RnoINT0131647 @ rn6
Intron Retention
Gene
ENSRNOG00000015049 | Scn5a
Description
sodium voltage-gated channel alpha subunit 5 [Source:RGD Symbol;Acc:3637]
Coordinates
chr8:128198493-128201519:-
Coord C1 exon
chr8:128201361-128201519
Coord A exon
chr8:128198614-128201360
Coord C2 exon
chr8:128198493-128198613
Length
2747 bp
Sequences
Splice sites
5' ss Seq
GAGGTAACG
5' ss Score
9.65
3' ss Seq
ATCCCTCCCCTCCCCCACAGACC
3' ss Score
12.35
Exon sequences
Seq C1 exon
GAATCCCAAGTTGTGTCTGGTGGCCACGAGCCCTACCAGGAGCCCAGGGCCTGGAGCCAGGTGTCAGAGACCACGTCCTCTGAAGCTGGGGCCAGTACATCTCAGGCAGACTGGCAGCAAGAGCAGAAAACGGAGCCCCAGGCCCCGGGGTGCGGTGAG
Seq A exon
GTAACGGCGGGGTCTGCTGCTGGGGCCAGGGCCAGGCCATGAGGCCACAGAGCCAGTGTGTCACAGACAGCATGGAGGCGTGTTACAGAGAGGAGGGTGGGAAACCAGTGTCCTGACAGGGAGAGACAGTACCCACCCCATGGCCACGCCACGAGGAAATCAACCAGCTCAGGACTCTGAAGCCTGACTGAGTAGTCCTCCCGAGTGTTCACCCTTCTCCTCACGCTTTGCCCTCGTGTTCTTGTGCCAATCAGCAAGCGTTTGTCCTGTGACTCCCCGTATCCAAGGAGGACTTGACTGATCTTCAGAACAGTCCTCACCACATCAGTCAGCTTATGCCTTTCCCCTGTCTTCCCTGCAAAGAAAAAAAAAGGGGGGGGGGAATGGGGCATCTCAGCCTGTCATCAGGATTTACTGTGGCTTTCCTTTGGATTAATTGACACACACTTGGGAGCTTTTGTGGGATTTTTTGTCCTTTTTTTTTCTTTTAAATCTGCATTTCTTGTTTCTCTTGAAAACTTGAGAATGGCACTCCATGTTGCAGACAGGAGGTAGCCATTCTTCAGCCTCCCGCTGGAGCTCTCTGGTTTGCCTCAGCACCACCTGCCCGATTGCATGTGTGACCTGCCTGGCCCCTCTGCATATCTGAGTTTTAAGGCCCCAAGTCAAGGGCCAAACAACCGCGCTGTTCGGCCTCACTTGCTTCAAGCGTGTGGAAAGGAAGTCATGTGCTCAGAGAGTGCAGGGTGACCTCCCTCCTCAGCCCTGTGCTTGTGACTTTGGTCCTGTAAGACAGGCCCTAGGATGCTCTGCCATCATGGCTGGTCTTGGAGCACGAGGCCCTGGTGCGTGTCCTCACTGAGTGAATCAGCCTTCTCCCTAGATGGCCTAACACTTGACATGGAGTAGGAGGATCCAGGATCCCAAGCCTCGGGAGAGAGTGTGAGTTTTAAGGCTTCTTCCCTTCAGATGCTTGTGTCCCAGAAGAGGCGAGAGAAATGATGTGGTAGTCCCAGGGAAAGGACTTCTTCCAGGCTGGGCCTGTAGCTGGGTTGGTAGAATGCTTGCCTGGTGCACAAGCCCTGGGTTCCAGCCCTCGGACAGCATAAACTGGGAGTCACGGTCCACAGTTGTAATCCCAGTGCAGCCTCAGGCCCAGAAGTTCTAGGTCTACAGCAGCTGCAGTGAATTCCTGTCTCAGACAGGAAGAAGGGAAGAGGCAAAGGGAAGGAGCTTCCTCCCTCCTGCAGTAGGATCCCGAGAACTCCCTGACAGCCTTCCAGGCCTTGCTCAGCTCAGAGCCTGCAAAAACCCCACCTGGGATAGCCAGCCTCAAAACCATGGGCCAGGAGACTCAGCCCCACCCCTCTGGCCACTCCAAGCAGGCTGTCCCCTCCCCTGAAACCACCAACCTTGGAGGTGATGAATCAGGAGAAACAGGAGGTGCAGATGGGCAGATGGGGATTCATCCCAGGAAGGGGAAAGAAGGCAGCAGGAGCCGCAGGGCCAGGCCCCAGCCTTCAGTAGAGAGCCTAGACTGGCCGCAGGCAGCCAGCTGAGAGGGGACGGAAACAGGAAGCAGATGGGGTGGGGTTAGGAGGGTGGGAGTGGAGTAGGACAGGATGAGGGGGTCCTTTCTCTACAGAGGCCCTCCTGACTCTTATGTTGTTAAGTTCTGTTTCCCACAAGCAGAAATAGGGACAAGGACCTCTGTGTAAATGACTTATAGGGTCAGTGCTCCCTAGAGAGGCCAAGAAGGACACAGTCGAAGCAGATTCAGAGAAGAAGGGAGCTAGACCAAGGCCAAGAGCAGGTTTTCTGAAGTAGACTTCAACGTGTGCTAGTGCAGAGCTACAAAGTATCAAACCACACCCTTGTGCTATCACCAACTGGCAGTCCACTGGCTAAACTGTTCTGGAGAAGGGGCCAGCTAGGCCGCAGGTTTCACAGTGGTAGGGCAGGGTGTTCTACCTACCCATAGACATGTGGCATTACCCACAGTCACAAGGCACAGACACTCACAGGTTATCAAATGTCCTATAGCAGGGGTTCTCAGCCTTCCTAATGCTTTTTGATACAGTTTCTCCTGTGACCCCCAACCATAAAGTTACTTTGTTGTTATTTCATAACTATAATTTTGCTACTGTTATCAATGATGATGTAAATATTTGGGGAGATAGAGGTTTGCCGGAGGGGTTGCAACTCAAAGGTTGAAAACTGCTGACCTAGAGGACCAAACAAGTTATCAAGGCCTAGGGCCAGGGTGGAGAGGTTCCAGCGCTTTCTCTGCCCCAGTTCTAACATCTGTGTGAGCTGAGTGGGAAGCATGGTCCGCTGCTGGCATGTTCTCTGCATGTCTGACCTGCTGCTGTGTGCCTGTCTTGGTTTTGGTTCTGTTCTGGATCTGTGTCTGTGTGCCAATGGGTGCTCCTATAGTCCCCCCACTTTGTCTGTCCTGTCCAAGCTAGATGCATTCCTTACGCTGAGTAATCCCCAATCCCCTCATTCCAACACACCGCAGCCCTAAACCCCACACACCAGAACCACAGACCGGGGAATCCTGAAGTCCAGCCTCCACTCCTCCCTCCTTCAGTGGCTCTGTGGCAGGCATTGACCCACCCCCACCTCAGAATCACGGTGTGCAAAGTGGGAGCCCTCTGGACTCAACCTAGGCTTCCCCCAGATGCTAGGCTGGCGCTGGAGGCTGATCCTCAGCCCACCACGGCTATCCCTCCCCTCCCCCACAG
Seq C2 exon
ACCCCTGAGGACAGTTACTCCGAGGGCAGCACAGCTGACATGACCAACACCGCCGACCTCCTGGAGCAAATCCCAGACCTTGGTGAGGACGTCAAGGACCCAGAGGACTGCTTTACTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000015049:ENSRNOT00000064555:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.683
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=FE(19.8=100)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(15.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
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]