GgaINT0046960 @ galGal4
Intron Retention
Gene
ENSGALG00000011009 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr7:19322229-19323589:-
Coord C1 exon
chr7:19323536-19323589
Coord A exon
chr7:19322367-19323535
Coord C2 exon
chr7:19322229-19322366
Length
1169 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGT
5' ss Score
8.62
3' ss Seq
GTGTCTATGCCTTTCTGCAGGTT
3' ss Score
9.95
Exon sequences
Seq C1 exon
GCTACATTTAAAGGATGGATGGATATCATGTATGCAGCTGTGGATTCTCGTAAT
Seq A exon
GTAAGTATACTCCCTTGATTCCATCAGTTTGACTGTATGAGCTCTAAGACTTAAGAACATAATTTTAACTCCATCTTTTAGAAGTAACAGTAAAAATGAGAGAACAAGGTATTATTGCAGTTTTATAGTCAGAGAAAATTGAAACCATAGGAAAAATACAGGAGATGAAGAAAGCAGAGGAGCAGTCCTAAAAGATCCAAATTCTCTGCAGTGCAGTTGGACCAAGATTCCTTAATTCTGCAGCAGACTGAACTGTTGCCATGAAATGCCTTTTCCTCCTCTCATAATGTGCATTGAGGTATTAATTACATTTGGAAACAGCATGGATACATAGCTTAGAGATGATGGTTTGTACCACTGATCTTTTTTTAAAGGTGAGATTTTCACTATCTTCTGCAAGCAGCCTGACTTTTCTTCAGGGCACAGTTCCTATTCTTAACTCAGCCTGTGAATTTTCATATTGTTTTACCTTCTCCTTGCTTCCTTGGTGCAAATTGTGCTCTAGCTCAAGTAAACAACTGAATAAACTATACTGGTGAAGCTCCAAGATTTTTGCAAGCTACATTCACAACAGGAGGTCTGTTGTAATATAATAAATGTGCATAGCTATAACAAGAAAATATGCTTACTCTGAACATTGTTTGGATGCCTTTCTTTGGCCTACCTAGGCCAATTAAGCTGCAAAGAACATGTGCTGTAACCTGCATTGGTCAGGTTTTTGAGTTCAAACTCAGGTTATAATTAGGGTAGACTGCAGGAAAAGTCCGACAAAACAGTGAGATATAAAACAATAAGAGAAGAAGTTGTACAAAACTGATAGCCCTTGTAACAAATACTAAAACCCAGGGCAGCTTACTTAGTGCCTGTAGTAGTGAAGCTCTACAAGCCTACACTGGTGGCTTCCCACAAGATACACTAAAATGTTCACAGCATTCAAAATTGATGTTTCTGGTTGTGTACAGATTCAGATGGATGGTAATCCTAGTTTAAAACAATTGTGCCTTCAATATTTATTCTACAGTAATTTAGTGAGTAACAGTTTTGGAAAATGAAGTATCAAGTTCAATAGCAGAGTCCTTTGTCAAGAGTATTTCTTCATAAATACTCAACAGCTACTCAACTCTATGTCCACATTTAAACTAAGGCTTAGTGTCTATGCCTTTCTGCAG
Seq C2 exon
GTTTTGGATCAGCCTAAGTATGAAGATAACCTGTATATGTATCTATACTTTGTCATCTTTATAATCTTTGGATCATTCTTTACCCTAAACCTTTTCATTGGTGTCATCATAGACAATTTCAACCAACAGAAGAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011009:ENSGALT00000017933:20
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(7.4=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(15.3=76.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTACATTTAAAGGATGGATGGATAT
R:
TTTTCTTCTGTTGGTTGAAATTGTCT
Band lengths:
190-1359
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]