RnoINT0131554 @ rn6
Intron Retention
Gene
ENSRNOG00000005018 | Scn2a
Description
sodium voltage-gated channel alpha subunit 2 [Source:RGD Symbol;Acc:3632]
Coordinates
chr3:51771126-51776337:+
Coord C1 exon
chr3:51771126-51771473
Coord A exon
chr3:51771474-51776207
Coord C2 exon
chr3:51776208-51776337
Length
4734 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
CTGGAACCCTGGTATTGCAGGGC
3' ss Score
2.73
Exon sequences
Seq C1 exon
TCTCTCTTGAGCATCCGAGGCTCCCTATTTTCTCCAAGACGCAACAGTAGAGCAAGCCTTTTCAGCTTCAAAGGTCGAGTGAAGGATATTGGTTCCGAAAATGACTTTGCAGACGATGAACACAGCACATTTGAGGACAACGACAGCAGAAGAGACTCTCTATTTGTACCACACAGACATGGAGAAAGGCGTCCTAGCAATGTCAGCCAGGCCAGCCGTGCCTCCCGGGGGATACCCACTCTACCCATGAATGGGAAGATGCACAGTGCAGTGGACTGCAACGGTGTGGTGTCCCTGGTTGGAGGCCCCTCTGCGCTCACATCGCCTGTGGGGCAGCTGCTGCCGGAG
Seq A exon
GTGAGGACCAGTAAAACTACAGCTGAGAGCACAGAAAGAGAAGGGACATGGGCACAATCAGTAACATGGGTTTTGAATTCCACAGATGATAATTTTTCTGCATCTATTATTCCGAGGCTAAGAGGTGGCTGATTTTATCAAGCTATGAACTTAACTTATTAAAAATCTCTCAACACATCTCTACAAATTAATATTATGCAATGAGTTTCATAGATGCATTTGTCCATTATTATTCCTATAGTTCGGAGTTTAATATAAAAATCAAACCACATTTTTGTTGTGCAAACACGCAACTATTATTATCATTGTTGTTGCTGTTATTATTATTATTATTATTATTATTATTATTATATTTTTTGAAACAAGGTTTCTCTGTGTAGCCCTGGCTATACTGAAACTCTCTTTTATAGACCAGGCTAGCCTTAAACTCAGAGATTCACCTGCCTCTACCTCCCAAGTGCTGGGAATAAAGGCCTGTGCCACTACACCAAGCAATATAATTAAATACTAAGAACTTAAAGAATATAAACATGAGCGTGATCACACACACACACACACACACACACACACACACACACACACACGCGCGCGCGCGCGCGCATGCATTTCAAAGGTTTTGCTATCCTGTTCCTTTAAAACAACTTCACACCTCCACTTGGTGTCATGCTACCACTAATTCTATCTAAATCCCTTACTTAGCAATTCTTCACATTTTTCATACTGTGCCCTTCCCCTAGTACCAACTCAAATGACCCAGCCACCCTGTGTCAGTAAAGAGGCTGCTTGAATAGCATAGGCTACAGTCAGATGTTAGACTTTTTCTAATGGATTTCAACTTCCTTATTATTGCCATGAATTCTTCTTATATGCAAAGTCACCCTAAATCAAGCATTCAGAAAAGATTTTCAACTTAATAATGTGTATCAGGATGTATCACCAATGGCCCCTTTATAAAGCAAGGCATTCTTCAAGTTGGCATTAAATGAAACGTTACTTGACCTTTATAAAATACTTCAGCCATGTTGTCTGATTACATCATAGTTTCCCTGGCTGGGTTAAAATCTCCCTTGTATAATTACTTTTATATCATTTCAATTTTTAAGTGGCCACACCCCTTAGGGCCATTTATAATGGTCCAGATAGTTTGCAATCAACATCTTGCCCTGGAATATGGTAACAGTGGCTGCTTGTCACTGATTTCCCATGGCATATTCTCAGCCTTTCCTCCCAGGGAAGTTTCCAAGTATCCTGGAAAAATAGCAAGCCGCAGAAGCAATAGAACTTTGTTGTGAAGCAGATGAGAAAAATGATAAGGAAATGTCACGTCTTCTTAGAGAAATAATTTTAGCCAGTTATGTACAACACATTGCCCAGAACACTGTGGGGTTACTTCATTGAACCTTTACAACTACCCGTTATACTAATTATTAATTTATGCCCATTTTACAGAGGGGCAATTGAGGTCTGTACATTCTGGAACTAAGATTTGACCCCACATATGTTGTCTACAAGCCCTGCCACCTTCCATTCCTAGTGAAATATATTTTACTGAATTTTCTTAAATGATAAGATCAGATGAGGAAGAAAGAAAATACTTTCCTTTAAACCAGTGTTTCTTTTTCTTTTTCTTTTTTTCTTTTTGTTGGAGACAGGGTTTCTCTGTGTGTCCTGGAACTCACTATGTAGACCAGGCTGGCCTGGAACTCACCAAGATCTGCCTGCCTTAGCCTCCAGAGCACTGGAAGCAAAGTCATGAACCATCACTGTCTGGCTAAACCTTTTTCTTTCTTTCTGTCTGTCTTTCTGCCTCTTTCCTTCCTTCCTTCTTTCTTTCTTTCTTTCTCTTTTTCTTTCTTTCTTTCTTTCTTTCGTTCTCAAAATCTAAACACAGTTTAATTAAAATACCAGAGACATATAAAACAAACCAATCAAATGCCTTGGAACGACCTTAACCAAGTGTCTTAGGGTTTTACTACTGTGAACAGACACCGTGACCAAGGCAACTCTCATAAGGACAACATTTAATTGAGCCTGGCTTACAGTTTCAGAGGTTCAGTCCATTATCATCATGGTGGAAACATGGTTGGAAAGCATCCAGGCAGGCATGGTGAAGGAGGTGCAAGAGTTTTACATCTTCTTTTGAAGGCTGCCAGCAGAATACTGGCTTCTAGGCAGTTGGAATGAGAGTCTTATGACCCACACCCACAGTGCACACCTACACCAATGGGACCATTCCTTCTAATCTTGCTACTCCCTGGGCTGAGCATAGACAAACCATCACACCTAGGATATGAATGAGTGCTTTGATGAAATGGAAACACTGACAAAGGAAGGAGATACCAGAAGCAGAGAGTTCCCATGCGTGCAATGCATGTGCCGTTTCACCAAGCTACTTCAATCCCGGTTCTAATTGATTCCTGTAATACCTTAATGTTACTGTTTTAATGAGTAGACAAAGAAAAACCAGTGTTCCTTAAGCTATGCTTCAAATTCTCTCAGGTGATTCTCAGAAATGGTAAATTCAAATTTTCTGGCTGAATCCAGAACTACTCAGAAGGAAGCTTGCAGAGGGGCCTGGAAATCGTTTTCTTACAAAACAGTTCACATGGTTCTTGAATACAGAAGTAGGCCCACCACAGATATTGTTACCCTTGGGATAAATCCCCCAATTTCATTGCACAAATATAACTGCAAATCCATATATCAGAACTGCCACATTATTAATCAGGAGTCACCATACATTTACCCTATCAGAAAAGGTAGAACAAATCACAAAGTTTGATTGAACATAGTTTGACTCCAAGCCTATTGTAACCAGGTAAGCTGTGGACTCCCACACCTGCATCCCTTCAGCCATGAAGTCAATGCTTTAGGGCAGGACTCTGTCCTGTGGAAGAAGCTGAAGGAACACACAGTTGGCAATGGGAATGTGTGAACCGAAAACAGGCCACAACAAGTAAATGGCATGTACCAAACAAGGCACACTATTTCCTGTTCTTTAAACATAAATTCCATTGAGACAATTAAACTTCAGAAGAATATTATTAGAGATTTTTGGAATCTATCATTAAAATTTCCATAGATCTGGAGTTTTTAATGTGGTTTTGCCTATCGCGAAGAGATTGGATGATATTTACGTGGCCTCTGCTTTTTTTTTTCTTAAAAGACTCATCTTTCAGGAGGTAAATATTTACTTTCCATGAGCCCATCTTTACATCTTGAATAGTTTTATTTTCAGTAATGGATTCTCTCTTTCCTCCTTGCTTCAACTATTCCTTCACCTGGCAGTTACAATGAGCTGAGAGCATGGACCTTTATACCCACTCGTGGTAACATCAGTTGAGTAGAAATCAGTTTGAAATTCACCATCATGCAAATGAGTGAACAGGACAGAAATGGTCGGTGCTCACATCCCTGTGATGTCCAGACCCCTAAGCAACACTTACGTTGCTATTTAGACTACAGCAGCAGCACTGGCAGACCAGAGAGTGGCTTCCTTCTCACTGACTCACTTTGAAACGCTTAAGATTCTTTTCCTTTGTCCTGTGACTGCTAACTCCTTGTCTGATGTCTTGGAGTAGGAACATGTTTCTACCTAGCTCCAAACCTGGGGAGTTTTTTAGAGCAAGGAAGAACTGAGCCATTGCGTGATTGCTAACATTCAAACACTCCAATTGACGTGTCCTAAGAGTTGTGATGTTTTAGGTAGCTCAGCTGTGAATAGAGCTGTTTCATAAGTATAAGGTAAAAGGATAGGTTAGCTAGATTTTTTTTAAAAAATATGAATATTGGGAAATGATATCTGTCTCCAAAAGAAGAAATATTTTACATACAGAGTTTATATTTTAGGGAACTATTAAGGTATAAGATGACATGATAAGACTAAGATTTGTTTTTTTCTTAAATATGGATATGGGAAATTATATCTGTCTCCACAGAAAATAAGAAAATATTTTACATTCAGTGTTCACATTTTAAGGAAACTGTTACAGACACATTGGATAAGGAAGTCTTTTCACACCTGTCTGTAAAGTACATCAGGAATAATGTATTTCAGCTTGAAGCTTGAGGTTGAAATGGGTGAGATGCTCCACATTTATACAGTTGATATCAATGTTGGTCCTTCCAAGCCAAATCTGTAGCACAGAGAAAGCTGGCACAGAAGCACAGAAGACTGAGGGGCTGATGGACTTCCCAAAAACAGTCCTAATATGGTAATTGTAGGGATATCACATGGAGCCATTGTGGTCTGGATATGGACGGTATGCCATGGGTCCATATGTCTCAATCATTGGTGCCTAGCTGATGGCCCTATCTGGGAAGGTTGTGGGTACAGAAAAGAGGAAAAGGGTGCTGGGTCGCTGAGAGTGGGATTTGAGGCTTTATAGCCAGGTCTCACTTTCTGTTCACTGCCTGCTTCATGGGTGCAGATGCCAGATGAGTGTGAAAAGCCAGTCCCCTCCTCTTGCCGCTATGCTTACCCTTTGTGCGGCCATATTTTCCTCTTCCATGTAGGCCGTACCAGCTTGAAACCTGTATGTGTCAAAAAAGAATTTCTCTCTTATGCTGCTTTTGTTTGGTATTTTACCACTGCAATAAGAAAGTAAGACACTCCTTACATCTGAGGGAGCATGTAGAACTCTTGGTTAAGTGGTGTCTACAGCTGGGGTGCTTTGAGGTTGCTTATGGCCAAAAGTGATGATTAGTTTGCTTTCTGGAACCCTGGTATTGCAG
Seq C2 exon
GGCACAACTACTGAGACAGAAATAAGGAAGAGGAGATCCAGTTCTTACCACGTCTCTATGGACTTGTTGGAAGACCCTTCAAGGCAAAGGGCAATGAGTATGGCCAGTATTTTGACGAACACTATGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005018:ENSRNOT00000007069:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.578 A=NA C2=0.449
Domain overlap (PFAM):
C1:
PF119333=DUF3451=FE(51.6=100)
A:
NA
C2:
PF119333=DUF3451=PD(16.1=81.8)
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]