GgaINT0047682 @ galGal4
Intron Retention
Gene
ENSGALG00000010943 | SCN1A
Description
sodium channel, voltage gated, type I alpha subunit [Source:HGNC Symbol;Acc:HGNC:10585]
Coordinates
chr7:19149356-19151896:+
Coord C1 exon
chr7:19149356-19149626
Coord A exon
chr7:19149627-19149968
Coord C2 exon
chr7:19149969-19151896
Length
342 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGT
5' ss Score
9.66
3' ss Seq
TATTTGTCCTCCTATTTTAGGTA
3' ss Score
11.5
Exon sequences
Seq C1 exon
AACAAGTTTCAAGGCATGGTCTTTGATTTTGTGACACAGCAAGTATTCGACATTAGCATCATGATTCTTATCTGTCTTAACATGGTTACCATGATGGTAGAAACTGATGACCAGAGTAAAGAAATGGAAAATATTTTATACTGGATAAACTTGGTGTTCATTGTCCTTTTCACTGGAGAATGTGTCCTGAAATTAATTTCACTCCGCCATTATTATTTCACTATAGGCTGGAATATTTTTGATTTTGTAGTTGTCATTCTCTCAATAGTAG
Seq A exon
GTAAGTCTCATTTATTAACCTATAAAGAGGGTAAAATGAGTATAAATTGAACTTTCACTCAGTAGTACTATATGGCTAGCTTTTGCCATTCCAAGGCTTCTAAGTCTTGCATGTTCTCATTTTATCTAATGATTTACCTAATCACCGTGATTGTTGTAATCATTCAAAATACATTGCACTTGTAAATATTAACTGTAACTGGTAGAAATTATGCAAGTGTAATCTACAGAATATCTTTAATTGCTGCATAGAACATCAGTTTTAAAACTATTTTTCTAAATTATCACTACAATATGGAGAGTGTGGTAATATATCCTTATTTTATTTGTCCTCCTATTTTAG
Seq C2 exon
GTATGTTCTTAGCTGAGATGATTGAAAAGTATTTTGTGTCCCCTACTTTGTTCCGAGTCATCCGACTTGCCAGAATAGGCCGCATTCTGCGTCTCATTAAAGGCGCAAAGGGAATCCGCACTCTGCTTTTTGCTCTGATGATGTCTCTTCCTGCTTTGTTCAACATTGGCCTGCTGCTCTTCTTGGTCATGTTTATCTATGCGATATTTGGCATGTCCAACTTTGCCTACGTTAAGAGGGAAGCTGGGATTGATGACATGTTCAACTTTGAAACATTTGGCAACAGCATGATCTGCCTATTTCAAATTACCACATCTGCTGGCTGGGATGGCTTGTTAGCCCCAATTCTTAACAGTGGGGAGCCGGACTGTGACCCTAACAAAGCTCACCCAGGGAGCTCTGTTAAAGGTGACTGTGGCAACCCTTCAGTTGGGATTTTCTTCTTTGTCAGCTACATCATCATATCCTTTTTGGTGGTGGTGAACATGTACATTGCTGTCATTCTGGAGAATTTTGGTGTTGCAACTGAAGAAAGTGCTGAGCCCTTGAGTGAGGATGACTTTGAGATGTTCTATGAGGTCTGGGAGAAGTTTGATCCAGATGCAACACAATTCATGGAATTTGAGAAGTTGTCTGATTTTGCAGCAGCTCTTGAGCCTCCTCTTCACCTTCCCAAACCAAACAAGGTCCAGCTGATTGCAATGGATCTGCCCATGGTAAGCGGTGACAGAATTCACTGCCTTGACATCTTGTTTGCTTTCACAAAACGTGTGTTAGGGGAAAGTGGGGAGATGGATGCCCTCAGAATACAGATGGAAGACCGATTTATGGCATCAAATCCTTCTAAGGCTTCCTATGAACCGATTACAACAACATTAAAAAGAAAACAAGAAGAAGTATCTGCTGTCATTATTCAACGTGCTTTTAGACGCCACCTTTTAAAACGAACAGTAAAACAAGCCTCCTTTATCTATAACAAAAACAAAACTGAAGGAGGGGCTGGTCTGGGCATTAAAGATGAAATCCTTATGGACAAGTTAAATGAAAACTCATTTACAGAAAAGACTGATATAACTGCATCAACAGCAGTTTGTCCACCTTCTTATGATCGTGTAACAAGGGCAGTCAAAGAAAAGCATGAAAAGGAAGACAAAGATGTTCATAAATAAAAATAAATAGCAAGCAAAATCATCTATGTGCAAAGTAGTTCATAGCCTGCAAAGGTCATGTGTTTGTGTCAACAGGACTCCTGCTGGAGGTCTATGCCAAACTGACAATTTTTACAAACATACTATACGTTAAAGGTCAGTGCCTATTAAAAGACAGCGACCCCTCGTCAGTAACTGTGACTGTGACATGGGGAAATAACCTTGACAGGATTTAACTGTTCTCACTACCAGCTGACACTGCTGAAGAGGAGAGAAAAAATGGCTACTCAGGCTGTAGGGACCAGCTAAGGGGTGCAGTCCAAGTTCTAGTTGTGTGTTTAGCGTAAAACAATACAATAACTGTATCCACTGTTTGCATTTCAACTGCCACATACATCATATTTTTACAAATCTGTGTTGGTGGATTCATCTTTTCTTTATTCATATGTTGTTTATTATATGTGACTATTTTTGTAAATGGGTCTTCTGTTGGGAAAGGGGGTCAAGCACTACTTTACAGGTATAAGAGCCAGGTGTTCTACTATGCGACTAATATACACACAGAAATGATTTGCATGAAGGCATGCTGCACTTATAGATCATGCATGAAAATAACATTAAGTCACAAAGAACAACTGATTTTAGCTCAGTGTTTCTGGGAAGGAATAATAAATTCTGAGGTGCTTAATTAATGTATTCATGTTGTATCGCGTCTGAACCAGTCTTGGTATGCCTGTAAAGTCCCCTGTAACTCACAAAAACAGTAAAAACAGATATTTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010943:ENSGALT00000017814:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping 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:
TGTGACACAGCAAGTATTCGACA
R:
TTGCGCCTTTAATGAGACGCA
Band lengths:
350-692
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]