RnoINT0131588 @ rn6
Intron Retention
Gene
ENSRNOG00000005007 | Scn3a
Description
sodium voltage-gated channel alpha subunit 3 [Source:RGD Symbol;Acc:3635]
Coordinates
chr3:51568209-51571154:-
Coord C1 exon
chr3:51570798-51571154
Coord A exon
chr3:51568680-51570797
Coord C2 exon
chr3:51568209-51568679
Length
2118 bp
Sequences
Splice sites
5' ss Seq
GTGGTACGT
5' ss Score
8.61
3' ss Seq
TTTTACTCTCTCCTCTTCAGGTT
3' ss Score
12.41
Exon sequences
Seq C1 exon
CTCCGAGTCTTCAAGTTGGCAAAGTCCTGGCCCACACTGAACATGCTCATTAAGATCATCGGCAACTCGGTGGGCGCACTGGGCAACCTGACCCTGGTGCTGGCCATCATCGTCTTCATTTTTGCCGTGGTCGGCATGCAGCTGTTTGGAAAGAGCTACAAGGAGTGTGTCTGCAAGATCAATGTGGACTGCAAGCTGCCGCGCTGGCACATGAACGACTTCTTCCACTCCTTCCTGATCGTGTTCCGAGTGCTGTGTGGGGAGTGGATAGAGACCATGTGGGACTGCATGGAGGTCGCGGGCCAGACCATGTGCCTTATTGTGTTCATGTTGGTCATGGTGATTGGGAACCTTGTG
Seq A exon
GTACGTATGTACTGCAGATCTTTGTGAATAAGAATGAGTGGGGTTGGGGATTTAGCTCAGTGGTAGAGCGCTTGCCTAGGAAGCGCAAGGCCCTGGGTTCGGTCCCCAGCTCCGAAAAAAAGACCAAAAAAAAAAAAAAAAAAAAAAAAAAAGAATGAGTTTGGGCCGTAGGAAACAATGGCTTAAGCAGTAAATATATCTCCAATTTTACTGCCAGCACTTCAGTGTCAACACCCCCTACAGGAATTACAGAATGACATTATTTAAATTCTCTGAGGTCAGAGCTAGCTCCCTGTGACCATGGAATAAAATGTCTGCTATGGAGGATATGGGGATGAAAAGCATGTTCGCGGGTTACAGCTACTAAGTTTACTTTTTTCATGTCAAAAAGTGTATTTCCTTATCTAGACTCACTATATCATTATTTGATATGATAATCTCTTTAAACCCTAAAAATACAACTACCTCTTACATGTCCATAATTCACACTGTTTTATTTAAAGGTGTGGATTAGACACAAATTCTAAGGTCAAACGTTAAAGATATAAAGTAATTTACTTCAGTTGTGGTTTATAATTACTGTAGGGTACAAAATATGTTCTTATCTGCATTTGTTTTATTAAAAGAAATAACATTGGAGGGTGAATAATTCCACACATACAAACGTGTATGTATGTATATACAAGCATACACAGAAAGACACAAACACACAACACACACACACACACACACACAGAGAGAGAGACAGAGACAGAGACAGAGACAGAGACAGAGAGGCAGAGAGAGGCAGAGACAGAAATGAAGATAGACACAAGAGAGATCAGATTTTACATACTTTCAGCCATTCCTTAGATTCTAGAAGAGGATGGACAAACTGTCATGAGCTGCTTCCCCACAGCTGAGCCTGCTTACCTCAAAAAAGCCATGCTAACAGCAGCGCTCCAGTTGATCACATCGAATAAAAGGAATCGACTTGAACGCAAAAGAGAGCCTTGTGAATAGGTGTAGCAGGGGTGGGGGTGAGGAGTGCATGGCCAGTGTATCTTGTATTCGTGGATGAAATTGTCCAAGAACAAATGGAAACTATTTTAAAAGCCCTAACATAAAGGCATGTGTTTTCATACTTAAATTCCTCTATCATATATGTATATAGTAAGTACCTACATAGTCATATAAGGTCTTCCTTTTAAGGGGTACACTTCAAATAATACTCAAAAGAACGATAGTGGGACATACACATTATTTTCTTAAAATAGAAAAGTGCCCTAGATTCAGATAAAAATATGATGTTTAAATAGAAAACAACCCAGAGATCCTAGTTTGCATTTGTCCTCCTACTATATAAAGAGACTCAGTAATTACATTTTAGGCTAAAATGATCCCTGTGCTTAAATATCCTTTTACATCAGACATTGTGAGTTATCCCTGTAATAGCCACAAACCCCCAGGTATCCACTGCAGTGAGTCACAGCGACACTCCACAAACCTAAGGAGAGAAGGGATTTACATTATATGAGTATGGCTGAACCTTAGAACGTTCTGGAATTTTCTCCAGTTTTCTACACGATTTGAACACCCATGTTTTAAAGTATGCTTGACAGGAAATATATTAACCCTTGTGTAATTCGCTATCTCTGCCATCACAGTTTGTAGCCTCTGGACCAAAGAAATCTGTTTCTGCTACGTACTGGCTTTATACAAATTAGCAGGTTATTAGATAAATTGGTTATTTGTACACATGAAGCTAGACACTCCATAGGCAAGCTGGTAAGAGGAAATAAAACAATGGAACTGAAAATGCCATTGTGTGTGTGTGTGTGTGTGAGTGTGTGTGTCAAACGCCATTGAAAGGGGGATTTTTGTCTTTTCACTGGTGAGACTTTTAATAGTTTCTTTTTTTCCCTGCTATTCTCAGTGGAGAGGGGCTTCTAAGTTATCATTCCCCTTTACCACAGGTAGACATGATCATGTGTGGTTTTAACGTGGACCCTGATGTACACTAATCATTCACTAAGCACTGAGTGAAACCACTATAGTAAAGATCTGAGCCCCTTGTCCACTTCCTATTGTTGCCCGTGTGTCAGTTTTAACTTAGAGCTTTTACTCTCTCCTCTTCAG
Seq C2 exon
GTTCTGAACCTCTTTCTGGCCTTATTGTTGAGTTCCTTTAGTTCAGATAACCTTGCTGCTACTGACGATGATAACGAAATGAACAACCTCCAGATCGCGGTGGGAAGGATGCAAAAGGGAATTGATTTTGTGAAAAATAAGATACGGGAGTGCTTCCGAAAAGCGTTTTTCAGAAAGCCGAAAGTGATAGAAATCCAAGAAGGCAACAAAATAGACAGCTGCATGTCCAATAACACGGGCATCGAAATAAGCAAAGAGCTTAACTACCTTAAAGACGGTAATGGAACCACCAGCGGCGTGGGAACCGGAAGCAGTGTGGAAAAATACGTAATCGATGAAAATGACTACATGTCATTCATAAACAATCCCAGCCTCACCGTGACTGTGCCAATTGCTGTGGGAGAGTCTGACTTTGAAAATTTAAATACGGAAGAGTTCAGCAGTGAGTCAGAATTGGAAGAAAGTAAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005007:ENSRNOT00000006646:17
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=0.134
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(62.1=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(4.2=5.1),PF065128=Na_trans_assoc=PU(60.7=84.7)
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]