RnoINT0131516 @ rn6
Intron Retention
Gene
ENSRNOG00000032884 | Scn11a
Description
sodium voltage-gated channel alpha subunit 11 [Source:RGD Symbol;Acc:3630]
Coordinates
chr8:128450801-128456086:-
Coord C1 exon
chr8:128455816-128456086
Coord A exon
chr8:128452359-128455815
Coord C2 exon
chr8:128450801-128452358
Length
3457 bp
Sequences
Splice sites
5' ss Seq
TTAGTAAGT
5' ss Score
7.79
3' ss Seq
CACTGGTCCTCCCTCTCTAGGTA
3' ss Score
10.93
Exon sequences
Seq C1 exon
AACAAATGTCAAGCCTTTGTGTTCGACCTGGTCACAAGCCAGGTCTTTGACGTCATCATTCTGGGTCTTATTGTCTTAAATATGATTATCATGATGGCTGAATCTGCCGACCAGCCCAAAGATGTGAAGAAAACCTTTGATATCCTCAACATAGCCTTCGTGGTCATCTTTACCATAGAGTGTCTCATCAAAGTCTTTGCTTTGAGGCAACACTACTTCACCAATGGCTGGAACTTATTTGATTGTGTGGTCGTGGTTCTTTCTATCATTA
Seq A exon
GTAAGTAAAACCAGTAGCCAGGACTTTCCAGGAAAGGCAGACATAAACCCTAAAGATAATCATTTGGAAGTGTATCAAGGGTTTCCACAAAGCAACAGATTATGCTTAATGTAGCCCCAGGGGTGGCGGTAGGGGGCTAAGAATGGCCCGCTCTGTTGGAAAGTTGCCACAGGCGGTAATTTCCTTTCTTGACCCGTTCCCTTGTTCAATGGAGAGAAACAAAGTATCTCCATTAACAGTTGTTGCCATGGTTCCTGACATCTCAGGTGGCTGAATAGGAATTCCCACCTCTTTCATGCTACCGTAAACCCCCCCCCCCCCCCCCCCCCGTGGGCAGTTTGTGGTTTTAGGAGCTTGTCGGTTAGTACTGATGTTTGTGTCTGGGTTCAAAACCCACAAGGGTACTAGAGCAGCTATTGGACCAGTATCCATTGCTGGGGCTCCCTTGCTTCCCATTCAGCTGTCAAGACTGCCTCACATGAGAAGCAGTACACACTCCTTGACCTGAATCCCCTGTTTACTTAGACAGGGTTTGGGCTGCATGCGTCTCAGCTGACACCATGGCCGGCAAGCCTCTTTCTATAACCAGTGGGGTTTTCATAGCTACAGTCCCGCCGTATCAAGCGCAGAGCAAATGGGAGAAAGAGCGTTATTAGCACACACTCATTCCCTTTCTTCTTTCGTGTTTTTAAAATTATGTGTATGGGTGACCAAGGAGACCAGGGCCAAAGACATTGAACTTCTGGAGCTGGAGTTCCAGGCCCCCACCTGATGTGGACGTTAGTGATCAAACTTAAGTGCAACACAACAGAAGCTCATGTTCTTCATCTCTGGGCCGTCTTTAGCCCGCCTGCCTGCCTGCCTGCCTGTCTTTCTTCCCTCCGGCCTTTCTTCCTTCCTTCTTTTTTTCTTTCTTTTGTGCTGAGAATCAAAATTCAGTCCTGTGCATGTTAAGTATTATACTTCTTCATGGCTAAGAGATTAGAGTTTATTTGGGTCCTTGAAATTTGATTGGAACTAATCCATTAATTTGACTTTTTCCCCTCTTTCTCTTTTTCTGAGAAGGAATGTTAAGATGGGGTGTCACTCTAGTGCAGGTTGACCTGGGATTTATCATACAGCCTAGGCTGGCCTCAAGCTCATTTAAACCTCTTACTTCAGCCTCCTGAGTGCTGGGATTATGGGTGTGTGCTGTCACATCTGACTTAACCTCGTCTTTCACATGGTGCAGGAGGGTCCAAGAGTCTTTCTCGTAGTTCAGAAAGCAACGAAGACAAGGAGAACCACATTTTACAAATGGAGGCTTCATCCCATCTCAGAAAGACTGCACCACAGGTTTACACCTGAGTGGCTTCTCTCGAGTAATGCGGGCTGTCAGGGAGTGTGCTTGGGTTCTAAGCTCGGAGGTTTATGTAGTTAGTTTAAATAGGCTCATCTCTTGGCAGCAAAATAGACCTATGATCCTTATTAATTAGTCCCGATCCTAAGTTCTGGTGAAATTGATGTCAATTGAGGTTGGAGAATGGTGAACAGATGATTCGGGGATCTCCTTGCACCAAAGGGAGCACCATGAGCCCCTTCCTCTCATAAGTGAAGAGGGTCCTCATTCCACCACCCATTCTAGGGTGACTGTGCAGCTTCTAGAACTATATCTGGGATCCTTCTAACAGCTCCCAGATGATGGAAATCCCACATGCTCCAATGTAGGACCAACCTTCACAAGAAGCCAAACACTTTTCACTGACATGCAGAGTCCCATGTGTGTCTGCATCCAGCACCTGGTCTCCACACACCCAGCACCTGGTCTACACACACACACACACACACACACACACACACACACACACACACAGCATCTGGTCCCCACACACCCAACACTTGGTCTCCTCCCCCGCCCCCACAACACCCAGCACCTGGTCTACACACACACACACACCCAGCACCTGGTCTACACACACACACACACACACACACACACACACACACACACAGCACCTGGTATACACACACACACACACACACACACACACACACACACACACACACAGCATCTGGTCCCCACGCACCCAACACTTGGTCTCCTCCCCCGCCCCCACAACACCCAGCACCTGGTCTACACACACACACACCCAGCACCTGGTCTACACACACACACACACACACACACACACACACACACACACACACACAGCACCTGGTCTAACACACACACACACACACACACACAAAGCACCTGGTCTCCACACATCCAGCACCTGGTCTCTACACTTTCCCCAGGCTTCTCCCTGAGCTTTTACAGTAACGCAAAATGAGTGAGTCTGGGAGTTAGCTGTCTAGTTGCCAAGTAAGGCTTACTCATTTTAGTTGAATACCAAACATGGGGTTCACACAAAAAGAAAAAAGAAAAAAAAACTGCACTCAGAGAAAAGACTGATTCACACAGACCCGGTTAGTCCAGAAAGGATTTAAGGCCGAGCCTGAAAGGGCTGGTATTGCTGAGCGAGCACCATCCTTGCTAGGATTGTCTGCCCAACTAGCGTATGTCTTTTATACAGTCAGATGACAAGGTTTAGCCAGTGAGCTCTCTGTAGTCATTAGGAGACTGGCAAAAGCATTTTCACTGCCATGATCCCTAATGACCTCAGAGCAAGGGGAAGACCATGCCTACACAAGGCAAGCATGTTCCAGCCATTCTATAATATTTGGGCCAAAATGTAAATTGCCTTAACTGCTCATAGCATGTACCGGCTGGACAAGCAATGAGAAAACAGGGTGACATTTTAGGCCCAAATATTCACCAGTTTTCACAAAGCTCAGAGACACCATTTCTGGGTTGTCCACAGCAGAGAACATGTGTGAGCTTTGTGAGACCTCAGCGGGTCCTCAGGGTGAGCAGAACATCAAACAGGGATCAGTGGGCATCTTCGGAGTAGAGGAAAGCTCAGTTCTGCGTCCCTGCAGCTCTACACAGCACAGTTAGTCCGTCCTCATGGCAGAGCCCCATTCAGAACCCAGATGAAGAAGCATCCGTCCCTTTTAATAAGCTTGGGTCTCTCAGCCATACTCTAGGAGAAGCATCTCCGTGCACTCTGGGAGAGTCAACATTTGAAGAAAGGGCCCGTGTCCCATCTACATCCAGTAAATAGGGAAACATCGTGGCAGGTGTGGCCCTGTGGGAAAATGCAACAGGTAAAACCCTGCATAGTATAAGCTGCCATAGTTTCCTTACTTGCCTTCAGTGGCGTGGGCATCCCAGCCCCCACAAAAGTTCCATCTAAAATTCTATGGCCCTTAGAGATTATTCTTCAAATTGAAACACAAGTGACCAGTTCTTAGTTTTGTGTATAAATGAGAAGGTGTGTGTAACAAGTTGGTCCCCTCAGGATTCTGAGGTGGGAGAATGGCTGGGTTCGAAGCTGGAGTGCTTGTTGGGAGCTCACTGGTCCTCCCTCTCTAG
