GgaINT1024516 @ galGal4
Intron Retention
Gene
ENSGALG00000027702 | SCN11A
Description
sodium channel, voltage gated, type XI alpha subunit [Source:HGNC Symbol;Acc:HGNC:10583]
Coordinates
chr2:5335005-5335798:+
Coord C1 exon
chr2:5335005-5335106
Coord A exon
chr2:5335107-5335533
Coord C2 exon
chr2:5335534-5335798
Length
427 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGA
5' ss Score
6.29
3' ss Seq
ATTCTTCTCTGTCTCCACAGAAT
3' ss Score
11.81
Exon sequences
Seq C1 exon
GGTGGAAAAGATCTCTTTTTGACTGAGGAACAGAAAAAGTACTATAATGCCCTAAAAAAACTCGGATCCAAGAAACCTCAAAAACCCATCCCAAGACCATTG
Seq A exon
GTGAGACCATTTAAGAGGGAGCATGGTAGAAAATGTAAAGATGATGACCAGTTTAAATCAAGCAGCAGGGGATCTGGAAGTAAATTTACAAGTTGGAGCCCATCATTGGTCTACAGCTCTGCTTATACTAGAATGCCTGCTTCAATAAGTATTTCTATGCACAGAGCAGTCACAATGTACTCTGAATGTTTTCCTTTTGTGTAATTTTTTTCTAAGGAAATGTAGTTGTACGATACCTGAAAATACTTGGCCACATACTGAGTGTTACCTTAAAATGTCTGAAGAAATTGCCTACAATGCTTCTAGCACCTTATTGTTAATTTTTTATTCTCTTAAATTCCCTTTTGAGCCAAAAATTACTGTTTAATATTTGAATGTTGCCTGAGTCTTAGAAGTAACATTAATCCATTCTTCTCTGTCTCCACAG
Seq C2 exon
AATGCATTTCAAGGATTTTTCTTTGACATAGTGTCACACAAAGCATTTGACATTAGTGTGGTGACTCTCATCTGTCTAAATATGGTTGTGATGATGGCAGAAAGTGACAATGGAGAAGTCAGGGATGTTCTTAAAAAAATCAACTACTTCTTTGTGACAGTATTTACTGGGGAATGCATCATAAAAATAATAGCCTTGAGACATTACTTCTTCACCACTGGCTGGAACATATTTGATTTAGTTGTTGTGGTCCTTTCACTAGTTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000027702:ENSGALT00000042757:24
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(21.0=48.3)
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:
AGATCTCTTTTTGACTGAGGAACA
R:
AGTGAAAGGACCACAACAACT
Band lengths:
354-781
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]