RnoINT0131728 @ rn6
Intron Retention
Gene
ENSRNOG00000006639 | Scn9a
Description
sodium voltage-gated channel alpha subunit 9 [Source:RGD Symbol;Acc:69368]
Coordinates
chr3:52591484-52595989:-
Coord C1 exon
chr3:52595852-52595989
Coord A exon
chr3:52591589-52595851
Coord C2 exon
chr3:52591484-52591588
Length
4263 bp
Sequences
Splice sites
5' ss Seq
AAGATAAGT
5' ss Score
2.82
3' ss Seq
TTTCTTTTTTATTCCTTTACCTT
3' ss Score
1.26
Exon sequences
Seq C1 exon
GTAAATGAACAGCCGAAATACGAATACAGTCTCTACATGTACATTTACTTTGTCATCTTCATCATCTTCGGCTCATTCTTCACGTTGAACCTGTTCATTGGTGTCATCATAGATAATTTCAACCAACAGAAAAAAAAG
Seq A exon
ATAAGTATCTTAGGTTTCCTTCATTGCACTGAGAAAAAATGCACTTCATGTAAGGGGGTTATTTTGATTTTAATTTTTCAAAATAATTGGTCAAGTATGCAATTGCATATATGCATAATCTTATCATATTTGTTGTGTAGTTTTGAATATTATATTAATAGTTTTAATTAAATCATTACATCATATTGTATGTAGTTATATATTATTATATAGTATACTCATTATTTAAACTATCATTTAGTTATATGCTATTATATATGTATTTAAAATATTAAAATGTAATTAAACATAATAATACTTTTAATTATATTCTCTGCTTTCTCTGATCTTGCATATAGAGGACTAAACAATAAATATACTACAACTCAAAGCAGTGAGCTATTTTGTTCAAAGCAGTTATAGTAGTTTATTTCAGGGTTTTTTTTCCTGCTAACCACTCTTCTGTGATGAATCTTATGATGGTCATGGGGTGACAGTTACCTAGGACATGGCTGGTGAACCCAGGTCACTTATGTCACACATAAGAAATAGTATAACTAGTGAAAATAAGGTCTGCAGAGTGTGTGTGCCAATCACTCTCCTTAGCTTTTAAGCTCACTAATCCACGTGTCAGCTTTCGATCCTTTTGACTGTCATAATAAAATACAACCAAGAGCAGGACTTAAAAACAACAGTAATTTATTCCCCACTCATCTAGACATTAGAAGTCAAAATCAAAGAGCTGGAGGAGTCATGCTTTTTGTCCTGGCCCCTAAGAGAGGACTCATCTTTGTATCCCTCAGTCCCTGTCAGCCCAGGCTCCCTTTTGGGGTGAGAACAGGGTACATCTAATATATATATATATATATATGTATAATATTCCTTCTATATCATCTCCTCTACTGAGTACCTGATTATGAATCTGCTCTACTTCTCTTGGACCTCCTCTTAATCACACTAGGCAATAACAGTATCTTCAATCAATGTCATATACTGGGGTGCTAGGAATTAAGATTTCCATATTTATTTGAAGGGAATACAATTCAATTCATACAGTCAACCATTATAGTCTGAATTGTTGCTACAATAACCTAGAAAGGGGGATATGAAGTTGGGGATCTAACATATGTAAAGCACTTACTTAGGAAGCACGAGGCCCTGTTTTTTGTCCCAGCATGAAAATAAATAACTAAATAAAATTAGGAAAGTAGAAAATAGGAAGGGCACAAAGAACAAGTAATTCCTCCAAATCAGATATCAGACTAAGTAGAATCTGTAATATATCCCTTATCTGTTGGGTATTTAATCAAGTATTTTATTCCATCTGCCACACTGCACATATAAAATAGCAATAAGCGCAATGATAAAATTTTATGATAATGCAAATGAGCTGTCAGGAAGTGGATGCTGTGGTACTTGATTTGCTTTCTGAAGGTAGGAAAGAGAATATGCAGCAACTGGGAGGTCAATGGATAGACTGTCTTCATGAAGAACAGAAATATGTGGGCATAATGTCTAGCCCTAATAAAGGAGGAAGATCTTCAGGATGAGTAGCAACTCACTCCATTATTATAGAGTTCAGATTTGAAGATAGAAATTTTTAAAAATACATGCTGTTTGTAGTTTTGGAAAAGCAGATTTGAAAACCCTTACTAACTACCATTCAGTAGGAGCTGATATGTCATTGGGTATTCCAAGCAAGGAATTACATGTAAGCATTGACATTTTTGGAATTCTGTTCTGTCTGATATTGCATAAGATGCCTTGTGTGTAATTTAGAGGAATGATATCTAGTTAACTTCTTAGAAACATTATGTAATATTTACAGTCTGACCCTAGAGAGTAGCTTCATCAAAAACTAAGCCCCAGAATTCTTTCAATCACAGATTATGAAACGGGGCTTTAGTAGATGTGTCTGTGACTAGGAAAACACAAGTTGATCCAGGTCCTGTGTAATCTGACAACTGAGCTGCTCTTGGAAACCCAAAATAGCCCACCATGACAACTGGGAAAGGGAACATACTCAAATGAGACATTCTCTCAAGGAGTGTCTACATGGTTGTTGTGGATTTCAAGAGAGCAGAATCTATGTCTCAGGTTTCTTGATGATTAACTTTGACCTGGTTACCATCTAAGGAAAAGAGATGCTTGGAGAATTAGAAGTAGGATCTCTACAGAAAATTATTCTATGTGCTAATTCTAAGTAACAACAGCCCTATTTAAATAGCTACATCCTTATAGGGAAGATGAATGCAAATACACAAAAACATCTTTCATTCAAAATTTTGGAGCCCCACATGTTTCAAATGTCACACTTTCTTGTATTTTTAAATATCAACATATATAATAAAGTATTGAGGTATGAGGCCCAACACTAAACAAAAAAAACAATCATTTATGATTCATAGAAATGAGAAGAATGAAATTTAGCATAAAATTTGAAGTGTATCTGCATGTTCACTAAGACCAAGCCACTGGGTTAGTAACAGAATTCTCCACTTTGAGTATCATGCCAATTCTCAAAACATTCAGAATTTGAAAGATTTCAAGTTAATATAGAGCATTTATAAAGTGTTTCTCTGTCCTAGTTTTATACTGTTTGGCAAGTCTGATTTCATTTGATCCTCTCAGCAAATGAATGGTGTATTTGCTATATAACAGCATAATAATAGTGTGTTTGGGGAAATCAAGGAACTTATATATGGACAAGAGAGATGAGATTTGAACAAAGATAAGAGCCTAGTCTTAACTGATACAACTTTGACATCCAATAAACATTCGGATAGGAAAAACTGACCTATATATAATGTCCGTCTGGCCTTTCTAGGAGGCGATTTTGCACAAGGACTATATAGTCTGCAGTAAAACACAACAGTTTTACTCTGGGTCACACAGTCTCCCCTACGGTTCATCATACCCATCATGATATTTTGAAAATAGAATATTTTCCCTGGAAAACAAAGTCTGCAACATTATTTTATGCTTTAAATTTCTTCTCCATGTGTTGTTACCAACTTTTGTTTAGTTTCTGATGTGTGAAGATAGTCAGTCACTACTAATAATGACTAAGGACCAAGGCTGCTCTCTTAACATTAGCAGGAACTCTCTGCCATCAGATGAGTACCAAAATGAATGGCATGAAGACAGTGGGCCAAGTAGGCAGAGTGAATAAAATCTAAGAAAAAGAAAGTATGACTATATGAAACCAAAATAAAGCTGAATATAGGTTAAATCAGGAAAACAAAATGGAAGCCACAGTCAGATTGTCCTCAACTTCAACACACTGTAAGTTAAGCAAAGCAGTTGAAGCTTCAAGTCCTCAGAAATGAATCTGTAAGATCACATTACTCTGCATTATGCTGTGAGTTTAAAAGAGCAATAGCAAAGACCATGGCAGAGTCCATCCAAGTCTGTGAAGATTGTGGATAGTCTTCAAAAGTCAGCAAAGGATAAAAAAAAATAACCAAAGTTTCTAGACTTTCTTTCTGAAGTTTTGTCTTTTCTGATGAAGAAAGGGTTAAAATGTGATTTTGACATCAGCTTAGGCTATTTAATCTAGGTGACTGCATTTCTTTTTGTTTAATTATTTGATAATCTTTCAGACCGCTCAAGACTGATGACTGGTAGCTTCCTTTGTACCTGAACTTTACAAGTATAATGCTGATATCCAATAAAATATTTATATTGAAACCAGAGAGGGATTATTAAAAATCCAGTTTCTTTACATGAAGACAGAGACATACATGGATGCTGACATAGATATAGGACTGCCCAAGCACTTCTAGAATTGCCTGTGTTTTTTCCTCCATTAATGAAATGGTGCCATTTGGAAATTATAAATCAATAGAAAATTAGTGCTATCTTAGTTGTTATTTCTGAACCCTACTTGTGATTAGAGTCCAAAACATCTGCCAATGTGTGAAAGACATTTTTAAATTTTCCTAATCTGTCCGTTACTTAGCACAAATATTTTCCAGTAAGAGAGATAGCAGAGGAAACAAAACCTCAACACAGAGGCTAAAGAATAACGTATTAGTATATCATAGGTAATGTGGCCACTCATGATCATATGTTGTGCATACTCTATATATTTGAATTACAGCATGTCCATGTTTATACAAGGTTTATACAGGTAACCCTTTTTAGGCATCTTATGTATGGCTCCTAGGTATTAGCCAAGTGAATAATATCATCTCTATGTTTATATATTTAACCTTTATGAAGGAGAAGAAAGAACTGCACTTTGGTTCTGGTTTTAATTGGATTTCTTTTTTATTCCTTTAC
Seq C2 exon
CTTGGAGGTCAAGATATCTTTATGACAGAAGAACAGAAGAAATACTATAATGCAATGAAGAAGCTTGGGTCCAAGAAACCACAAAAACCAATTCCAAGGCCAGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000006639:ENSRNOT00000065126:24
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=PD(15.3=76.1)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
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]