DreINT0131462 @ danRer10
Intron Retention
Gene
ENSDARG00000062744 | scn1lab
Description
sodium channel, voltage-gated, type I like, alpha b [Source:ZFIN;Acc:ZDB-GENE-060906-1]
Coordinates
chr6:10065479-10066268:-
Coord C1 exon
chr6:10066150-10066268
Coord A exon
chr6:10065569-10066149
Coord C2 exon
chr6:10065479-10065568
Length
581 bp
Sequences
Splice sites
5' ss Seq
TTCATATCC
5' ss Score
-14.87
3' ss Seq
ATTCCTTGACTGATGCTCACTCT
3' ss Score
-7.57
Exon sequences
Seq C1 exon
ACCTTTATAGTTTTGAATCGTGGGAAGGCTATATTCCGCTTTAACGCTACGCCGGCCTTGTATATTTTGAGTCCCTTCAATCCATTAAGGAGAATCTCCATCAGGGTCCTGGTGCATTC
Seq A exon
ATATCCTTTATGAGCTGAATGGATGTATGTACGCACGTTTTCCTGTACTGCCAGAGCTTTTACCTGTGAGATAAATCCTGATCCACATTCATCTCATTTTGACCAACAACAATCACAACCAACATCTTCCAGATGGAAAGGGAGTAAACACAGTTTGTTTATATGTGTATATACATCATTCAAAAGATTTTTTTAAATGTTTTTGTTTTGATTGCACTTGCTTTCATGACAAATACAGCAAAACGATGATTTAAATATCTAAAATCTGGCAATTTAACAGTATTGAAAATGTTAAGGTCCTATCATGCGATGTTGTGTGTGTATATACACTCACAAAGCAATGTTTTACTGCTTGTTCAAACTACTGATTTAAAATTAGCTAAATCAACGCAATTATCAAGTTTTTTGGGGGACAACTTAATTGTTTTATGTTTAATCCACTTACATTTGTAAGAACAATGAAGTTAACTTAATCGATTTGTGTTGGGACAACATGAAGGAGTTGTGCAGAACCCAGCATTTTTTACAGTGGCCATTTACTTGTGTGTTTTCTTTGTATATATTCCTTGACTGATGCTCAC
Seq C2 exon
TCTGTTCAGTTTTGTGATCATGTGCACAATCTTGACCAACTGCGCCTTCATGACGCTCAGCAATCCCCCAGAATGGGCCAAGAACGTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062744:ENSDART00000151247:3
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=6.5)
Main Inclusion Isoform:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTATAGTTTTGAATCGTGGGAAGGC
R:
TCCACGTTCTTGGCCCATTCT
Band lengths:
206-787
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]