RnoINT0131616 @ rn6
Intron Retention
Gene
ENSRNOG00000012134 | Scn4a
Description
sodium voltage-gated channel alpha subunit 4 [Source:RGD Symbol;Acc:3636]
Coordinates
chr10:94516350-94518826:-
Coord C1 exon
chr10:94518353-94518826
Coord A exon
chr10:94516486-94518352
Coord C2 exon
chr10:94516350-94516485
Length
1867 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAC
5' ss Score
8.14
3' ss Seq
CTGCCCTGTGGTTCCCACAGAAG
3' ss Score
9.34
Exon sequences
Seq C1 exon
GTCCTGAATCTGTTCCTGGCTCTCCTGCTGAGTTCCTTCAGTGCTGACAGCCTGGCGGCCTCGGATGAGGATGGCGAGATGAACAACCTACAGATTGCCATCGGGCGTATCAAGTGGGGCATCGGTTTTGCCAAAACCTTCCTCCTGGGGCTGTTGCGTGGCAAGATCCTGAGCCCCAAGGAAATAATACTCAGCCTCGGTGAGCCCGGGGGTGCCGGGGAAAATGCCGAGGAGAGTACTCCCGAGGATGAGAAGAAGGAGCCGCCACCGGAAGATAAGGAGCTGAAAGACAATCATATCCTGAACCACGTGGGCCTGACCGATGGCCCCCGCTCCAGCATCGAGCTGGACCACCTTAACTTCATCAACAACCCCTACCTCACCATCCACGTGCCCATTGCCTCCGAGGAGTCTGACCTGGAGATGCCCACAGAGGAGGAGACAGACGCCTTCTCGGAGCCTGAGGATATCAAG
Seq A exon
GTAAACCCGCTGAGGGTCTGGCTGCAGAGGTCAAGGGCCAGTAGGATCCAGCTTTAAAGTTTAGTTCGACTTTAGACAAGTCATAAAACCGTTCTGGCCTTTAGTTTCTCCATCTGTGGAAGGTTTTTGCCCTGTGCGCGGTGTTGGCTCACCCATAGTCCTCTGAAATGGAGACTGTTAGAGAAGGTACCATGACTGTTATAATTGGCGAGGCCAAAGCTCTACCTGGGCCCTTTCTGCCACCAGGTGGCGTTCTTGGACAAGTGCTTCTATCAGCTCGGACACTGGGAAGCCGAGAGACCTTTCTTAAATACCTGCCTGGGCTTTCTTAAATAGCCCCCTGAAGACCCTGCTAAGCCTTTGCTCCAAATATGTTCTGATCTTATCCATAACCCTGAGGCCCCCATGCTGGCTGACAATTGGCATATCCACATTTCTACATAGAGTTCCTCTGAGGCTGTTCCAATCTTCCTTGTGAAGGACAGGGTACCAGTTCCAGACCAAGGCTACTAGGACGGGAGTAAGAGAACCCAAGGAGAGTTGGGAGACACAAATAGTGGTCTCTTTCAAAGTCTGGGACTCTGTCAGGCCTGCCTCGGGTGAGCTGGTCTGAACCCCCTCACTCTTCTTGCAGCCCTAATAGGAAAAGGATCAATACGTGATTGGAAGCAAGGGACGTTACCCATGCCACCCTTCAGCCCTGGGCCTCTCAGGGCACCAGAACTTAATGAACTTTGCCCTAAAAGCTCTTGACTCCTTATCCCAGCCCCCAACACACACCAGTATGTGGTTCGTTGACTTAGCAGGGGCTTGAGTGCCTGCGTGAGGCTATAAATATCCCAGGAAACATGGCACCAACCTCGACCTCGGTATGAGGAACTCAGTGGGGGTGGGGCTAGCTAGTGGTAGGTCCAAGGCTCTGGGAAGGCAAGATATCTGAGGAGCAGCAAGCAGAGCTTAAAGAGCAATTATGGGTGTTGACGTGCAAGGGTGAGGCCTGCAGTCCGGTGTATACCCTGATTGACTAAGTGCTCTGTGCCTCGGTTTCCCTCCTGTCAACTGGTAGCAAGACCCACTCACTTGTAGCTTTCTGACTAGTGCCCTGGTTTAGTTACATGTGCAGGAGAGCCCACACACACACACACACACACACACACACACACACCCATATGCACATGTGGAAGGGGCCACCCGATTCATCTTTCTCTGCAGAGATTTCACTGTGAAGGATGAACTATGGAGGCCAGCCTGAGTTTCTGGCCTGGGACAGCATTGGGAGGTGGGAGGAAGCCTGGCCAGGCCGGAGCACCAGCCCCCACACCCTGCCCCCACCGTGATCAGATTCCCTTGGCGCCACACCGGAGCCTTGGCTGGGGAAAATTTTCCATCCTTTCTGAATCTCTCAGCCAAATAGACCCTGGGGGTGAGAAAGCTTGGACTCTGGGGGCACCATGTGCCTGAGCTCTGTAGCTGTGTGGCCACCCAGATCAATCTTGGCTGCACCGACCCCTTCATATATCCCTATACCTCCTAGGACCCCGCTGGGCTGAGCCAATCCTCAGCCCATCTCCTGTCCTCTATACCTTCCTCCCCAGACCTCCTCACGTCTTGTCTGTGTTTTCTCGATGCTAAGTGCCATGGAGGGCAGAGCTGAGGGCATTTTTGTCACTAGGGTGCTTTTGCCAGGGCACAGTGGTGGTTTTGTAAGGGCTGAATGAATGAATGAACGAATGAATGAATTAATTAATTAATGAGCGAATGAAGGAGTAGATCCTGCTCTGCTCTCTTCTTTCTCTCTGGTCTCCCATACTACCCCACCTATTGGGAGAGTGGGACCCAGGAGTCACCTGCCCTGTGGTTCCCACAG
Seq C2 exon
AAGCCCCTACAGCCCCTCTACGACGGGAACTCCTCCGTCTGCAGCACAGCTGACTACAAGCCCCCTGAAGAGGACCCCGAGGAGCAGGCTGAGGAGAACCCCGAGGGGGAGCAGCCTGAGGAATGCTTCACGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000012134:ENSRNOT00000016841:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.430 A=NA C2=0.696
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.2=5.1),PF065128=Na_trans_assoc=PU(59.6=84.8)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(20.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGATCCTGAGCCCCAAGGAAA
R:
GAGGAGTTCCCGTCGTAGAGG
Band lengths:
346-2213
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]