GgaINT1024508 @ galGal4
Intron Retention
Gene
ENSGALG00000027702 | SCN11A
Description
sodium channel, voltage gated, type XI alpha subunit [Source:HGNC Symbol;Acc:HGNC:10583]
Coordinates
chr2:5324844-5326020:+
Coord C1 exon
chr2:5324844-5324998
Coord A exon
chr2:5324999-5325835
Coord C2 exon
chr2:5325836-5326020
Length
837 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAAT
5' ss Score
6.06
3' ss Seq
ACTGAATTCTGAAATTCCAGGCA
3' ss Score
2.62
Exon sequences
Seq C1 exon
GTTGTGTCAAATATTTTCCTTGCTGCAATGTGGATATCACTAAGTTTCCAGGCAGCACTTGGTGGAAATTTAGAAAAACCTGCTACAAAATTGTCAAACATAGCTGGTTTGAAAATTTTATCATTTTTGTAATAGTATTGAGCAGTGCAGCACTG
Seq A exon
GTAAATTTCATTCACTTTATCAAACTTTGAATGGAGGGTTGTCAGCTGCTGGTGGTGGTGGGAACGGGTGGATAGATCACTAGAAATATTGGTCACAGGAGACATAAAGTGGAGATGGAGATAATATGGTAGAGAAGTAAAGGATGAAAGGAAGTATGAAGGCACTGCCAGAGGATTGGTGAGGAAATAATGCAGCTGCTAAAGGAATTGGAAATTGATTGGCAATATCAATAACTTACAATAAATTGGTAGAACAGCAAATCTGTTAAAGGCAAGTGAACAAGACAATGGAGCGATCACACAATAAAGCATTTTCCAAAACCCTTACTGACAGCAAGTAATGTCAGGGGGTTTGTGAGAAATTTGAAACTCAAAGATGAGGTCTTTGTTGTGTTTTTTTTATACCTGTGTTACAGCTCTGCAGACTCTCTGAGACAGCTCTGAGGGTGGCAGCTTTGGAAGGTTTAGGCCTGAAAGAGGTTGGTTAATGTGTTTAACTTAAACTTAGTTATGAAGGATTTTAGACTTCAAAAATTATCTACTTATTTGGGAAGCTAAGATTTTTGGTAGCTATATCAGGCACTCATCAGATGCTTATTGAATAAGTCTAGAACGGAAACAATCCAAAGCTTTTCAACCAACCTGAAAATGATGCTGTTTACTATTTAGGTTTTTATTTCTAACTATAAAAATAAGTTGCCAATAACATAAACATGAAATGGATAGAATAAGCCAAACTGTATTCTTGTGCAATTCTAAAATAATTTACTGTAAAACTACTAAAGTAATTTACTGTAAAACTACTAAACAGCTTTAAACTGAATTCTGAAATTCCAG
Seq C2 exon
GCATTTGAAGATATTCACCTTAAGGACAGAAAAACAGTTAAAAAGCTCCTAGAGTATGCTGATATGGTATTTACTTACATCTTTATTATGGAGATGCTTCTGAAATGGGTAGCTTATGGTTTGCACAGTTATTTCACAAATGCATGGTGTTGGCTCGACTTCATCATTGTGTGTGTAAGTATTAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000027702:ENSGALT00000042757:17
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(21.1=84.6)
A:
NA
C2:
PF0052026=Ion_trans=PU(19.5=69.4)
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:
TTGTGTCAAATATTTTCCTTGCTGCA
R:
ACTTACACACACAATGATGAAGTCGA
Band lengths:
334-1171
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]