DreINT0131489 @ danRer10
Intron Retention
Gene
ENSDARG00000098738 | scn4aa
Description
sodium channel, voltage-gated, type IV, alpha, a [Source:ZFIN;Acc:ZDB-GENE-051201-2]
Coordinates
chr12:4852458-4854360:+
Coord C1 exon
chr12:4852458-4852580
Coord A exon
chr12:4852581-4854081
Coord C2 exon
chr12:4854082-4854360
Length
1501 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
3' ss Seq
GGTGTTCCTACTCCATACAGGTG
3' ss Score
8.14
Exon sequences
Seq C1 exon
GTGTCTCTGGTCAGTTTAACGGCTAATTTAATGGGCTACTCTGAGCTGGGGGCAATCAAATCTCTCAGGACACTTAGAGCTCTTCGTCCACTTCGAGCCCTATCCAGATTTGAAGGAATGAGG
Seq A exon
GTAAGGAATGAATCTCTCTTCACTTGTGTATGTTTATTTGTGTTTGATTCTTTAGTTGCTAATTAAAGTGCTGGAATTGTCTTTAATATGATGTGTGACCATATTGATTTTACTATTTATTTTTAATAGCATTTGACAATGATAACATTTTTAGTTTATGTAGCATTTGTTATAGGGATAGTTCACCCAAAAATATAAGGTTACTCTTCGTCAAGTGGTTCCAAACCTTTATGAGTTTCTTTCTTATTCTTTCTTGTTTCTTTGTTATTTTCTGAACACAAAATAATATATTTTGAAAAAAAATGTTAAATATTGACATCTACTTAGGGGAGGGAAAATACTATGGAAGTCAATGGCAAGCAGTTTCAGAAATTCTTCAGTATATCGTATTTTGTTTTCTTTGTCAGAAGAAAAAAAAGTCCAACAAGTTTTTGATAGGTGAAGGATGAGTAAATCATGGCAAAATCTTTATTTTGTGCAAAAGCACAAAAAAGGCTTGTGCTTGCTTAAACAGGTTTTAATGTTGTCAATTAAATAGGTGTTGGTAATGACAGCATTACTGGGAAGAGGGATTGTCTATAACATGATATGATGTTAATCTTAGCATATTGCTTTTAAAAGGATGCCTACTGAGCAATTTGTAAAGTTATCAAAAGTCAAAAGGAAAAAGTGGCATGTAGAATTTTCTTAATTTTGACACTGGTTTGCAAGTTAAATACAGAAAATTTAAAATTCTTTATTAATGTATAAACATATTTAAATAATAGATAATTATGTAGAAATTAGGCAAATCAAGAAAGATTAGGTTAAAGGTACAGTAAGAGATTTCTAGTTTAAAGCTATGAAACATTTTGAGTGTATGAGGGCATTACGTTTTTGAATCTGTTGTGTGTGGGCCAGACAGAATCTGAGGACCTTTTTTGCTATTTCTATGGAGAATTTTGTCACAAATCTGCAGATTTATGCAGAATTATTTTAAGAGAATCATAACTAAAAATGTAATATATAAAATAATTAAAAATAATACATATTTAACTTTTATTAAATTTTTACAATGCAAATCAAATTAAATCCACTTATTTGGTAAACAAAGCAAGTCTCTCAAAATATACTAAAAGACAGAAAATATTACTTTATAAACTGTACTGTAAATAAATCAAATCAACATTTTAATATTACTTTTATTATGTCACAATAATATTAGTTGAATGAATTTAAAAACTGAATAAATATACATTTACACAAGCATTCATGGACTTATTGATGGGCTAAAAATCTGTGGAAATCTGCAGATTTCTGCACTTGCAGATTCCGTGTGGGCCTAAACAAGTCACTGGCTGCAGTTCACTTAATGGCCATCAGTGTAACCTAGCAAAGAAAACAACTGGAGGAATGAATGCATCATTTTTGACTAAGAAAGTCTTTTTTTCATATGCCCTTTTACATAAATATTGATTACTCACCTATGTCTAATTCATTATGGTGTTCCTACTCCATACAG
Seq C2 exon
GTGGTAGTGAATGCACTTGTAGGTGCCATTCCCTCTATTTTTAACGTGCTCCTGGTGTGTCTGATATTCTGGCTCATCTTCAGCATTATGGGGGTCAATCTGTTTGCCGGAAAATTCTACCACTGCATCAACACCACCACAGAGGAACGGATCCCCATGGATGTAGTCAACAACAAGAGTGACTGCATGGCACTGATGTACACCAACGAGGTGCGATGGGTCAATGTCAAGGTCAACTACGACAACGTGGGACTCGGCTACCTCTCTCTGCTGCAGATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000098738:ENSDART00000170961:19
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:
PF0052026=Ion_trans=FE(17.5=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(40.4=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:
CTGAGCTGGGGGCAATCAAAT
R:
CAGAGAGAGGTAGCCGAGTCC
Band lengths:
353-1854
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]