RnoINT0131631 @ rn6
Intron Retention
Gene
ENSRNOG00000012134 | Scn4a
Description
sodium voltage-gated channel alpha subunit 4 [Source:RGD Symbol;Acc:3636]
Coordinates
chr10:94536128-94537647:-
Coord C1 exon
chr10:94537333-94537647
Coord A exon
chr10:94536192-94537332
Coord C2 exon
chr10:94536128-94536191
Length
1141 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
GTGGCCTCTGATTCCCAAAGGGA
3' ss Score
4.78
Exon sequences
Seq C1 exon
GGCTGAAGACAATTGTGGGAGCCCTGATCCAGTCTGTGAAAAAGCTGTCGGATGTGATGATCCTCACTGTCTTCTGCCTGAGTGTCTTTGCCCTGGTGGGGCTGCAGCTTTTCATGGGAAACCTGCGTCAGAAGTGCGTGCGTTGGCCCCCGCCCATGAATGACACCAACACCACGTGGTATGGCAATGACACTTGGTACAGCAATGACACTTGGTACGGCAATGACACTTGGTACATCAATGACACTTGGAACAGCCAGGAGAGCTGGGCCGGCAACTCTACCTTTGACTGGGAGGCCTACATCAATGACGAAG
Seq A exon
GTGAGAAGGGAGGTAGAAGGGCCAGAGGAGACTACCTGACTCCTCAAGGACGCATTGTCTCAGCTGCTTCTTCATAGAAGACGTAGCTTAAATCCATCACTAGCCAGCTTGGGTTGTAGCCTCCCACAGGTCTCTCAGTCATGACCCTTAAAATGGTTGCGTATTAAATGGAGTATGACAAAACCTCCCTCGAAGGGTTAATGTGATGACGACACCCTGTTTTAAAATCCTGTGTCTGTTGAGGCTGAGGGAGCTCAATCTATAAAATGCTTGCCTCGAAAAACCGAGGACTCGAGGTCGATCTCCAGAGCCTGTGTAAACAACCAGGCATAGTGGCACATGTCTGTGGTTCCGACTCTGAGTGGCACATGTCTGTGGTTCTGACTCTGAGTGGCACATGTCTGTCTGTGGTTCCGGTTCTGACAGGTCCCAGGAGCTCACTGCACAGCTAGGCAACCCTGCCTCATTGGCCAGCCCCAGACCTTAATGAGAGACTCCTGAAAAAAAAAAAAGTGTACCATTGGTCCTGAGAAACAACACCCAAGGTTGCCCTGGGAGACACACACACACACACACACACACACACACTCATGCACACGTGTGTGCTAAGGCTCTCACTATACAAAGAGACAGTCCATCATCCTTCTGTAGCCTGAACATGTGTTGTTCTTCCCCACGTTCTGGCAGGGCTGCCGCCAGCCACATCCTGTTCCCATGGCTGTCCTTTATAGGCACACACAGCACACATACACATTCTCATGCAGTCACTAGTACACACAGTGTCTTCTCCTTGGAACAGTGTCCTTCCTTCACTGTGCTTCCTAGATTCCAACTCCAACCCCTCCCCAGTGCACACACAGAAACACGCCCTTTGACACAGGGCCGTATTGGGTCCCTGGTGAATCCTGACTTCGTAACCACAGCGGGTACAAGCTTATGTGGCTTAGTGCTGAGCCCATGCAGTTTATCCGCTGGAGACCCTGGAGCTTGGAACTGTTCATAAAAGACAGGAGGGGCCCCAGGGAGTGTCTGTGTAGCCTCTTTGGGCACACAGATGTGTTGACGGCTGTGTGGTGTGTGCACGTGTTTACTGGGCATCTGTGTGGTAACATGTCTTCTTTGTGGCCTCTGATTCCCAAAG
Seq C2 exon
GGAACTTCTATTTCTTGGAGGGCTCCAATGATGCTCTGCTCTGTGGGAATAGCAGTGATGCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000012134:ENSRNOT00000016841:7
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(37.2=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(7.4=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:
CAATTGTGGGAGCCCTGATCC
R:
CAGAGCATCATTGGAGCCCTC
Band lengths:
344-1485
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]