DreINT0131490 @ danRer10
Intron Retention
Gene
ENSDARG00000098738 | scn4aa
Description
sodium channel, voltage-gated, type IV, alpha, a [Source:ZFIN;Acc:ZDB-GENE-051201-2]
Coordinates
chr12:4834632-4835411:+
Coord C1 exon
chr12:4834632-4834750
Coord A exon
chr12:4834751-4835321
Coord C2 exon
chr12:4835322-4835411
Length
571 bp
Sequences
Splice sites
5' ss Seq
TTCATATCC
5' ss Score
-14.87
3' ss Seq
TTACCTTGACTGTACTTCACGTT
3' ss Score
-0.77
Exon sequences
Seq C1 exon
ACTTTTATTGTCATAAGCAAGGGAAACACAATCTTCAGGTTCTCTTCTGAACCGGCGATGTTTTGCATCAGTCCTTTTAGTATTGTCAGAAGAGGAGCCATCAAAATTCTTATACATTC
Seq A exon
ATATCCTTTTTGTGCAGTTGTTTCATTGCAATCATTGTATCTGATAACAATCATCATTTAGAGGGCAATTTTGGGTGTGGGCTGGTTACCCAAAGGTTGCTGGTTCAGTTTCTGGTCCTGGTGACCACTCCTCCTGGTGTGTGTGTGGTCACACTCACTCAAAATGTGTGTGCATGGATGGATTAAAAACAGAGGACTAATTGCAATTTTTGGGTAAAAACCAAACACTCTTTGAAATAAAGGTACAAAATCTGTCACAGGGCGGTACCATTTTAAAAGGTATATTTTTGTTCTTAACAGATCCTTAAAGGTACATATTAATACCTAAAAAGTACATATGTACCTCATAAGGGTACAAAAATGCACCTTAAAGGTACAAAAAGTGGTCCCTAAACTTACTAACGTACACATGTACAGTACAAAAGTGTACCTTTTGAAAAGGTGCCACCCCAGTAACAGATTTTGTACCTTTATTTCTGAGAGTGTACTTGGCAAGGCTCAGTTCACTTCACTCACTCACTCATTATTGAGTCTTTAGATGTTTGCAATATTTACCTTGACTGTACTTCAC
Seq C2 exon
GTTATTTAGCATGTTCATCATGATCACCATCCTGTCCAATTGCGTGTTCATGACGATGAGTAACCCTCCAGCCTGGAGTAAAACTGTCGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000098738:ENSDART00000170961:2
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:
NO
C2:
PF0052026=Ion_trans=PU(0.8=6.5)
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:
ACTTTTATTGTCATAAGCAAGGGAA
R:
CGACAGTTTTACTCCAGGCTGG
Band lengths:
208-779
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]