GgaINT0046957 @ galGal4
Intron Retention
Gene
ENSGALG00000011009 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr7:19331147-19333525:-
Coord C1 exon
chr7:19333352-19333525
Coord A exon
chr7:19331270-19333351
Coord C2 exon
chr7:19331147-19331269
Length
2082 bp
Sequences
Splice sites
5' ss Seq
GATGTATGT
5' ss Score
6.31
3' ss Seq
GCCTTTCTGTTTTTGTGTAGGTC
3' ss Score
10.94
Exon sequences
Seq C1 exon
GCATTTGAAGATATATACATAGAGCAACGTAAAACTATCAAGACCATGCTGGAATATGCTGACAAAGTTTTTACTTACATCTTCATTCTGGAAATGCTTTTAAAATGGGTGGCTTATGGCTTTCAAACATATTTCACTAATGCATGGTGCTGGCTGGACTTCCTGATTGTTGAT
Seq A exon
GTATGTATTCTTTTTCATATAATGTACCACAAACTCTAAAAATCCCAGTATTATGTGTTTAGATAAACATTCTGCTCTAGCCAAAGGAAGCTCTGTTTTAAAATTGCTGTTGTGATATGGTTTATAATTCTGTTTAGAAAAGAAAAATTATGCAGATGTACTTATTATTATAGATTTTTTTTTCCTGATATTCTGTAGTTTTATGAAGTTATTGAGCTTTATTGAAAGTGTGCTTTTTTGTTATTTTTTGCTGTGTGGAATGGATGTTGCTGATCCTTGTGAGTTTTAACTGTATATGGAATTTGAATATTTGAAAGCAATTTATTTAAAAGTTTCTAACTTCTAATCCATTAATGTGTATCCTATCACTTAGTGTGATGAAAGAAAAATACTGCTAGGAACTCTCAGTACTACTCAGTACTTTTGTGGTTTTCACTGTATCACATGTGCAACCTTAAACAGTCACTTAGAGAACTACAGCTGAGCTCCCTTGAAATGAGTACTCAAGTGATTTTCAAAATGCTGCACCACCAAGCAGATCGCATTTTCTGAAGGACCTAGAGGACAGAGTATTGTAATTTCAAGTCTTAACTGCCAAACAGTGTATGCATATTTCTGGGTAGCAAAAAATGGAAGACTACAGATCTTTAGCCATGTAGCAGACATCCATTTCCCTTCCATCCTCAATATCCTGACTACATCTGTCTGTGCTAATAGGGCATCACTCAGTTCTGCATGTGTAATTCCCATATAATGCAAGGTAAGAGTGTGTCTTGAATCTCTTGGTCACTTGCTCTGATCAGCAGCAGAATTCTGTAGAAACCACTGCATACCTCCCTAGTATTCCAATATGATAAACTATGAAGTGTTTACTACACAGAGCTTGGAAAACGTTCTAACTTTATATCCGTACCATCCCTAGAGATCCTATGCTAAAATGTGCCTAGGTGCCACGTTAGAATTCTGTGGTTGAGTAAACCCCTGTGAAATATTTAATGGCATAAGATTATGTAAATCATCGACCAGTAGTGTTCTACAGAGGCTTTGTACTTTACATTGTCACTCTATGTTCACTGTATTTATCAAAAAATATTCAAGTCTTATTTGATAATCTGTGGTTTAGTTACTTCAGTGAACTTTATGAATATCTTTCTGAGATTTTCATGGGAAACTTTTCTATAGCAATTGTTTGCATGGAAAAAAAAGCCCCAACAATTTCCACAGTATTTTTTTAACTGTTTAGTTGGAGGAGTGAAAAAACTAAGCAAAGAAGTTAATGTGGAAATGACAGAAATGAGAGAACAGGAAGGCTGAAAGAGAAAGGCATTAACTTGCAGTAGGTGTTAAAAATTTTCTTTACTGGGACCATTGCTTCCAAATGGTCTACTATAAATACAGTTCTATGGATTATTGATGAAAGGTAATTGTATTATTTATTTTACAGCTTTTCTGTTTTATTTACTCATCTGCCTGCAGACCAGACCAGCGTTATACAAGCCAAAATTGATGAAGTTGTTAAAGGATTCACAGGGAATGTAATGAAGTGTGGATATGCCTAACAGTGAAGGTCCTACCATTGTCTAACAAACAGTTGGTTATCAGTTTTGATTAGTCTTGTTAAATCTGAACAACACTGGTAGCTATGGCAAACTAGAAATTTGCATTTGACCGAAGGCCAGGTCTGAACGTAGTTTTAGAGAGCTTTTTCATTCTCAAGTTCTGAAGATGACATGGAAAGTCCTGTCCTAAATTGAGCATTTCAATTCAGCCAACTTCTGCAAGTTTTCTTTTTGCATGTGACTTCATTTTTCATTAAATACCACCAAATGTTGGCTGGTTTATGTGAATTTAGAAGACATTTTGTATACCATTCTACAAAGATGATTTCATCAACAGGTACCTAGGATATACTTTTATTCTGCTTTGTCTGACTTAAAAACTTTCTGCGTTACAGAGGGGTTCCTAGAGAAAGAGGTCTACCCTTGAATCTTCTTGGGAAGTTCAGGGCACATGTCATCCCACCATATGTATCAAAGGATATACAAGATGAATGAGCACTATTGCCTTTCTGTTTTTGTGTAG
Seq C2 exon
GTCTCTTTGGTTAGCTTAACAGCTAATGCCTTGGGCTACTCAGAACTTGGTGCGATTAAATCCCTTAGGACACTAAGAGCTTTGAGACCTCTAAGAGCCTTGTCGCGATTTGAAGGGATGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011009:ENSGALT00000017933:17
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:
PF0052026=Ion_trans=PU(17.0=67.2)
A:
NA
C2:
PF0052026=Ion_trans=FE(17.5=100)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]