GgaINT0099743 @ galGal4
Intron Retention
Gene
ENSGALG00000006072 | SCN10A
Description
sodium channel, voltage gated, type X alpha subunit [Source:HGNC Symbol;Acc:HGNC:10582]
Coordinates
chr2:5360857-5362215:+
Coord C1 exon
chr2:5360857-5361114
Coord A exon
chr2:5361115-5362094
Coord C2 exon
chr2:5362095-5362215
Length
980 bp
Sequences
Splice sites
5' ss Seq
AAGGTTAGA
5' ss Score
6.12
3' ss Seq
TCTTTATGTTTATTTTTAAGATC
3' ss Score
9.18
Exon sequences
Seq C1 exon
AAAATGGCTGACTTCCTACTACCTGGTACCAACAACTTCCGTAAATTCACTCCGGAATCCTTGGCTGCTATTGAAAAGAGAATTGCTGCCAAGAAGGATCATCAAAAAAGTACCTTAGATCAAAAACCTGAGGAGAAACCACGTCCTCAGCTTGACCTAAAAGCTTTCCAGAAATTGCCAGCTCTCTATGGAAATCCTCCTCCAGAGCTCATTGGGGAACCACTGGAAGACCTTGACCCATACTACAAAGATCGCAAG
Seq A exon
GTTAGAGCCAACCAAACTGTTTAGATCTTAATTTGTTTCGTTATGTGGCTACAAAATGTTCATGTGAATGATCTATTAAATGGTCTTGTTTATACTCCTTTGGAAAAACTATAATCCCTTCCCATGTTATAATAATGTGGGAAGTTGGCACGACTGAATGACATGCTGTAATTTTCAGGAAAAAAAAAATCTTAATTTTGAATTACAGGAATTAAATATCATGAACTGCATTAGCATTTAAATCAGAAGGGAAACATCAAAAGTGAAATGGACAAAGGAAGAAAATGAGGTTTTGACTCAGATTTACCAGAAATGATGATAACTTTGGAAACTTTCTTTATTTTCATGGTTTTAAACTCTCCTCCTCTGTCTCAACAGTTGTGCTCTATGAACGCACACAATGGGTGATCATCCAAGTATAAAAATTATTATAAAACGTTTGCTGGTGAATCCTTTAAACCTACTTATTCAAGCTCCATATTCTAGTCGTGTATACTTGAAGAAAATAAAGAGGGGAGAAATGGGAAATACTCCATTAAAAATGAAGCTTATTGCTTGAGAAACTGAGAAATACTTTGTGTTAATTTCTACAGTCTTAGAGCTATAGGATCGCTATTCATATTGACAAATAACATTTAAGTCTACAACTCTTTCTTCCACCTTTGCACAGCTTGATTCAGAGGTCCAACTTACCTCAAGAGAACAGTCATAAGCAAAATTTATTTTGCGTTCATTATAAGGATTTAGGTTTAAAGAAGGAAGTTCAGGGTAAGATTTTGTTCTGCTTTGATAGTTACTGGATATTAACTCATTCATCAGTTTATGATAAAAGTGTTGCAAAATATTACGGTCTACTCACTTAAGCAAGCAAACAAAAGTTATCGTCAAAGCCTTTCATAGAAAAAGGTGTAATAAAAAATATATATATTCTCTTAAGCTTCCTGAAAGTTTTACTTTGTTTCTTTATGTTTATTTTTAAG
Seq C2 exon
ATCTTCATAGTGTTAAACAAACAGAAAACAATCTTCCGGTTCACAGCTACGCGTGCCTTATGGATCCTCAGTCCTTTCCATCCAATCCGAAGAGCAGCAATTAAAATTTCAATACATTCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006072:ENSGALT00000038879:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.174 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCTGACTTCCTACTACCTGGT
R:
TGCTGCTCTTCGGATTGGATG
Band lengths:
352-1332
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]