GgaINT1024511 @ galGal4
Intron Retention
Gene
ENSGALG00000027702 | SCN11A
Description
sodium channel, voltage gated, type XI alpha subunit [Source:HGNC Symbol;Acc:HGNC:10583]
Coordinates
chr2:5303344-5304252:+
Coord C1 exon
chr2:5303344-5303464
Coord A exon
chr2:5303465-5304164
Coord C2 exon
chr2:5304165-5304252
Length
700 bp
Sequences
Splice sites
5' ss Seq
CATATCCTT
5' ss Score
-20.06
3' ss Seq
CCTTAGCTTATCATTCACATTAT
3' ss Score
-5.87
Exon sequences
Seq C1 exon
ACTTTCATGGTGATCAATAAAAGAAGGACTATTTTCCGGTTTACTGCCACACCTGCCTTGTGTATACTCGGTCCTTTTAATCCAATCAGAAAAGCAGCGATTAAAATTCTCATCCATTCAT
Seq A exon
ATCCTTTGGTTGAGTTCTGTTTTAATTTTAGAATGTATGGTGCACATTTATGTGATTCTCTTCTTTTCATATTAATCAAATTGTGGCTTTGATTCTGAGAGCAACAATATTTACAAGATACAATATTTGCAAATATTTACTACATTCTACTGTTAAAAAACACCTATTTAAAGAGTTGGATTTGAAGATGCTGTTATGAAACCACATTTAGATGCTACAGTGTGATATTTTAGCCCTTTTCCAGAAGTTTTTGTGAATCTCCAGTGTAGTGACAAGCTTAAAGTTTTAGTTAGAAACAAACCAGGGACTTCCTCATAATTAAAACACGGAGAATGGAAATTTCAGCAATGCTTTGCTGAAATTTTGAAATTTTTGAAATTTTGTCTGGTGTTTCCCTAAAAAGGATATTTCATACTCAAGTTTATACAGCTCTGAGCACCAACTTCTCATGTATTTGGAAAAAGATAAATATATTTTGAAGGAAGTTAAAATATAAAGGCCTGCAGGTGCAGAGCTGTAGGCTGAGTAGTTTCTGTTCTTTCTGCCAGACATGTGTTTTCCTTTAGACTTGTTCATTTGTGGGAATAGATTCCTCAATATGGCTGACTTTGAATACATGGTCATGCCATTACTAAAAGCAACTTTCCTGAACTTCACTCTTTTATAATACAGCACTTTTTCCTTAGCTTATCATTCACAT
Seq C2 exon
TATTTGTTGGCTTTATTACGTGTACTGTGATACTCAATTGTGCTTCCATGGCTATGAATAACTATCCACTAGATTTCAATGGGACTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000027702:ENSGALT00000042757:2
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(0.4=3.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCATGGTGATCAATAAAAGAAGGAC
R:
TCAGTCCCATTGAAATCTAGTGGA
Band lengths:
206-906
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]