GgaINT1024513 @ galGal4
Intron Retention
Gene
ENSGALG00000027702 | SCN11A
Description
sodium channel, voltage gated, type XI alpha subunit [Source:HGNC Symbol;Acc:HGNC:10583]
Coordinates
chr2:5329951-5331084:+
Coord C1 exon
chr2:5329951-5330205
Coord A exon
chr2:5330206-5331030
Coord C2 exon
chr2:5331031-5331084
Length
825 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGT
5' ss Score
10.36
3' ss Seq
AACTCAGTGATTATTTTCAGGCA
3' ss Score
3.74
Exon sequences
Seq C1 exon
GTTGTTGTGAATGCACTTTTGGGAGCTATCCCCTCGATCTTGAACGTTTTACTCGTCTGTGTTGTCTTCTGGCTCCTGTTTAACATTGTAGGAGTAAAACTACTTGGACAAAAATTTTGGAAATGCGTGCTTAAGACAGGAGATAACAGAGAAGTTCAGAACATAAATGACTGTAGGAATTATGGTGGAAAATGGACAAACAGTTATGTAAATTTTGATCATGTTGGGATGGGATACTTGGCTCTTCTCCAGGTG
Seq A exon
GTAAGTTCTGTAAAAATATGCTCATCTTCAATTTCTTCAAGAAAAGAGCAGCCCAACCACAGGACACCACCGCACTTCTGTCTTTTTTGCTGAAAGTGGCAATATTTTCTAGCTTAAATAAATATTTTTCATGCCTATAAGCTGCTCAGTTTCTGATAAAGTACACTTTTGCATATGCAGCTTTGTTTCATGATTTTTTGTATTTTACTGCAGTATTGATAAATATACTAAGCCTGAAATGTTTGTGGATTTAAATTACTCATTTTATCTAGAGTAAAATTTGTCCTACAGAGGGGAACAGAGAAATAGCTCAATGCACTTTGTTTCTTTTTCTGATATTATATCAGTCATGAAGCGTTTGGATGCTGACTTACTGGTCTTAGTACCACAAGATAGGTGCTGGAAACACCTGAAGTGTTTTTGAAGTGCTTCCTATCCCCATGTTCTATCTAGCTGTTCTTTGCCCTGCATCCTCGAAGCCTTCTAGAATCCTTCAGAAGTGCTAAAACTGCTGTTTGTCTTAGAATTTATTTTCTGCCTTTTAGGACATGCTTGCTAACTGAACATAAGCATAGAATTTACAAAAAACCTGATTAAAAATTAATGATAAGAGAGATTTGGCAGGGCTCACACCCCCTTTTTTCAATACATAATGTTAATTTGTTTCTGTTTACCAATCAAGTAGAGCATTAGAACATTTTTTGTAGCACGCTTCTCACTTTTCCTGAACTGTAAACAAATTTATGTTAGCTCTACCTCATCTTTTATTTTTGTTTTTATTTTTATTTTTATTTTAACGAGAATAAACTCAGTGATTATTTTCAG
Seq C2 exon
GCAACTTTTAAAGGCTGGATGGACATTATGTATGCAGCAGTGGATGCGCGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000027702:ENSGALT00000042757:21
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:
PF0052026=Ion_trans=FE(38.2=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(7.7=100)
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:
TGTGAATGCACTTTTGGGAGCT
R:
TCCACTGCTGCATACATAATGTCC
Band lengths:
294-1119
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]