GgaINT0143172 @ galGal4
Intron Retention
Gene
ENSGALG00000000252 | SCN4A
Description
sodium channel, voltage gated, type IV alpha subunit [Source:HGNC Symbol;Acc:HGNC:10591]
Coordinates
chr27:1630447-1632050:-
Coord C1 exon
chr27:1631780-1632050
Coord A exon
chr27:1631640-1631779
Coord C2 exon
chr27:1630447-1631639
Length
140 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
TCTTCTTCGTCCTTTCACAGGTA
3' ss Score
11.51
Exon sequences
Seq C1 exon
AACAAGTTTCAAGGGATGGTGTTTGACTTTGTTACCAAGCAAGTGTTTGACATAACCATCATGATCCTGATTTGTCTTAACATGGTGACCATGATGGTCGAAACAGACGATCAAAGCGAGACCAAAACAGACATCCTCTACAAAATCAACCTGATCTTCATCGTCATCTTCACTGGAGAGTGTGTGCTAAAGATGTTTGCCTTGCGCTACTACTACTTCACCATTGGCTGGAACATCTTTGACTTTGTGGTGGTCATCCTCTCCATCGCAG
Seq A exon
GTAAGCTTTGGGGGTTCCACTGGATAATGAGGAGTAGAAGTGGTGTGGGCAAGGGGAAACCAGTGAGACCCTGTGCCACCTCACCTCCCTATCTCATGTGCAGAGTGTGCCAAATTCACCTCTTCTTCGTCCTTTCACAG
Seq C2 exon
GTATTGTCCTCTCAGACATCATAGAGAAGTACTTCGTGTCACCCACACTCTTCAGGGTCATCAGGCTGGCGAGGATCGGCCGCGTCCTCCGGCTGATCCGAGGAGCGAAAGGCATCCGGACTCTGCTCTTCGCTCTCATGATGTCCCTCCCTGCCCTGTTCAACATCGGCCTCCTGCTCTTCCTCGTCATGTTCATCTACTCCATATTCGGGATGTCCAACTTCGCCTACGTAAAGAAGGAGGCGGGGATTGATGACATCTTCAACTTTGAGACTTTTGGGAACAGCATCATCTGCCTCTTCCAGATCACGACGTCGGCCGGATGGGATGGGCTGCTCAGCCCGATCCTAAACAGTGGTCCCCCCGACTGTGACCCCAACCTGGAGAACCCTGGCAGCTCAATAAAGGGCAACTGTGGCAATCCATCCATCGGCATCTTCTTCTTCTGCAGCTACATCATCATCTCCTTCCTCATCGTGGTCAATATGTACATTGCCATCATCCTGGAGAACTTCAACGTGGCCACGGAGGAGAGCAGCGAGCCCCTCTGCGAAGACGATTTTGAGATGTTTTATGAAATCTGGGAGAAGTTTGACCCGGATGCCACGCAGTTCATTGCGTACAGCACTTTGTCTGACTTTGTGGACACCCTACAGGAGCCGCTCAGAATCCCCAAGCCAAACAAGATCAAGCTGATCACCATGGATTTACCGATGGTTGCTGGGGACAAAATCCACTGCCTGGACATCCTCTTTGCCCTGACGAAGGAAGTGTTGGGGGACTCCGGAGAGATGGACGCCTTGAAGGACACCATGGAGGAGAAGTTCATGGCTGCCAACCCCTCAAAGGTCTCCTATGAACCCATCACCACCACTCTGAAGAGGAAACACGAGGAGGTGTGCGCAACGAAAATCCAGCGGGCGTTCCGGAGGTACTTGCTGAGGCGCTCGGTCAAGCAGGCGTCCTACATGTACCGGCACAGCAAGGATGAGGAGGCACTGTTAGGGGATGCCCCTGAGAAGGAAGGTCTGATTGCAACCAAAATGCACGAGATATATGGGAACAGTGGGACCGATGCGGAGATGGGCGCTGCTATTGATCTCGCACCCGTCCCGAGCTCAGAGACTCAAAGTGCTCCCATAGAAGCAAAGCCACCGGGCGGGCAGCGTGTCGTGAAAGAGTCATTGGTATAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000000252:ENSGALT00000040680:28
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.141
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.4=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.1=42.0),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:
TTGTGGTGGTCATCCTCTCCA
R:
GCGAAGTTGGACATCCCGAAT
Band lengths:
253-393
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]