DreINT0131567 @ danRer10
Intron Retention
Gene
ENSDARG00000018032 | scn8ab
Description
sodium channel, voltage gated, type VIII, alpha subunit b [Source:ZFIN;Acc:ZDB-GENE-060906-2]
Coordinates
chr6:39410276-39412409:-
Coord C1 exon
chr6:39412255-39412409
Coord A exon
chr6:39410450-39412254
Coord C2 exon
chr6:39410276-39410449
Length
1805 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGG
5' ss Score
6.9
3' ss Seq
TCTTCTGTTTTGTTTTTTAGGCA
3' ss Score
11.99
Exon sequences
Seq C1 exon
CTTGTGTGGCGCGCTACAAATGTTGTGATGTGCCTATTACTGAGGGCTGGGGGAAGTACTGGTGGTTTCTGAGGAAAACTTGCTACCTCATTGTTGAGCACAACTGGTTTGAGACGCTCATCATTTTTATGATTCTTCTCAGCTCTGGAGCTTTG
Seq A exon
GTGAGGACACACACATTGCATAACTTTCTAAGAGACAAAAAAAACAGCAGCTGAAATTATTTGTTACTAATTTCTAAAAAGTGTGAAGACGTACACATTGGTGTTCAAATCAGCTTTGTATACAACTGAAGTCAGATTTATCAGAACCCTTTGAATTTCTCTTTCTTTGTAAAATATTTCCTAAATAATGTTTAACAGAGCGAGGACATTTTCACAGTATGTCTGATAATATTTTTTCTCCTGAAGAAAGTCTTGTTTGTTTTATTTCAGCTAGAATAAAATCCGCTTTTAATTTTTTAAAAATCATTTTAATGTCAAAACTATTAGCCCCTTTAAGCAATATTTTTTTCGATAGTCTACAAAACAAACCTTCGTTTTACAATAAGTTGCCTAATTATCCTAACCTGTCTAGTTAACCTAATTAAGCCATTAAATGTCACTTCAAGCTGTATAGAAGTGTCTTGAAAAGTATCTAGTAAAATAATATTTACTGGCATCATGGCAAAGAAAAAATAAATCAATTATTAGAAATGAGTTATTAAAACTATTATGCTTAGAAATGTGTTGGAAAAAATGTCTCTGTTAAACAGAAATTGTGGAAAAAATAAACAGGAGGCTAATAATTCAGGGTGGCTAATAAGTCTGAGTTCAACTGTATATATTTTTTTCCTGTAATTTATGAAAAATGCACATTTTTTTGCAAATCTAATGCATAATTTAATCAGGATCTCACTATCCCTCATGAATGACAGTTTATTTCAGATTAATTTTCAAAAATTTTAACCATTGAAGCAAGTGATAGCAGTTGAAATATATATATAAGAGCCATTATATTATTTAATACATCTCTGATTGTGTTAATCTGAAAATATTTCTTGGATTGTATTTAAATCATATTTGATAACAGGGTATCATTTGAAATAGTTTAAGTTTGGTCTTTGAAGCTAAACATTTCTTTTAAAGTTTAATACATATTTAATTTATTGTTGAAAGGAAAAAAACATAAGCAATTAATCTAATATAGGCCCTTATTTTGTTCCCTGTTGTTCATTGAAAGCGATGAAAATAACTTGACAGTGTAACTAACCTCAAAAACTCCTTAAGGCATTTTGGGGAGTCAGTGATATAGATTTGCAGAAGCTAAAATAATTAAGGACCATGATAAGTATTCTCTTGGAAGATACACGGGTACTGTATAGATTTTTCATCCTTGCACAATGTATATGTGCAGAACTAATGGTCTCCAGGTAGATTGTAATGTGATTGAGACTGCATAGCATGCAGTGTGCTATATGATCTATGTAAGTAGGTAATGGCTATCACTATATTGCAATGAACCGGCCACTGCACCTCAGCAGTCTGTCTTGGGGCTGCAGTATCTCATGTCTGCTGTTAGGGAGCGTAGCCAAATGCTGTAGAAAAACGTCCACATGCAGAAGATGCTGCTGCTGCCTTTCTTACAGCTACTATTAGGGACCGTGGCCAAACTCCAAATAAAGTGAGCATCTGTGAACTGATGTATGTGGGACTGCAGTGCCACACTCTGGGGATGGCAGGGACTGAAAGTAAAAAGTGTTTTTAGGAAAGTTGTAGGTGAATCGTCATCCATTCATCAAACAAAGTAGTTTATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAAGATGATTTAATAAATTTGTTAATAATTATTAAAAACTGTTAAATACATATTTTAAAAATAAAAGTTACATTTATATATAAATCTCTTCTGTTTTGTTTTTTAG
Seq C2 exon
GCATTTGAGGATGTATATATTGAACAGAGGAAAACCATCCAGATCATTCTTGAATATGCAGACAGAGTCTTCACATACATCTTCATCCTGGAAATGTTGCTAAAATGGGTGGCCTATGGGTTTGTCAAATACTTCACCAATGCATGGTGCTGGCTGGACTTCTTCATTGTGGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000018032:ENSDART00000151299:19
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:
PF065128=Na_trans_assoc=PD(20.0=84.6)
A:
NA
C2:
PF0052026=Ion_trans=PU(17.0=67.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTGTGTGGCGCGCTACAAAT
R:
CCACAATGAAGAAGTCCAGCCA
Band lengths:
327-2132
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]