DreINT0131423 @ danRer10
Intron Retention
Gene
ENSDARG00000086819 | scn1a
Description
sodium channel, voltage-gated, type I, alpha [Source:ZFIN;Acc:ZDB-GENE-040426-751]
Coordinates
chr9:50224315-50225382:-
Coord C1 exon
chr9:50225209-50225382
Coord A exon
chr9:50224438-50225208
Coord C2 exon
chr9:50224315-50224437
Length
771 bp
Sequences
Splice sites
5' ss Seq
GATGTAGGT
5' ss Score
4.9
3' ss Seq
TCCTCTGTGTATATGTGTAGGTC
3' ss Score
7.71
Exon sequences
Seq C1 exon
GCTTTTGAGGACATTTATCTGGACACAAGGAAGAGCGTTAAGACCATACTGGAGTTTGCTGATAAAGTTTTCACCTACATCTTCATTCTTGAGATGCTGCTAAAATGGGTCGCATATGGATTCGCCAAATACTTCACCAATCTGTGGTGCTGGCTGGATTTTGTCATTGTTGAT
Seq A exon
GTAGGTTGCCCTGCACAATATTAGTTACACATTTGATCAAGATTAACCTATAAAATGTTCACAGTTTTTTTCAGAAGAAGAGGGTTCACAAAAGTTTTCAATTACACAGTCCACTTTAATCAAGCGTTGATACACTGTACTAGTGTTTATCAGTCTGTTATGGTGAGCACATGCAACCATAATCATTGGTTCATAGTAGGCCATGTGTTTTCTCAAAACTACTGTTGCGCTATTACTTTTACACCTTTAAAGCATTAGTTCACACAAAAATGCAAATTGAGTAAATAATGGGAGCTTGAGAGAGCTCCAGGATTTCATCTAAAATATCTTCATTTGTTTTCTGAAGATGAACAAAAGTCTCAGGGGTTTTGAGGACATGGGTGGGCGATTAATAACAGAATTTACATTTTTGTGTGAACAAACCCTTTAAGTTTGCATTTGTTTCTCAGAACTTGACATGTTTTGCATGATCTGCTTTAGTGAAAAGAAAGCCAAATCAACTCCACAACATATGACATCCTCCACAATACCAACGAAAGCATCATTATCCAGAAAGCAGTATCATGTGCGCTTGGAAATGATCATTTCTGGGTGTGTTATACTGCGTGAGTGCTCGTGTCTCTGAGAGTTTAGATTGTTTGATGACAGCTGCTTGAGTGAATGGTGCATTTGTACATCTAAAAAGGCCATTTTCCCCTGAGAAGACAGAGTGAAAGGATCAGGAAGGAAGGGAATGGCTTTTCTACTAATCTCCTCTGTGTATATGTGTAG
Seq C2 exon
GTCTCGCTGATCAGCCTGGTGGCCAACGCCCTCAACTATTCAGAGCTGAGTGCCATCAAATCCCTGCGAACACTCAGAGCCTTCCGGCCGCTTCGGGCTCTCTCACGCTTTGATGGAATGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000086819:ENSDART00000161648:13
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=PU(17.3=66.1)
A:
NA
C2:
PF0052026=Ion_trans=FE(18.1=100)
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:
GCTTTTGAGGACATTTATCTGGACAC
R:
CCTCATTCCATCAAAGCGTGAGA
Band lengths:
297-1068
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]