DreINT0131514 @ danRer10
Intron Retention
Gene
ENSDARG00000034588 | scn4ab
Description
sodium channel, voltage-gated, type IV, alpha, b [Source:ZFIN;Acc:ZDB-GENE-051201-1]
Coordinates
chr3:22142961-22143823:+
Coord C1 exon
chr3:22142961-22143091
Coord A exon
chr3:22143092-22143742
Coord C2 exon
chr3:22143743-22143823
Length
651 bp
Sequences
Splice sites
5' ss Seq
TCAGTATAA
5' ss Score
-7.29
3' ss Seq
CTTCACAACAAATTGTTTAGCTT
3' ss Score
1.57
Exon sequences
Seq C1 exon
ACGTTCATCGTTATAGACAAAAAGAACACGATATACAGATTCAACACTGAACCAGCCTGTTACTGTCTGAGTCCCTTCAACCCTGTTCGACGAGCTGCCATAAGAATACTCATACACTCATATCCTATTCA
Seq A exon
GTATAACCCATGTGTGTGCGAATAGATGTAACAATGCTCTTCATGTTTTTTCATTTTCATGTACACTACAAAAGTTTAGGGTCAGTTTTATTATTATATTTTTTTTAAAGAAAATTATTCTGTTCATCAAGGCGCCATTTATTAAATGTAAAAAAAAAAAAAAGTTAAATGGTTAAATATTTATCAAAATTTTAAATAACTGCTTGATTGAAATTATTATTCCAGTCATTATTGCTTTTATTACTATTATTACCATTAATAATAATAATATTAATTATAGTAATAATAATTAATATTATTATTATTAGAGTGATTTCTGAAGGATCGTGTGACTCAAGACTGGAGACATTGAGCTGAAAATTCATCTTTAAAATCAATGGAATAAATGATTATGTTAAATTATAAATTACTTTTAAACAGTTATTTTATAGTGAAATAACATTTCACATATTTGATTAAATAAATGCAGCCTTGGTGAGCAGCATACATTTATTTTAAAACGTTTCAATATCGTACCGACCCCAAACTTTTGACCGGTAGTGTATGACTTAACAATTCAGGTTTATTTGTAAAGCTCTGGCTTTTTGGTTTAATTAGGAGCCAAATATCATTCCTTCTTTGTTTTCCTTCACTTCACAACAAATTGTTTAG
Seq C2 exon
CTTAGTCATCATGCTAACCATCCTGACAAACTGTGTGTTCATGGCGATGAGCGACCCTCCAGGCTGGAGCAAAATATTAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000034588:ENSDART00000044157:2
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(0.8=7.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATCGTTATAGACAAAAAGAACACGA
R:
TCTAATATTTTGCTCCAGCCTGGA
Band lengths:
207-858
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]