GgaINT1024531 @ galGal4
Intron Retention
Gene
ENSGALG00000011040 | SCN3A
Description
sodium channel, voltage gated, type III alpha subunit [Source:HGNC Symbol;Acc:HGNC:10590]
Coordinates
chr7:19448405-19449727:+
Coord C1 exon
chr7:19448405-19448559
Coord A exon
chr7:19448560-19449553
Coord C2 exon
chr7:19449554-19449727
Length
994 bp
Sequences
Splice sites
5' ss Seq
CTAGTAAGT
5' ss Score
8.78
3' ss Seq
ATTATTATTTTTTTACACAGGCT
3' ss Score
7.17
Exon sequences
Seq C1 exon
GTTGTGTGCAGAAATTTCCATGTTGCCAAGTAAGTATAGAGGATGGCAAAGGAAAAATCTGGTGGAATCTTAGAAAAACCTGCTACAGCATAGTTGAACACAACTGGTTTGAGACTTTCATTGTCTTCATGATTCTCCTCAGCAGTGGAGCACTA
Seq A exon
GTAAGTTGAAAATAAAAATTAAAAATTGCAGATGCTGAAATATCTAGATGTCTCCTCACAGGTAACAGCAAAATTCAAATTGAATCAGAAAGGCCTGATTGACACAGCTTGATTGGAGCTGTGTACTACTTGTATTCCATGATTTCATGATTTATTTACTGAAAATTGGCTCAAACTTGAAAATGTTTGTTTTACATGCAGTTCTTCAGTGATACTTTTGTTTTACCCCTGAAAAGCTAGAGCAACGTTATTTAAGCCAGTGACTGTAGATCCAAACTGTCTACCAATTCTCAGCATGTTTATACAAAGATCTGAGTACAAAGAAACTCAGTTAACAGCTAAATGTACGATTTCAAGCCCTTAATTCCTTCTGTGCCCTGCCATTCCTAGGATGGTGCTTACAAAAAAACCACAGACAAACTGAAGCATTTCTTCATTTTGTTGCTGCTTTGAAGGCAGAAGGTAGAGAAGAGTGTGATAGCAAATGAAACCAAAAAGCTGTTTTCCAATAGGATTTACATTACCCACCTTCCCAGCTGTGAATGTGCATAGTATAAACTGCAGCAAATACATCACTCGTTGACTTTTAGAGAGGAGTTTGATTGATGGAGGATGAAAATGTAATCTCTCAAACTGCTCAGATTAGATTTTTGTTGAAGAGAGGGTTTTGTTTTTGTTTTTTCTTTTTTGTGTCTGTGTGAACATTTTTTTGATACAACAGTGGAAAAAAATCATGTTTTGAGTTTGTCTCCTCTTTCAACAGTAAAATAGGATATATATGTCATTCAATACACTTTACTGGAGAAATCCCAGAGAAGGCTGAATGATGTTGCTCCAATTTGCAGCATGGTTATAGGTGAGAAATAGGTAAAATGAGAGGATACAGAAGAACAAGGGGAAAGATTATACCTCAACTGCTTATTTTAATCATTCATATTCTGTGAAACATTAGTAACATCTGATTTTTTTTTATTATTATTATTTTTTTACACAG
Seq C2 exon
GCTTTTGAAGATATATATATTGAACAGCGTAAAACTATAAAGACCATGCTGGAATATGCGGACAAAGTTTTTACATACATTTTCATTTTGGAAATGCTTTTAAAATGGGTAGCATATGGTTTTCAAATATATTTTACTAATGCCTGGTGCTGGTTGGACTTTCTGATTGTTGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011040:ENSGALT00000017981:18
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:
PF065128=Na_trans_assoc=PD(19.6=84.6)
A:
NA
C2:
PF0052026=Ion_trans=PU(17.0=67.2)
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:
GTTGTGTGCAGAAATTTCCATGT
R:
AACAATCAGAAAGTCCAACCAGCA
Band lengths:
326-1320
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]