GgaINT0143171 @ galGal4
Intron Retention
Gene
ENSGALG00000000252 | SCN4A
Description
sodium channel, voltage gated, type IV alpha subunit [Source:HGNC Symbol;Acc:HGNC:10591]
Coordinates
chr27:1631780-1632752:-
Coord C1 exon
chr27:1632648-1632752
Coord A exon
chr27:1632051-1632647
Coord C2 exon
chr27:1631780-1632050
Length
597 bp
Sequences
Splice sites
5' ss Seq
TCGGTACGT
5' ss Score
10.06
3' ss Seq
CACCATCACCCCTATGACAGAAC
3' ss Score
4.62
Exon sequences
Seq C1 exon
TTTGGAGGCAAAGACATCTTCATGACAGAAGAGCAGAAGAAATACTATAATGCCATGAAGAAGCTCGGCTCCAAGAAACCCCAGAAGCCCATCCCCAGGCCCTCG
Seq A exon
GTACGTTGGGGTAATCCCCATGGCATGCAGTGAGCCACCAACTGTCCCAGAGCGAACAGGGAGGGTTTGGGGATGAGCTCTTCCACTACAAAGAGCCAATTCTTGGCTCCTTGGAAAGGACCTTGCTAAGAGTTGGGGTATCAGAAAAGGTTCACATCTGGCAACCTTGTTTGGGTCTGTTCTTCAGCCCTGAACCTGCAGAACAAGGGGAGATCGCTTTTGTAGGGGCTGAGGATTTCCTCCCATCTCCCCTCTCCAAGGAGTCAGACTGAGGGAAACCTCAGCTTCCATTGCTCCTAGAAAGGAAACTGGTCCACCCAATACATACACAGTTGTGATTTGGGCTTTCCCAGCTCAAGTGAGGTATTTTCCCATGGATTCATTGCTGTCCTGATGGATATGCTTTGGAAACAACTATCTCCTGTGCCCACACCTCCTGGCCATAGTGGTTCCAGGTGCTGGGTATCCTCCTCCCACATCTTCCTGCACGCTCCTAAATCTGGTTCCTTCTTCTCTTTCTGTTGTGTCTTTGTTTTGTTTGTGTGTGTCCCGTGTTCCCACCTCACGTCTGGCTCTCCACCATCACCCCTATGACAG
Seq C2 exon
AACAAGTTTCAAGGGATGGTGTTTGACTTTGTTACCAAGCAAGTGTTTGACATAACCATCATGATCCTGATTTGTCTTAACATGGTGACCATGATGGTCGAAACAGACGATCAAAGCGAGACCAAAACAGACATCCTCTACAAAATCAACCTGATCTTCATCGTCATCTTCACTGGAGAGTGTGTGCTAAAGATGTTTGCCTTGCGCTACTACTACTTCACCATTGGCTGGAACATCTTTGACTTTGTGGTGGTCATCCTCTCCATCGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000000252:ENSGALT00000040680:27
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:
TCTTCATGACAGAAGAGCAGAAGA
R:
TGGAGAGGATGACCACCACAA
Band lengths:
354-951
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]