Seq C2 exon
GTACCCTGGTTTCCCGCTTGGAGGACAGTGACATTTCTTTCCCGCCCACGCTCTTCAGAGTCGTCCGCTTGGCTCGGATTGGTCGAATCCTCAGGCTGGTCCGGGCTGCCCGGGGAATCAGGACCCTCCTCTTTGCTTTGATGATGTCTCTCCCCTCTCTCTTCAACATCGGTCTGCTGCTCTTCCTGGTGATGTTCATTTACGCCATCTTTGGGATGAGCTGGTTTTCCAAAGTGAAGAAGGGCTCCGGGATCGACGACATCTTCAACTTCGAGACGTTTACGGGCAGCATGCTGTGCCTCTTCCAGATAACCACTTCGGCTGGCTGGGATACCCTCCTCAACCCCATGCTGGAGGCAAAAGAACACTGCAACTCCTCCTCCCAAGACAGCTGTCAGCAGCCGCAGATAGCCGTCGTCTACTTTGTCAGTTACATCATCATCTCCTTCCTCATCGTGGTCAACATGTACATCGCTGTGATCCTCGAGAACTTCAACACAGCCACGGAGGAGAGCGAGGACCCTCTGGGAGAGGACGACTTTGAAATCTTCTATGAGGTCTGGGAGAAGTTTGACCCCGAGGCGTCGCAGTTCATCCAGTATTCGGCCCTCTCTGACTTTGCGGACGCCCTGCCGGAGCCGTTGCGTGTGGCCAAGCCGAATAAGTTTCAGTTTCTAGTGATGGACTTGCCCATGGTGATGGGCGACCGCCTCCATTGCATGGATGTTCTCTTTGCTTTCACTACCAGGGTCCTCGGGGACTCCAGCGGCTTGGATACCATGAAAACCATGATGGAGGAGAAGTTTATGGAGGCCAACCCTTTTAAGAAGCTCTACGAGCCCATAGTCACCACCACCAAGAGGAAGGAGGAGGAGCAAGGCGCCGCCGTCATCCAGAGGGCCTACCGGAAACACATGGAGAAGATGGTCAAACTGAGGCTGAAGGACAGGTCAAGTTCATCGCACCAGGTGTTTTGCAATGGAGACTTGTCCAGCTTGGATGTGGCCAAGGTCAAGGTTCACAATGACTGAACCCTCATCTCCACCCCTACCTCACTGCCTCACAGCTTAGCCTCCAGCCTCTGGCGAGCAGGCGGCAGACTCACTGAACACAGGCCGTTCGATCTGTGTTTTTGGCTGAACGAGGTGACAGGTTGGCGTCCATTTTTAAATGACTCTTGGAAAGATTTCATGTAGAGAGATGTTAGAAGGGACTGCAAAGGACACCGACCATAACGGAAGGCCTGGAGGACAGTCCAACTTACATAAAGATGAGAAACAAGAAGGAAAGATCCCAGGAAAACTTCAGATTGTGTTCTCAGTACATTCCCCAATGTGTCTGTTCGGTGTTTTGAGTATGTGACCTGCCACATGTAGCTCTTTTTTGCATGTACGTCAAAACCCTGCAGTAAGTTAATAGCTTGCTACGGGTGTTCCTACCAGCATCACAGAATTGGGTGTATGACTCAAACCTAAAAGCATGACTCTGACTTGTCAGTCAGCACCCCGACTTTCAGACGCTCCAATCTCTGTCCCAGGTGTCTAACGAATAAATAGGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000032884:ENSRNOT00000034025:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.017
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(21.1=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(78.4=46.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
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]