RnoINT0131670 @ rn6
Intron Retention
Gene
ENSRNOG00000029342 | Scn7a
Description
sodium voltage-gated channel alpha subunit 7 [Source:RGD Symbol;Acc:61922]
Coordinates
chr3:52796890-52800055:-
Coord C1 exon
chr3:52799621-52800055
Coord A exon
chr3:52796996-52799620
Coord C2 exon
chr3:52796890-52796995
Length
2625 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGA
5' ss Score
10.06
3' ss Seq
GGGACTATAATTTTTTCTAGAAA
3' ss Score
3.71
Exon sequences
Seq C1 exon
ATACTTTACCTCTTTGTGGCATTGGTGAGCTCATTTGCTTCATACGATGCTACCACAGAAGTGAGCAAAGAAGCCAAAAACCTTCAGCTTGCAGTGGCATGGATAAAAATGGTAATAAACTGTGTGCTTCTTAAAATACTGTGCAAAGAAAAAACTGTTTCTACAGAAGCAACAGACCAAACATGTGATCCAAGTGTTAAAGAGAATATTTCTGGTCATACTCTTTCTGAACTGAGCAACACCCAAACATTCCTCAGATACAAGGACCAGAGCAGTGGTACTGAGAAAACTCCAGTGACTGAGTCTGAGAGCCAATCCCTGATTGCTAGTCCCAGTGTATCAGAAACTGTGCCAATTGCTTCAGGAGAATCCGATATAGAAAACCTGGATAACAAGGAGACTCGGAGCAAGTCTGCAAATGGAAGCAGTAAAGAG
Seq A exon
GTAAGATGATCTATTGTTATTCATTGTGGATTTGTGGTTTTGCTCAAAAGAAGTAAATCAACACTGGTGTTACAGAGTTAAATCGCACGTTTGACCCTAATTCCACCTTCCCTAACTACTGGATTTCATGGTTTTAACCAAACTACTTAAATGTCCAAGCTTTTGTTTCCTTATCTGAAAATGAAGATATATTTCTTTTACAGGGAAGAAGTGAGAGAAACAGTAGTGAATTCGCTTAAAGTGATATTTGGAAGATATACTATGATTTAATTGTGAAGTTCTATAAATCAATATGTAAGACAATTTGTGGTTCTGAAAATCATCTCTAAAGCACATACAAACCTTTGTAAAACTCAATGTGTATGATTGAAATTTCTTGTGCGTTATCATCTTCAAGCTGTGAGAATAGCTTAAAAGACTGTGACATGATTGTTTCTTCATTGCTAAGAATGAAAGTCTAGTCCATTCACATTTACCATATTTAAAAATATAATTGATTAAGACTAAAAAATAATAACAAAATCAATAAGTTTGTATTGTGACTAGTTAGAACTTTATAAATTTCTGATTGATAAAAAAACAAACATTTAAAAGGCTAAACATTGTTGTTCACTTAGCTTCTGAAATATTTAATGTTCTATCCTTTCCACTTAGAAATGACCTAACGCACTATCAAAAGGTACAATTTAGTAAGAGCCATTCTTACAGAGAGCGTATGTGCTATATCAGCTTCAAGCTCTGAATCTTATTGGACATCATCTCAGGTCAACCGAAGGCCCCAGAGAAGGACAGATTATGTCTTTAATGTGTCCCCATTGTGCCTGGCATCCCTTTCCCCAAAATTCTGCTGGTTAGGCAGATGTGGCCCATTATAATGCCTCAAATGTATCTTCTGACACAATTTCAGGATCAGTAATTAGTAGATCCTCAACTTTCCTCTGAGCATATCAATATTCTTGGCTTTCTTTTTCTTTAATGACAAATGATGGGAATTTCTATTCCTCAAATATTCACACACACACACACACACACACACACACACACACACACACACACACACATCTTTCTTCTCTGAAGACTTGGCGTCCATGCATGTCAAGATGAAACTGTTTTGTGTAGTAAATAGAACAGGATTTTCATTGGAAAATCTTGATGATTTCATTAGAAATTCTAAAGCACAAAATGCAGAATAAAGCAATAATGTGAAATAACTGTAAATATTGGATTTCAGATTCTGTCAATAATATTGTGTGCTTATCTAAGCCTTTTTTTGGTTAATTAACTTCTCAAAGATTTATCCATGATGCATATCCCTAGCTATATATTTAATTAGGCAATTTGTCAATTATATGGTCCAAGAATATTTAATGTACACTGGACTAAAAATTACCACAAATAAAGCATGAAAAAAGACTAATTTAAGAAATACATTTTTATTAGTATACATGTATTCTTCCATTAAAATATTATGTATGCACATAAGACTGATCAAACTATATTTCATATTGTTAAACTTTTTAAAAAATATAGAACTACATCACAATACATTTTTTCATGATGTTCAATAACCTACCAAAATGAATTATAATTATAATTTATATTTTGAGCTATATATGAGGTAATAAAGTAAAGCTATTAATAGGTCATATTAATAGCATATGGAGAAGTGTTTGATAATATCTATAGTAAGTGTACAATTATTTATCTAAATAATACTTTTCTGCTCATTTTGTTTCTTTGCTCAAGCAACAGATTTTACTGAGATGACAACTAGCTATGTAATAAAACAAAGAAAGTTTTCCATTATAGTGATCCTGCATAAGATCACAAGGAATGAACAAATACCAATAAGATCTTTCTCCAAATTCTGTCTAAACAATCCCGTAGTAATAACATTTTATATACTTTTATATGATTTGTCTACATTAGGAAATATCTTTTAGTGCTATTGACTTATGGGATGCTGATTTATTTAAATGATGTTATGTTTGTGTCCATCTCAAAGTAAAGTCAATAGAAGCATTTGCCACAGGTACAAAGCAATCAACACCCTGACTCGGCAGCCTAGAGCCTCAGTCATGGCCGAGTGGGAATGGAGAACCTCTCTATCTCCAGGATCTTCCTATGTGACTTTATCCACTTGCCCCATTCTGTCCAGATACTTCTCTGTGTGTTTCTTTTCACATCAGTGTAATCTCATGTGCAAAGCTGACAAGCACAAAAGTATCTGGATTGGATTAAGCAGTTATAATGAAATGTATTGTCTACTCAGTAATAGGATGAATTATTGTGATGTATCTGCCTAACTAAAACAACATATATATGTCCCATGTGAATTGCCTTAAAATTCAAATCCCAATTATTTTAGAAACAATAAATGAAATGCTTTATACTTAAACTTCAATTTTACCTCAAGTTATTATCACTTAAGTACTTCAAAGTAACTTAAAAAACCAAATCTATACACAGTGAATGTCATTTCAGGTCAGCCTCAACTACCTTGATGTCTTTTAACTTTGATAATATTTTTGTATATCATATTTACTTCTGAAAATAAAACAAAACTACCACAATCAAGTTGAACTTTGGATGTAACTTTTTTATTGGGACTATAATTTTTTCTAG
Seq C2 exon
AAAATGAAGCAATCTAGTTCATCTGAGTGCAGCACGGTTGATATTGCTATTTCTGAAGAAGAAGAAATGGTCTATGAACATGAAAAGTCGAAGCTTCATAAAAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000029342:ENSRNOT00000041096:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.421 A=NA C2=0.194
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.2=5.5),PF065128=Na_trans_assoc=PU(60.3=84.8)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(17.2=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:
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]