RnoINT0131534 @ rn6
Intron Retention
Gene
ENSRNOG00000053122 | Scn1a
Description
sodium voltage-gated channel alpha subunit 1 [Source:RGD Symbol;Acc:69364]
Coordinates
chr3:52406543-52408953:-
Coord C1 exon
chr3:52408672-52408953
Coord A exon
chr3:52406597-52408671
Coord C2 exon
chr3:52406543-52406596
Length
2075 bp
Sequences
Splice sites
5' ss Seq
GTTGTAAGT
5' ss Score
8.3
3' ss Seq
ATGCATGTCCTTTCCAACAGGCG
3' ss Score
9.61
Exon sequences
Seq C1 exon
GTGGTTGTGAATGCCCTGTTAGGAGCAATTCCATCCATCATGAATGTGCTTCTGGTTTGCCTTATATTCTGGCTAATTTTCAGCATCATGGGCGTAAATTTGTTTGCTGGCAAATTCTACCACTGTGTTAACACCACAACTGGTGACACATTTGAGATCACCGAAGTCAATAATCATTCTGATTGCCTAAAACTAATAGAAAGAAATGAGACTGCCCGGTGGAAAAATGTGAAAGTAAACTTTGATAATGTAGGATTTGGGTATCTTTCTTTGCTTCAAGTT
Seq A exon
GTAAGTGAACACTATTATCTCTGAAATTTTATTGCTCGGAATAATAACAAAGTGATTATTGCAGCCATTGTTTAGTTAAAAAGAAACTTTATAATATTCTTCTGCATTATCTGTTAGTACAAATGTGTGAATCCAGATGAGTAGAATCATTTACAGACATAGTCAAGAGTGGTCAGGTATTTCCATCTTTTTCCAAAGGTCTTATTTCCTTCTTTCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCCTCTCTCTCTCTCTTACATTCCTATCACTTATGAAAAACTGTTATTTTTTTCTATTGCAATTGTAAAGCTTGATATTTGTAGAGTGTCCTTCTTTGGTACACGTGTGCACATGCGTACACACACACACACACACACACACACTTGATGTATAGGAGTTCACTGATGCTTAGTTACCTCAGTCTGGATTGTGAACTTGGGAAAGATGGTTGGGTGTGAAGATTTTATTCTCAGAGTGTAATGGAAACCACAGAGCATCAGCACACAGGAGTCAAGCACAGGCAATTCTAGTCTCAAACCAGGAGCTCTCGTTACCACGATTGAGTTCTGTTTTACCCTAAACATCCTCAATTCCCAAAGAACTGTTTATAGCTTATTAAAAAACCACAAAAGATGGTGATCCCTTAAACATATTTATCCAATGACACTTCCAGCTGCAACAAAGCAGTGAGTGTAAACAGAGGTCAGGTTATTTTAAAAAGAAATAGGTTTCAGTTACTCAACCAGATGCAACAAATACACTTAGGCTGTTCCTCTCACGCCTGCAGTTCTCACACACACTCTTATTAGGATTATTTTATAATGCCCTCTCATTTTTTTTCTTGGAATTACTGTCTTTCTGACCCTGCAGCTGACTCTGAGTGTTTATAACTTAACATGACTTTTTTAATGTATCAAGAATGATTTCTTAAATATTACACTAGAGTCACCACCTTTCTCTTGCATATTCACCCTGAACTGTACTGATTATTGCAGTATAGCGTTTCTAAAACACATCACTCTGTTCATAAAACCAAGGAGAGAAAAATCAGATCCTTTCAATGATCCTTTGAAATGCTAAGGGATTCAGAAAATGAAGAAGGCACCTTCTGCACAGAGCTCTTAAATATGTTCTGCTACTAAATAAAAATGCCAACATGCCATTTCACACTTGACTATACTGCCCTCCTCTCTAGTGAGTAGTGATTTCATAGAAATAGCTCAAACCACTTTTTTTGTTCCTGTAGGAAATGTGTGATAGATGGGTTCTATAATTGACCTAAGCCACTGACACATCTCTCTCCTTGATATGAAAAGAATTTGTTTTCTGACTAAGATGAATTAGTCTCCAGTCACACTCTGTCATTCAAGAGTCAATGATTTAAGAAACAAGATACATCACAAAAAATCATATGAGGCTTCCTCATTGACTGAGGAATATGCATTTCAGGCCCGGTAGCCTCAAACTTGTATTCTAAGACACAAGGCAAATGACTGCAAGAGATAGAGGAGGAATCCCTCTTCAATGTGCAGACGACAAGTGTCAGTCTTATTTTGTCACACTTTTATTATTTTATTATTTACATTAACGCAATATCTTCAGAGGTTACCTCATAGAAAGCGAATATTCCTGAAATTTCTTGAAAGGATAGCTTCATTTTTTTTAATTATGCCCATATGAGTCATAGTGTGTAAGAGTAAAGAAAAACCTTAAATACTATCAATTTGATCACCCAGAAGACAAGATTTCTTGCAGAAAATCCCAGATCTAATTTGATATTGCTGTAGCTGTTGCCAAGTATACTTATATTTCTAGGACTTTCTTCCAAATTATAGTAGCATGTTAAGCTTGAGAATTACTTTAGAGGTAGTTATAAAATAGGAAGATATATTGCATCGTCATTTGTTGACTTTCTATCTCGTTTCAAAATCCAAGAAAGTTTGGTTTGAAATGACCTTAAAATAATTCTTTAAGCATGCACAGTCAGAATACTTAGTAAGTTTCCATTTTGAAACTTAACCCAAAGTAAGATATGCATGTCCTTTCCAACAG
Seq C2 exon
GCGACGTTTAAGGGTTGGATGGATATCATGTATGCAGCAGTTGATTCCAGAAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000053122:ENSRNOT00000083552:19
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:
PF0052026=Ion_trans=FE(40.6=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(7.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]