RnoINT0131646 @ rn6
Intron Retention
Gene
ENSRNOG00000015049 | Scn5a
Description
sodium voltage-gated channel alpha subunit 5 [Source:RGD Symbol;Acc:3637]
Coordinates
chr8:128201361-128203242:-
Coord C1 exon
chr8:128202802-128203242
Coord A exon
chr8:128201520-128202801
Coord C2 exon
chr8:128201361-128201519
Length
1282 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGC
5' ss Score
7.16
3' ss Seq
TCATGGGGTCTTTTCAGCAGGAA
3' ss Score
5.89
Exon sequences
Seq C1 exon
GTCCTGAATCTCTTCTTGGCCTTGCTGCTCAGCTCCTTCAGCGCAGACAACCTCACAGCCCCTGACGAGGATGGGGAGATGAACAACCTCCAGCTGGCCCTGGCTCGCATCCAGAGGGGCCTGCGCTTTGTCAAGCGGACCACCTGGGACTTCTGCTGCGGGATCCTGCGGCGGCGACCTAAGAAGCCCGCGGCTCTTGCCACCCACAGCCAGCTGCCCAGCTGTATCACCGCCCCCAGGTCCCCACCACCCCCAGAGGTGGAGAAGGTGCCCCCAGCCCGCAAGGAAACACGATTCGAGGAGGACAAGCGACCCGGCCAGGGCACCCCTGGGGATTCGGAGCCTGTGTGTGTGCCCATCGCCGTGGCTGAGTCAGACACTGAAGACCAGGAAGAGGATGAAGAGAACAGCCTTGGCACAGAGGAAGAGTCCAGCAAACAG
Seq A exon
GTCAGCTACCCCTCCATCCCGTCCTGATGGGACAGCCACCTGCTTGTATGGAGTCCAGAGTGCAGCTCCTAGCCTCAACCAGACTACCTCAGCCATGGCACAGGAGGGGAGAGGAAGCCCCATGGCAGCTGGCCCCTCAGGAGGGAGCCAACTCCAGCTTGCCCATTTATCCTGTTAATCAGTATTCACCCCTGGCTAACCTTACAGACCGGCATGCCTAAGAACTCTTGATGAATCTCCCAGTCGCCCACCCCACCCCCAGCTCTGACCGTGGTCCAGCCCCAGGCCAGCAGAGACAGATGTCCCTGTGAGAGAGGGCCACTGTTCGGTGACCTCACAGCCATCTCTTTTCCCTCCTCCCATGCCTGAGGCTGATTCTGAGATTTAAAAATAAGTACCCCTGAGACGGAGGTGTCAGGGACACCACTATCTTATCTCTCAACCTGTTATTTTTAACACTTAGGACCAGAGTCTGGACAAAGCAGAGGGTCTGTCCCCCAGGTTTCCCTTGACCTGAGCTGGGCTCCGTGCAGCTCCTTAGGTCCCTAGGTCAAGCGTAACCAGTTCTCCCTCCGTGTCCGCATCCCTTCCTGGCTGCTTCCTCAGCTGGCATTAGCTGGGCCAGGCCCCGGGGCTCTGCCTCCTCCTGCCTCAGTTGGCCTCACAGACCAGCCTTGGCTCTTTTACTCGAGTTGTAGGACTCTAACAGGGGTGGTTGAGGGAGGGAGAGCTGGGGTCACTAGGACCAACATAGTATCTCCTGCACAGGAGATGAGAGTTGGATTCTGGTTGTTCCCTCTTTTCCCTTTCCCCTGGAGCCAGGATAAACGTGTGTGCTTGGGCACACTCACGTGTGTGTGTGTGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAGACATGCGTGCGTGCTTGTGTGTGTGTGTGCCTTGTGGGAATTGGTGCAGGCTAACTGCAGTATCTTCAGAACTTGGGAAGTCAGTGCATCCTCCTGAGTAGAGTTGGTAGCATTTGTAAGATGGGCATTGTGGCCGGGCCGCACCCGTTCAGGGAATCTTAAATACGTTGAGCTTTGGCCACAGGGCCTTTCCCATACTTTCCCAGAACCTCTCACTTACTGACCTAAGTCTGCAGAAGAAGGGTCTTTAGTTGATGGAAGTTCATGAAGAGGCCAGGAAGCAGTGGGCAGGGGCTGCAGCCCACATAGCCAGGGCCCTGGAGACCCTCTGCCCCGGGTGTTTGGGCTCTGCTCATGGGGTCTTTTCAGCAG
Seq C2 exon
GAATCCCAAGTTGTGTCTGGTGGCCACGAGCCCTACCAGGAGCCCAGGGCCTGGAGCCAGGTGTCAGAGACCACGTCCTCTGAAGCTGGGGCCAGTACATCTCAGGCAGACTGGCAGCAAGAGCAGAAAACGGAGCCCCAGGCCCCGGGGTGCGGTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000015049:ENSRNOT00000064555:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.531 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.2=5.4),PF065128=Na_trans_assoc=PU(46.9=83.7)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(19.8=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:
CTTTGTCAAGCGGACCACCTG
R:
GTGGCCACCAGACACAACTTG
Band lengths:
343-1625
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]