RnoINT0131509 @ rn6
Intron Retention
Gene
ENSRNOG00000032884 | Scn11a
Description
sodium voltage-gated channel alpha subunit 11 [Source:RGD Symbol;Acc:3630]
Coordinates
chr8:128510523-128515250:-
Coord C1 exon
chr8:128514977-128515250
Coord A exon
chr8:128510642-128514976
Coord C2 exon
chr8:128510523-128510641
Length
4335 bp
Sequences
Splice sites
5' ss Seq
AAGGTACGT
5' ss Score
10.75
3' ss Seq
GTTGTGATTTTTCTTCACAGACA
3' ss Score
9.01
Exon sequences
Seq C1 exon
GGTGAAGATGGAGGAGAGGTACTACCCGGTGATCTTCCCGGACGAGCGGAATTTCCGCCCCTTCACTTCCGACTCTCTGGCTGCCATAGAGAAGCGGATTGCTATCCAAAAGGAGAGGAAGAAGTCCAAAGACAAGGCGGCAGCTGAGCCCCAGCCTCGGCCTCAGCTTGACCTAAAGGCCTCCAGGAAGTTACCTAAGCTTTATGGTGACATTCCCCCTGAGCTTGTAGCGAAGCCTCTGGAAGACCTGGACCCATTCTACAAAGACCATAAG
Seq A exon
GTACGTTCACATGCAGGTGGGATGTCCCCTTTCTGTGCTCACACGTGCATTACTGGGTCTCTGAATCCAGTCTCTGAATCTGGGTCAGTGGCAGGCAGGCACACCTCCTTTCCTTTGCCATCACCCCATCTTTGTAGCTCTTACTTGTTTCCTCTAAGAAAAAGAAAGAGATGAGGCAGACTGTGCCGAAAGGTTAAAAGGTCAGCACAGGAAACAGTTATAAACAAAAAGAACATAGTGGTCAGTCAGGACAGGAAGTAGGGCCTCCCTTGAGCCTGGCTTCATGACTCCAGACAAATGTACACCCAGATCCTCATTTCCTATGTCTAGAGTGGGAACAATGTCTGATCTCCCTACTCCAAGGTAAGACATGCAGTCAACAATTCACAGTGCTGCACCGGGAAGGGGAAGGGACGTCCTTTTCAGCAAGAGCATCACCTCCCAAAACATTTGGACCATATGTAGGCTTTCTAAGCTGTTAAAGTGAGATTAACGAAGGTCAAGCTGATAGTTGATGTAAGGTAGGTGCTCAGCCATTGAAAGCTGGGTCCCTGTTAATCAAGTGAGCTTGTGCAATTCTACGTGACCCTCACAGCAACCTATGGAAGCCTCCATGGTTTACCCACGACCTATAATTCTGATTTTTTTAAAAAAACAATTATTTATCTATCTTTGTTATGAATGTGTATATGCATGTGTCATGGGCATGTGTGTGGACAGAGGATGATTTCAGAGTTGGACCTCTCCTACCGTATGCACCCTGGGGTCTGCCTCTCCCGCTTGGCGAGTGTCTTCAGCTGCTGAGCGATCTCACCACCCCCTAGAGGGAATTCTTCTTTTTCCAAATTAGTTTTTATCTGTGTGCATGGGTGTTTTTGTCTGTAGGTGTGTCTATGTACCATGGAGACTAGAAAAGGGGGTAAGGTCCCCGGAACTGGGGTTACACATGGTTGCAAGCTGCAATGTAGGTGCTGGCAATTGAACCCAAGTCCTCTGGAAGAGCAGCCGGTGTTCTTAACTACAGAGCCATTGCTCCAGCCCTCTCTGATGCAATTCTTGCTGTAAATTCTAGAATGACTTCAGAATGAGGAAGTCTGATTCCTGAGCTGTCCTTGGCTCCTTGAAAGCCTGGGCTGTGAGGCCACCCCCCCAGCCCTCTGAGGGGATTCCTTCTTTGGAAAGACCCAGGCGTCCTTGCTGTTTCATGGTTCAGCAGAGGTTGGAAAGTCCCTCATTAGACCAGGTCTGGGAGCTTGGGAAAACTTTTAGTATAACGACCATGGTGCTAAGACCACCTTTTGCTGATACCTGTGACCTCTTAAGAGTCGTTTCCTGGGTGCATGGTCTGTAAGTGGGGACCCTAGAGTTGCCAGACCAAATGGGGATGGGCCATTTAGAGGAAGTTGGGAATATATGTGGAAGGGACAGAGAGAAGAAGGAGAAAAAAAAAACACCCCACTTCCTTGTTTCTCCTTTCATTATGCCCCAGAATCCCAGGTATCTCTTGGAGACATGGTTGTCAGAGGAGAGTTAGTCAGGAGAATTCTCTTTGTCCTGGAGCTGGGTAGGAAGCCGGCAGGACAGGCAATAGCTCATGAGCTTCAGACTCCTGGAAGGCAGGCTCTGGTTTTAGGGCCACCCCTTCCTTCCTAGTTTGGGCTTGTCCTTTGATCTGGAAGGCATGTTTTGAGCCCTGCATGCCTATGGTCTCATGTGGTATGTGTGCTCAAGAGTGACGAGAGAGCCCTTTACCCTACAGATGAGGAACGGAAAGTTTATAAGGTCAGACAACTGGGAATGAATCTCAAGAGTTCTTTAGCTCTTGGCAACTTAGCGTCCCCCTCCTTTAGAGGCTCCTACTGAGGAGAGAGTTGGAGATGAGTCCGAGAGCAGGTAGGAGGAGCTGGTCCCTATCCCTCTAGTCATTAAAGCCCTGGCAAGTGTTGTTAAATGCACCATTAGCTGAAATATTTAAAGCAATGAGAGGAATCTCCAGAAGAGCCAGAGTACACAGGGGCAGAGCTGTACTGTACCTCCCTGTCATTGGTGGTGATTCTCTTCCCCTTGTCATCAGGGGTGGCCATCCTCTCTGTGGCATCAGGGGTGGCTGTCCTCAAAGAGAAGGTCATTATCAGTCCTGAAATGGTCTGTATACTCAAAGGAAGGGCACAGAGCCCTCTTAACAAGTCTTGGGCTCATAGACTCCCAGCACTGAAGGAGCCCCATGGCCGTAAGACTGACAGACACTGTGGCCGTACTTTTCCTTGCAGACAGATGGCTTCCAGGTCAGTATGTCCAGCAACTCCCTGATGGGAAGGAGGTGGCTAGAATGCTCTGGTGTAGAGCCTATGCTACACTATTCTTCTAGCTTTGCCCTCTAACCTGAGAACATGCTAGACCATGAGGTTAAGTGGGATTTCCCCTCACACCAAAGGAGCAGCGGAATGGGGTACCAGAATGGCCCTCACTCTGTGATCTGTCATCCTCAGAGCAGCAAGGAGAGCAGATCAGCTGTCAAAGGGAGAGTTTGGGGTGGATGGCAGAAGCTAGTGAGTGACAAGCCGCTGTCCAGAGCTGCTCAGGGACACGTGTCAGGAGGAAGAACGGAGCACAGTGCATATGCTGGTTGGTTTGAGAAAATGCCTTCGTGAGATTGGCCCGTGGACAAGTCTGTGGGGGCACTTTCCTGATTAGTGACTGGCGTGGGAGGGCCCAGCCCACTGTGAGAGGTGCCACTCTTGGGTAAGTGGTCCTGGGGTGTCTAAGAAAGCAAACTGAGCAAGCTATGGGGAACAAGCCAGCAAGCAGTGCTCCTCCATGCCTTCCCTTCAGTTCCTGCCTCCAGGTTCCTGCCCTGACTTCCTGTCATGATGGACTGTGACGGGATGTGTGAGCTGAGCAAATCCTTTACCCCCAAGAAGCTTCTGATAATGAGCTTCGTCCAAGCGACAGAAGGGAAACTAAGGTAGCCCACTGGGCTTTGTAGAGGGGGGACTCGTCATCTGGCAGAACTGCCCTGTATCCAGCATCTGTAGACCTGCTTCTAAAGGCCAGTAGAGGCCCCATCCCTGACAGATGGCTAAACCTCCATGCACAGGGGCAGTGCCCACCTCCTTCCTCAGGCAACGACCACAGGTAGATCTGCCCTGTGTGTGTTGGAGGCTGAGAGGAGGCCTTTGTGTGTTAGTTACTCTCCCTGGAGTTGGGACAAACCCCTGACATGAAGCGACGTAATGGAGGAAGTATTAATTTTGACTTACGCCTTGAGGGCTATAGTCTGTGAGGTCAGGAGCGGGAGGCAGCTGGAGTGCGTGGTGGCCGGTCACTCGGCTCCCGCAGTCAGGAAGCAGAAGGAGATGAACGCTGGTGCTCAGCTCACTTCCTTTTACTCAGTTGGGACTCCAGACTGTGAGGTGCGGCTGCCCACATTTGGGGTCTTCCCACCTTAATTAACACAATCTAGACAGTCCTTTCACAGAGATGCACAAAAACCGTCAACATTATACATCATACTGTGTCACACCTGGTGACTTTTTCCTTGGAACAGTCTGCATTTGTTTATTTAATCAATTAATTAATCTCTCTCTCTCTCTCTCTCTTTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTGTATGATGTCTTAGCACATGTGTGATGGTCATAGGACAAATTGCCAGTATCAGTTCTCTCTTACCATCATATGGGTCCTCCGGGTTGAACTCGGTTCTCCAGATTTGGTGGCAGGCACCTTCACCTCTTAAGCCCTCTTGCCTGCCCCTGAAGTAGTTTAAAGGTTAGAAGCAGATCGGTTATTTCATTAGAGCTGCTCACACTTGCTGCATACCCATAGAGTCTCTTTGTAGCTTAAGACAAATTGCAAATATTTCTTTGAGAGTGGTAGCCTTTTAAGAGGCTGGCTACGTGCGTGTGGCTGTTTAAGCTTAGTTTCTGTGCATTCTCCTTCTAGTCCTGACTCTATACATACATACTGTGAATGTCAGCACCAAAGATTTCCTTGCCCAGATATGATACCATACCCTGGCTTCTAGGGCTTCAAGGCTGTGCTCTCCAGTGTGCCCTGTGATGTAAACAGCCCACAGCACAACGCTCATCTTGAGGCCGATGGGAGCAGCTGGCCTCCAGAGTCTCAGGGTCAATAATTCTGCCACCAGAGACTGCCGTTATTAGGGCTCTGGATGTGGTTTCCCTAGAACTTTTTCTAATGGGTCTTGGAAGAATGCTGTCTTGCCAGTGTGTTAATATTTTCACGTTGTGATTTTTCTTCACAG
Seq C2 exon
ACATTCATGGTGTTGAACAAGAAGAGAACAATTTATCGCTTCAGCGCCAAGCGGGCCTTGTTCATTCTGGGGCCTTTTAATCCCCTCAGAAGCTTAATGATTCGTATCTCTGTCCATTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000032884:ENSRNOT00000034025:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.180 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Chicken
(galGal3)
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]