GgaINT1024500 @ galGal4
Intron Retention
Gene
ENSGALG00000027702 | SCN11A
Description
sodium channel, voltage gated, type XI alpha subunit [Source:HGNC Symbol;Acc:HGNC:10583]
Coordinates
chr2:5301781-5303464:+
Coord C1 exon
chr2:5301781-5302053
Coord A exon
chr2:5302054-5303343
Coord C2 exon
chr2:5303344-5303464
Length
1290 bp
Sequences
Splice sites
5' ss Seq
AGGGTTAAA
5' ss Score
-4.15
3' ss Seq
TCTTTTTTCTTTTTTAATAGACT
3' ss Score
9.27
Exon sequences
Seq C1 exon
ATGGAACCCTTGTTTTGGCCACTGGAAACTATCAGCTTTCAACGTTTCACTCCTGAGTCCTTGGCAGCAATTGAGAAAAAAATTGCTGAGAAAAAAGAGAAGCAAGCCAAACTTAAGCAGGAAACTACTGACCAAGAAGTTGAAGAGGATAAAGTGACTCCTCAGCTTGATCTGAAAACCTGTAAAAAACTGCCATCTCTCTATGGTGATGTTCCCGCGGAGCTTATTGGGGAACCTCTGGAAGACTTGGATCCATACTACAGTGATCACAGG
Seq A exon
GTTAAAATTTTAAAAACTTTTTTTTTTCAGTTTAATTTTATCTGCTATACTCCTAAGAGATAATGAAGATTGTATTCAGAAGTTGCTGCTTTTGGATTGCAGACAGATCTGTAGACAGATTTCAGAACATTACTAGTATTTCTTGGGGTAGGCAAGCTAGACTAAGTCACAGAATCATAGAATGGCCTGGGTTGAAAAGGACCACAATGCTCATCTAGTTTCAACCCCCCTGCTATGTGCAGGGTCGCCAACCACCTGACCATGCTGCCCAGAGCCACATCCAGCCTGGCCTTGAATGCCTCCAGGGGTGGGGCATCCACAACCTCCTTGGGCAACCTGTTCAGTGTGTCACCACCCTCTGTGGGAAAAAATTCTTCCTAATATCTAACCTAAACCTCCCCTGTCTTAGTTTACAACCATTCCTCCTTGTGTCTTACTATGTAACTACAAGGTATTTTTAAGGCCCAGTCAGTAATCAGAATGGATTCTGAGAATAGAATACACTGGATAGATTTTGATCAAAAATAGGTTCTGAGATAACTGATACTTTGTTACTCAGAAGAGTTTCTATGAAGTACCTGAGGCTGAACTCAGTGCCCCTCAAACAGTGGGTCACCCTGACTTATTGCAAATGCTTTTGCTTAATTGCAAATATACAAACGAGATGAGGCATATTTGAAATGTTTCCAGCACTCTGTATAGCAAAAAGATGAGTTTGCTTTAGACAACATCAATTCTGTGTTACTTTGTAATGTCTCATCAGCTTTGTTAATTGTACGGTATTGAGATTGCATATACTCCATTGCACTGCAAAATGTCTTCTCTTGTTGCCCATAGCAGTACGTGAATTAGATGCTGTAGGATTCTCTTCCAAATTAAATGTCTGTTGTATGATTCCTTATTATTATACCTGAAGAGCAGAATGTTCCATTCGGTCTGATGTTGCTGTCTGTCAAATATACCAGCAACTCACTGGAATGTGATCGTTCAATCAGAGAACTTGCAGAAGGCTTTGTAATTATTGGTGAAAAGGGCCTTCCAGAGACTTTTTTTCAAAGTAAACAGAATGACTGATGTAAAGAAAATAAGGCTGATTCAACTGAAGGCATCTACATAAATGTTACTTAGCTGTTTTTGATTAAAGACCCTTAATTTTTACTTCATCTGCCAATAGTACTGAGCAGCAATGGACCTTATGGTAGCTAGGAGATAATTTACACAGCTGCTTGATAATTTTGTTTCTTTAAAATATTTCATATGCTATGATTTTTCTTTTTTCTTTTTTAATAG
Seq C2 exon
ACTTTCATGGTGATCAATAAAAGAAGGACTATTTTCCGGTTTACTGCCACACCTGCCTTGTGTATACTCGGTCCTTTTAATCCAATCAGAAAAGCAGCGATTAAAATTCTCATCCATTCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000027702:ENSGALT00000042757:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.165 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
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGGAACCCTTGTTTTGGCCA
R:
AGGACCGAGTATACACAAGGCA
Band lengths:
348-1638
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]