGTGAACTTCAGAAAACAATACAGAATAAACAAAAAGGCTGGTCCTTGAGCCCCTTTAAAAGAATCAGACGTCTGTTCTTGTTCGTTCATATGTAGAAAAAAGATCAAGCTTGGCAGAAGTCATTTACTGAGATTCTCCTCTGACAAGCATTGTCTTGCAATTCATAGAGTGATGCCAAGTCATTATGGGTCGTGTGCTCTCTTCCTCTCTCAG
Seq C2 exon
TCGCTGTCCTGAAGGTTACACATGCATGAAGGCTGGCCGTAATCCAAACTATGGCTACACCAGCTTTGACAGTTTTGGCTGGGCTTTCCTGGCTCTCTTCCGCCTCATGACGCAGGACTTCTGGGAGAACTTGTACCAGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000005775:ENSDART00000022042:8
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(8.3=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:
CCAATTTCTACTTCCTGCCAGACC
R:
CAGCTGGTACAAGTTCTCCCA
Band lengths:
206-2055
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]