RnoINT0131537 @ rn6
Intron Retention
Gene
ENSRNOG00000053122 | Scn1a
Description
sodium voltage-gated channel alpha subunit 1 [Source:RGD Symbol;Acc:69364]
Coordinates
chr3:52394997-52397436:-
Coord C1 exon
chr3:52397332-52397436
Coord A exon
chr3:52395268-52397331
Coord C2 exon
chr3:52394997-52395267
Length
2064 bp
Sequences
Splice sites
5' ss Seq
GGAGTAAGA
5' ss Score
4.36
3' ss Seq
GTGTCTTTGTTTCTCCGCAGAAC
3' ss Score
13.06
Exon sequences
Seq C1 exon
TTTGGAGGTCAAGACATCTTTATGACAGAAGAACAGAAGAAATACTATAATGCAATGAAGAAATTAGGATCAAAAAAGCCACAAAAGCCTATCCCTCGACCTGGA
Seq A exon
GTAAGAAATATGAAATGAAAATTATATAAAGCAACAACCTGAGATACGTTTTGTTACACAGCGGAAATCAATTATCATTTCCAGCACAACAAAAACAAAACAAAAACAAACCTTATCCTTTTTGAGTATCTTTAATCCATGTTTTTGATATTTTTAACACCAAAGAGAATAAGAATATACAGGAAACGCACATTTGTCTTCAAATGACTTAAAACTATAGACCTAGAATCCAAACTACATAGATAAATGTGGTTCTCACAATAGTTGTGTCTTTACAGTAGCTGCTGTGCATTGTCAAGAAATGCAGAAACATTGGGCAGAGCTAGTATCCATTCACTTTCTGAGACTAAGATGCAGACAAAGATACTCAGTGGCATAACATCTCCATTAGCAGTTGTTGTTTAATAAGTAGAAATATGGACCATTTTAGAGGAGGTGAGGATTCCAGCAATATATTTCTGTATGGCTCTAAAGTCAGCAATTACTTACGTCAGTTACAATTTATGAGAACAAATAATCATTCTCATATTTCCAGGATAAATCTACAAACTATAAAGGAGAAAGAGCCCTTATTATAGCTATTTTTATGGCAGTGATTTTTTTCGATAAGTTATTATTTTTATTCACATTACATCCCAATCATAACCTCCCTCCCTTCTCTCCTCCTAATCCCACACTCACTACAAATCCCTCCCTCTATTGATCCCTCCCCTTCTCCTCATAGGAGTCCCCCCACCATTGGGTACCACCCCACCCTGGGATATCTAGTCCCAACAGGACTAAGCACATCCTCTCCCACCGAGGACTAACCAGACAGTCCAGGTAGGAGAAAGGGAGTTCAATGACAGGAAGCAGAGACTGAGACAGCTTGTTGGGGGACCCACAAGAAGAATAAGCTGCATATTTGCTACAAATGTGTAGGGGACCTAGGTCCAGCTCCAGGATGCTCCCCGGGTGGTGGCTCAGGCTCTGTGCGCCTAGGTTAGTTGACTAGGTTGGTCTTCTTGTGGTGCCTTGACTATGACAGTGATCTCTAAGCTTAAAATATTTCCAAGGATAAATCACAGAGCAGAATCATAGTGAATATTTCTATTGTGGAAACCAAATTTGTTTGTTTGCTTGTTAGCTTGTTTGTTTTGAGACAAGCTTTTTCTGTGTAGTCTTGGCTATTCTGGAACTCACATTGCACATCAGGCTGGCCTTGAACTCATAGATCCACCTGCCTCTGCCTCAGAAGTGCTGGGATTAAAGGCATGCTGCATAACTGCCCATTCAAGCCTTACTTTCTTAATGAGAACATTTTCCCCATTGAAACTTACTACTACCCGTCAAGTACTATCACATCAAGCATATTTTATGGTACTAGGATATGCTTAGGATTCTCGAGTGGCCCAAAGAAATAACCAGACAATGGCTTGCTGGGTCTAACATCAGCTGACTGGGGATTAAACCACAAATGGGTAGCAAAGGGCATGTGCTCCCTTTATTCTAATAGCAGAGAATGTCTTTTCGGTCTGATTACCCCTGTGAAGACTCATCATTGTATCTGATAATATCAGCAAAAACCTCTTGCTGGGAACAAATTAATGTCGCCAAGGTAGAAGGCAAATATTTCAGATGCATCCTTGAAGTCACAATGTTCCTTTGATAATTCCCTAGGAATAAAGCACATGTGAGCCTAATATTTACTACATGTATAAATGGCCACACTGTCTAACTGATCATTGGGAAAAATACTTCAGCCAGTGAGCTAAAGTTTGGGAACACAAATTCAAACAGGCTTCCTACATTCCTGTAACTTTGACTTGTTGAAATTCACTGTGTGTTTCTGAACAAAGTACAGGGAGAAAACCTTCAGCAATGGAATGATGTGCTCGGGAAGATACAAGCTTAAAAATAATTTAAATAACTAGATATAAAAAGGTACCTATTAGAAACATTTGTATCAGTAGGTAGGTACTATGAACAATACTAGAAAGTAGGTAGTATGGGAAATACATAAGGTGCGTGCTATGTCTACCAGAAAACTCCCCCATTGCTGAATGTGTCTTTGTTTCTCCGCAG
Seq C2 exon
AACAAATTTCAAGGAATGGTCTTTGACTTTGTAACCAGACAAGTGTTTGACATCAGCATCATGATCCTCATCTGTCTGAACATGGTGACCATGATGGTGGAAACGGATGACCAGAGCGATTATGTGACAAGCATTTTGTCACGTATCAACCTGGTGTTCATTGTGCTGTTCACCGGCGAGTGCGTGCTGAAGCTCATCTCCCTCCGCCATTATTATTTCACCATTGGCTGGAATATTTTCGATTTTGTGGTGGTCATCCTCTCCATTGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000053122:ENSRNOT00000083552:22
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:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(20.4=47.3)
Main Inclusion Isoform:
NA
Other Inclusion 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]