GgaINT0046963 @ galGal4
Intron Retention
Gene
ENSGALG00000011009 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr7:19318427-19319983:-
Coord C1 exon
chr7:19319713-19319983
Coord A exon
chr7:19319623-19319712
Coord C2 exon
chr7:19318427-19319622
Length
90 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGA
5' ss Score
9.14
3' ss Seq
TCTAAGTTGTTTTTCAACAGGAA
3' ss Score
8.07
Exon sequences
Seq C1 exon
AACAAATTCCAAGGCATGGTCTTTGATTTTGTAACAAAACAAGCATTTGATATCAGTATCATGATACTTATCTGCCTTAACATGGTCACAATGATGGTAGAAACAGATGACCAGAGTGAAGACATGGAAAACATTTTGTATTGGATTAACCTTGTGTTTATTGTACTTTTCACTGGAGAATTTGTCTTGAAATTGATTTCACTTCGCCATTACTACTTTACCATTGGCTGGAATATTTTTGATTTTGTAGTTGTCATTCTTTCCATAGTAG
Seq A exon
GTAAGAGCAATTCATTTTCATGAAATGGCTAATTTTGGGAAAACTGAAATGTAGTAGTATCTTTGACTAATCTAAGTTGTTTTTCAACAG
Seq C2 exon
GAATGTTCTTAGCTGAGATGATTGAGAAATATTTTGTGTCCCCTACTTTGTTCCGAGTCATCCGACTTGCCAGAATAGGCCGCATTCTGCGTCTCATTAAAGGCGCAAAGGGAATCCGCACTCTGCTTTTTGCTCTGATGATGTCTCTTCCTGCTTTGTTCAACATTGGCCTGCTGCTCTTCTTGGTCATGTTTATCTATGCGATATTTGGCATGTCCAACTTTGCCTACGTTAAGAGGGAAGTTGGGATTGATGACATGTTCAACTTTGAAACATTTGGCAACAGCATGATCTGCCTATTTCAAATTACCACATCTGCTGGCTGGGATGGCTTGTTAGCCCCAATTCTTAACAGTGGGGAACCGGACTGTGACCCTCATAAAGATCATCCAGGGAGCTCTGTTAAAGGCGACTGTGGCAACCCTTCGGTTGGGATTTTCTTCTTTGTCAGCTACATCATCATATCCTTTTTGGTGGTGGTGAACATGTACATTGCTGTCATTCTGGAGAACTTCAGTGTTGCAACTGAAGAAAGTGCTGAGCCCTTGAGCGAGGATGACTTTGAGATGTTCTATGAGGTCTGGGAGAAGTTCGATCCAGATGCAACACAATTCATAGAGTTCAGTAAACTATCAGATTTTGCAGCTTCGTTAGATCCTCCTCTTCTCATAGCAAAACCAAACAAGGTCCAGCTGATTGCAATGGATCTGCCCATGGTAAGCGGTGACAGAATTCACTGCCTTGACATCTTGTTTGCTTTCACAAAGCGTGTGTTAGGGGAAAGTGGGGAGATGGATGCCCTCAGAATACAGATGGAAGATCGTTTTATGGCAGCCAATCCTTCTAAAGTCTCCTATGAACCAATCACAACCACATTAAAACGGAAACAGGAGGAGGTATCTGCTGTTGTTATTCAACGTGCTTTCAGGCGTCATCTTTTAAGGCAGAAAGTCAAAAAAGTTTCATGTATATTTAATCAGGATAAAGGTAAAGATGAGGATGATCTGCCCATGAAAGAAGATATGATTATGGATAAATTAAATGAGAACTCCACTCCAGAGAAAACAGATATGACCCCATCCACAACCTCCCCACCATCCTATGATAGTGTAACAAAGCCAGACAAGGATAAATATGAAAAAGACAAATCAGAAAAAGAAGATAAAGGTAAAGACAGCAGGGAAAGTAAAAAGTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011009:ENSGALT00000017933:23
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.214
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.4=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.1=41.9),PF0061222=IQ=WD(100=5.3)
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:
CGCCATTACTACTTTACCATTGGC
R:
TTGCGCCTTTAATGAGACGCA
Band lengths:
175-265
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]