RnoINT0131532 @ rn6
Intron Retention
Gene
ENSRNOG00000053122 | Scn1a
Description
sodium voltage-gated channel alpha subunit 1 [Source:RGD Symbol;Acc:69364]
Coordinates
chr3:52416439-52418215:-
Coord C1 exon
chr3:52418042-52418215
Coord A exon
chr3:52416562-52418041
Coord C2 exon
chr3:52416439-52416561
Length
1480 bp
Sequences
Splice sites
5' ss Seq
GATGTAGGT
5' ss Score
4.9
3' ss Seq
TTGTTATTCGTATTTTACAGGTT
3' ss Score
10.73
Exon sequences
Seq C1 exon
GCCTTTGAGGATATATACATTGATCAGCGAAAGACGATCAAGACCATGCTGGAGTATGCAGACAAGGTTTTCACTTACATTTTTATCCTGGAGATGCTCCTCAAATGGGTAGCCTACGGCTATCAAACGTATTTCACCAATGCCTGGTGTTGGCTGGACTTCTTAATTGTTGAT
Seq A exon
GTAGGTATCTTCCATACCATGCCTTTTGTTTGAGGTAGTTTGTCTTGTTTGTCTCCTGATTTTAAATCAGTGAATGAATCCTTGACCATTGTGTTATGATGACCAGATGATCTGCTGAGTCCTAAACTCTCTAAGCAAATAATAGCATAGAATTTAGAAGTTCTGGACTAACTTACTAACTAATTTTAAAAGGGGAGATAAGATCTAGTGGGAAAAACAAATTTAAAAAGTCATGCCGGTAACATATAACATGAATGATGGAAAAAGCCATTTAAAGGGTGTTTATAATTCCATGTTGTAAAGCAGACAAACTCCAGATCTTCCCTCATTTATTCACTGATTTTCTTCCCCAATAGTAAAGAATGTCAAGAAACAAAAGGGATAGTGAGTACTAACTGTAATTTTATAAATCTTTCTTATCGGCTGGAAGATTTTATGGAGAGATTTTGAAGGGTAGGGGAAGACAAGTCTACTTCATGACTGGGAAGAAATATTCTTTGATGTAAATAAGATTTACAGAAAGTCCTTGATATACCAGATATGCTTATGGAGAAATTTAGTCATTAATAGTGAACATTTCATTCACTTAAAACGAGTAACAAGGCCTCTTGCTGAGGTCAAAACCAAGTGGGTGAATTGATGGAAACCTCAAAGGAATCATCAGTTTTACAGAATAGAGAGGGGACATGGATCAACAGACATCAACTCACGCTTTCACAACTCGTAGTGCAGTTAGGACTTTTATTACTTTTAAACGTTTCATGCAGTGTAACTTTGCATACAGTGGATTTTGCTTATATACTTCCGTTTTCTCAAGTCCTTCCAGATCCTCCTGCCCTACTACCCGGACAACTTCATTCTCTTGAGAAAACAAAAAAGGAAGAAAGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAATAAAAGTAAAAAAAACAGCAGAAAACCAAAACAACCACCAAACATAACAAAAAAAATGCACACAAACAACTAATCTGAGTCCATTTTGGGTTGGTCAGCTACTTCTGATCATACAGACTGCCCTCCAGTGTGATTCATATACCCAGTGTCACTCCATTGAGAAAAACTGATTTTTCTCTCTCCCAGTGGTATTGGTTGCAGATAGATAGTTTCTTGGTTAGGGCTAGAACTTCCTGGTCATGTCCCCTCCCCGACGCTTAGATTTAGTCCAGTTTAAATTTTCCATTGGTCCTGTGCATGCTGTCACTATCTCTATGAGCTCATATGTCCCTCACCCCATTGTGTCTGGAAGACAGTAATTTCCTTGGGGCCATTCCCCGCCTCTAGTTCTTCGTTAGGAGTCATTTCTGCTGTGTTTATTCAATAGAATAGCAGAACAGCTATGAATAAAACCTGTATCCGTTACATTAGTTGATAACAGCAAATTGAACAGAAGTTCAGTTTATGACTTATCCATTGTTATTCGTATTTTACAG
Seq C2 exon
GTTTCATTGGTCAGTTTAACAGCAAATGCCTTGGGTTACTCTGAACTTGGGGCCATCAAGTCCCTAAGGACACTAAGAGCTCTGAGACCCCTAAGAGCCTTATCACGATTTGAAGGGATGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000053122:ENSRNOT00000083552:17
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=PU(17.0=67.2)
A:
NA
C2:
PF0052026=Ion_trans=FE(17.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTGAGGATATATACATTGATCAGCG
R:
CCTCATCCCTTCAAATCGTGA
Band lengths:
294-1774
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]