GgaINT0046962 @ galGal4
Intron Retention
Gene
ENSGALG00000011009 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr7:19319713-19321114:-
Coord C1 exon
chr7:19321010-19321114
Coord A exon
chr7:19319984-19321009
Coord C2 exon
chr7:19319713-19319983
Length
1026 bp
Sequences
Splice sites
5' ss Seq
GCAGTAAGA
5' ss Score
4.95
3' ss Seq
TTTGTTTGTTTTTTTCCCAGAAC
3' ss Score
9.11
Exon sequences
Seq C1 exon
TTTGGAGGTCAAGATATTTTTATGACAGAAGAACAGAAGAAATACTACAATGCAATGAAAAAGTTGGGTTCAAAGAAACCACAGAAGCCTATACCACGACCAGCA
Seq A exon
GTAAGAATTAAAATCTTTTCTTTTTACATTGATTTAAAAGCTGTTTTGTGTATGTCTTAGACTGAATTAAGTTATAACCTGGGGAAAAAAAAAAAAAAAAAAAGATATACAAAAATCTTACTTATCTGAAATCCAGAATATTTAACTTTTGTAGCCTAAACATGAAGCACTCTTAACCTTTCCTTTTTTCCCCTTCATTTTCTCTTTACGGATGGCAATGACATTATATGTGGCAATTTTTTTAAACAAAGAAAAAGACTAAAACAATCACCTCTGACAATATATTTATCAAAATATTTGAAAGTTTTAGGGCATAGGCCTTTTTAGTCATCAAGGAAGACTGGGAAAAAATATCCTTCTACCTCTTGCATTCATTCTTGCTGCACAATCTTTACAATTTTTTTTTTCCTCCAGCTCTCCCCTGGCACTTCAGAGCAAAATTTAGATGGGGCAGTGATTCCAGCTCAGCAGTTCTACCTTGGACTGTGGAACCAGCTGATCCGCCCACTCAGCCATCAGTAAATTCTCTGTAGCTTAAAATGCAAAATGTTGTAAAGGTTATTTTGATGATATGAAGAGCACTGAACTTTGGGCTTGAAATTTTTCTGTATTTCCTTAAGATTTAGGACAAATGAAGTGCTATTAACTCTCAGCCTCTTTACAATACCCCTCCTTGTTTCTTTTTCCCAACTTTTGCCAGGTTAAGAGTTCATTTAATATTGTGTCACAAAAGCTTACAGTGAACTTGTTTGAGATATAAAATTGACCTTTGCAACTTTAAAAACTGCATCATGAGTATTTTGAAATCTTCCTTTTAATGCTTACAGATGTAGTATTTGCGTTTCTGTTTGATTTGTGTTTACATGTACAAACTGGAAAATTCATACAAATGAAAGACTTTATGGAAGACATGAAATCCCCTTACAATTACAAGCTAGATTAAACTAATTTGTAGCAATTTGGAAAAAAAGAAATTTTACCCTATGCATAACATAATAATTGTTTGTTTGTTTGTTTTTTTCCCAG
Seq C2 exon
AACAAATTCCAAGGCATGGTCTTTGATTTTGTAACAAAACAAGCATTTGATATCAGTATCATGATACTTATCTGCCTTAACATGGTCACAATGATGGTAGAAACAGATGACCAGAGTGAAGACATGGAAAACATTTTGTATTGGATTAACCTTGTGTTTATTGTACTTTTCACTGGAGAATTTGTCTTGAAATTGATTTCACTTCGCCATTACTACTTTACCATTGGCTGGAATATTTTTGATTTTGTAGTTGTCATTCTTTCCATAGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011009:ENSGALT00000017933:22
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(20.4=47.3)
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:
AAGAACAGAAGAAATACTACAATGCA
R:
TGGAAAGAATGACAACTACAAAATCA
Band lengths:
342-1368
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]