RnoINT0131558 @ rn6
Intron Retention
Gene
ENSRNOG00000005018 | Scn2a
Description
sodium voltage-gated channel alpha subunit 2 [Source:RGD Symbol;Acc:3632]
Coordinates
chr3:51784658-51790295:+
Coord C1 exon
chr3:51784658-51785014
Coord A exon
chr3:51785015-51789815
Coord C2 exon
chr3:51789816-51790295
Length
4801 bp
Sequences
Splice sites
5' ss Seq
GTTGTAAGT
5' ss Score
8.3
3' ss Seq
CTTCCTCCACTGCTTTGTAGGTC
3' ss Score
8.85
Exon sequences
Seq C1 exon
CTTAGAGTCTTCAAGTTGGCAAAGTCCTGGCCCACACTGAACATGCTCATTAAGATCATCGGCAACTCGGTGGGTGCACTGGGCAACCTGACCCTGGTGCTGGCCATCATCGTCTTCATTTTTGCTGTGGTCGGCATGCAGCTGTTTGGAAAGAGCTACAAGGAGTGTGTCTGTAAGATTTCCAATGATTGTGAGCTCCCGCGCTGGCACATGCACGACTTCTTCCACTCCTTCCTGATCGTGTTTCGAGTGCTGTGTGGGGAGTGGATAGAGACCATGTGGGACTGCATGGAGGTCGCGGGCCAGACCATGTGCCTTACTGTCTTCATGATGGTCATGGTGATTGGGAACCTTGTT
Seq A exon
GTAAGTAATAAAAACACTTTTCTGCTTTTCTGTCCCAGATGATGTTGTTTTAACAATGTTTGACTAAAGAGCATTCTATGTTCTAGGGAGAATTATGTTGTATATTTCTGGTTGTCTATTACCCAAGATTTCAAAAGCCACAGGTGATTTAGACTTCTGTAATATGTACACCCTCCAAATATCTCTTGAGCCAAAGTTGTTCTAAATAATGTGTATATCTATCAAAATATTACAGTGCTACTATACAAATGCATGTCAACATTATATGTCAATCAAAATGAAAATAAAACAGAAAAAAGTTCAATGTTAGACATGACATGGGAGGATTCATTGACACAGATTAAAAAATTATAATAGACAAAGACATTCTATTAATAAATCCAAAAAATAACTGTGGCACTGTAATTTGGTTTTCTTACAGATGAAAATTTAAGCAGTATTTAAATCTATTTTTTTATTTTATCTATTTACCATCCAAGAAAGAGATTCAAGGATGAGTCAGAGTAATAAAAGTGTATTAGTAAGTTTCTGAAGTACAAGGACAGAGAGCTCTTAGTGTGGCTGCCAGGAGCTACTGCAGGGTGATTGACCGAAGGTCAAAAGAGTCCTGGCTTCACCTTTCTTCTCGCTGACTCTTACCTGACACATCACTGTCAATTGCACTGAAATTTTAGCTAAAATCTACTGCAAGGTTCCACTTTTGAACTAATAACCTTTGCGTTTGGTCCCGTCTGTATTTTATTTGAATAATCGAGGGCTGTGTCAATCAAACCCCGATTTAAAAAAATGATGACAGATGTGTCCTCAACATTGCCTAATTCTTTTTTTTCTTTGACCCAATTGGTAAGGTATAATTGCCCACCTAAACATACAAAGCCCAGTACCATCCATCCCTTAAGAACATTTATAACAACCTGTAAAGGTACAGCATGGAATCTTAACATCACCCGCCATATTGTCCTGCCACGGCTTCTCTCTCCCTCTCCTCTCCTTCTTTCCATTCCAGTCTCCTCCCCTTCCTTCAAACTTCTCTCCTGCCCATCCTTCCTTCTCCTCCAATGACAGGCCTCCTTCTATCCTGTACCTGCCCCCCACCTGTATTTTAAAAATTCAATGGGGAGAAGGTTCTGGTGAAGTCACCTGATTCCTGAGTAGCGACTAGGCAGCTGTCCTTGGGGCAGTGGAATTAGCATTAAAGTACAGATAACTCCAGGGCAAACCACAACATTTCCCCCTTTTTGTCCAGCTAAAAAGGCTTTTTTACTTATATGTAAATTGAGTACAATTATTACCATTCTACAATTTATAAAGCATATGATATACTCAATACCCAGTCCATCACTATATCAATTAAACAGAACATTTAGTTACCCATTCCAGCTTAAGAAAGGCTTAAAATCTATATTATATCTTGGCTAGCTTGTATACTATCTGATAACTATCCGATAAAATATGTATATTCAGAGTTAAACAGCCTGACAGGCTATGAGACTATAATCAGTCTTCAACCCCGTCCGAAATCTGAGAATGACCTAATATCTATACACATAGGAAGCCTAACATGGCTTCTAGAAGTGAGAGGTTGTAGAGACAAACTTCCACTAGCACTGTTAGCAACATGTGAGTCTTCAGCCTTCTGGCTCAAAATCAACTGACAGACTCTTGAAATGCAGATTTTGAAGTCTTGGCAGAGTTTATCAGTCAACTATTCTGCATAATTTGTCCTTTTCAGGATAGTATTAGTCTGCAGATGAAACAGGCAGTTTTGTCTAGTGGCTGCCTAGCCACAAAGTATTGCCTCATCTGGACGTAGATGTTCAAATTCTTTGTTAAAACTGCCAAAGAGGAACTGTTAGGAGCAGATATGTCTCAACAAAAGATAAATAACTTTAAATCTCAAATTTTGTGGACTTCTGATGTTTTTGAAAACCATCTACCTGTATAAGACAATCTGTACTGTTGTTGTCTTTATATCTTAATAATATCTTGAAAGTACTCTCACAAAGTCAGCAATATATTTACTATTTGGCCCTTAACTCACATGTGTAATCAACTCAGAAATTTGTAATGACATCAATAGAAGGACTGGCTCTAAACCTTGTACTTTTAACAAATAAATTCTATATCAAAGCAAAGATATGATTTTAGCTTAGTTAACAAATGAGATTATGACTGTATAACAATCTAGCTAATTCCTCCCTGCTAAATTTCTAAATTCCTCATAAAAACAACTTTAGAATAACCACTTTCAGCCCCCCAAAGTCCAGGGAATTGGGGCGATGACTCCTCTATAACTTCTTCAAGCTGTACATGGGTGTTGAGATATCCTTGGGGCTAGGGGATAGGAAGAATGAAGCAAATGCTTTAGCCGATGTGTCCTGACTGGACCCAGCTGAAAGTCCTTGAGACCAGGAATCCAAGTAGGCACACTCTGTAAAATACAACTCTCAAGACAAAAGTTTAGAATTGAGAAATCTTTTTGTTTGATTCTCCTGAATAAATTTTTCAGGCAGTCTACCTCTATCAAATCTGATCAGAATGACTCTGTGAGGTTTCCAGAGCCTAATCACACTTTTTGAAAACACAAAGACAAAATCTTTCTCCCAAAATACTTTGTTCCTTAGTCTGTAACCAGAAAAGCTTGTATCTTGCACTCTCTCCCAGAGTAATAATATAACCATAAAACTCAAAGTCACACCCATTATGAAGATTAAACAATTTTTTAAAAAGAAGTAAGTAAACAATGAGCCTGGTAGGCTTTTGTACTCTGTGATATCAGGAAATTAACCCAAATTTCCTGTGGAGCCCATGTTAAGAGAATCTGAGCTTCCTGTTGTGGTAGATATAAAAAATAACCACAAACCCTCACTAGCTGGCATCAACGAGCCATATGGCCTTTAGCGGGATAATTCATAAAACAAACCAAATACCTTCTATCAATTCCAGTATCAATAAGCAACATATCAAACCAGGATTTTAGTCCAAAATATATCCATCTGTTAAGCTCTCTACCCCGAGCCACATATTTTTAGTTAACCTTATAACTTATAACTTCTATAATATATGTCTGCATTCACTCTCCCTAGTGTTACAGACATTTATCACAACTCTCTACTTGGAGTTAGTGACCAATTTTTCCCTATCTAAGTTCCGAACCATAGATGAAAATCCCCACGTAATTCGGGTAATCTCTTTACTCTCCTTAAAACAAACTTAAACACCTTCTATCAATTCTAAAACCAATAAGCAACTTAAAACTCAGGACTTTAGCTCAAAATATATCCATCTGTTAAGCTCTCTACCCGGAGCCACAGATTTTTCTTTAACCTTAATAACTTCTATAATACATGTCTGCATTCACTCTGCCTGGTGTTACAGACATTTATCACAACTCTCTACTTGGAGGTAGTGACTATTCCCTATCTAAGTTCTGAACCGTGGATGAAAATCCCCACCTGACTCAGGTAATCTCTTTACTCTCTTCTTTCTAAAAACAAACTTAATCACCTTCTAATAATACCTGTAATTAAGAAGTAGCTTGTCTAACTAGGATTTCAACCCAAAATTCCATGTTAAAAAGAATATGAGTATCCCGAAAGACTTTCTAGACAGCTTTCTTTAAAAAGCAGCTTTTAATCTCTAACTCTCTGAGCTGCCATTATTTATCACACAGCCTGGGACCAACAGCCAGCCAGCCCAGGCTACTTCCCTGTTTCTTTGTTAAATTCCCACGCTTGAGATATCACATGACTTAACATGGCGCTGGCCTCCTCTTACTTAGAAAATAAAAACTTTCTCTCACCTCTTAGGATTACTAGTGGATTCTTGCCCATCATGTTAGTTCGACACCTGTTGTTGTAAAAATATAAAAAATAAAAAAAAAGTATTGTCGTCTTTTACCTCGCTAGGTCCAGCACCTCCGCAGCCCAGCGTCTCCAGCCACCACACACTTTGCTACACTCAAATCGTCACATAAAAGGACACACAACACAATAATCTTTGACCCAATTGGTAAGATATAATTGCCCACCTAAACATACAAAGCCCGGTACCATCCATCCCTTAAGAACATTTGTAACAACCTGTAAAGGTACAGTGTGGAATCTTAACGTCACCTGCCATATTGTCCTGCCACGGCTTCGCTCTCTGCCTAATTCTTAAGTAACCTGCCTGGTCTGTGGGCTTAGCAGTTCCTGGTGATACAACAAACATCATTTTTAATTCGACATCACAGTGGTGTTATTAAACAACAACCACTTCTTTGTTGTATTTATAAGTCTTGCATGAACTAATAGCATCTAAAAGGTTTTTTAAAATCAGAGTTAAGAGTGTTGATCTAGCAATACGTATATTTTTTATTGCATTTAGCAAGTTACCGAGGTGAAAGAGGTTGAAATGCTGCAGAGGCCAAATCACATCTAAATATGTAGTTCTATGAATAAAATTACAAGAAATATTCAGTGTCCTACAAAATACAGATTATATGTTCAAACTTACGAGTATCCAAAATAGCTGGTTTCTTTTACTGTGGAGTGGTCTAGATTTGCCAGGACGTATAGTTAGTCTGGAAGTTTCATACCATGGTAGCTCAGGGATTTTAAGATGAGCCTGAAATGAAGAGTGTGAGTAGTGCTCGCTATCGGGGTGGGCGGGGGGGGGGAATTCGTTTGTTTTTACTTTTCTCTGCTGTGCTCCGGGAGACCTTGTCTTCAATGGGATGCGTGAAAACAGTTCCACTTCTCGTGGCTAGAACAGGGGAAACAACAGGCTGACTGATTGTTCTTCCTCCACTGCTTTGTAG
Seq C2 exon
GTCCTGAACCTCTTCTTGGCCTTGCTCCTCAGTTCTTTCAGCTCAGACAACCTGGCTGCCACAGATGACGATAACGAAATGAACAACCTCCAGATAGCCGTGGGAAGGATGCAGAAGGGAATTGATTTTGTTAAAAGGAAGATACGTGAATTCATTCAGAAAGCCTTTGTCAGAAAGCAGAAAGCTTTAGATGAAATCAAACCGCTGGAAGATCTGAATAACAAGAAAGACAGTTGTATCTCCAACCACACGACCATAGAAATAGGCAAGGACCTCAATTACCTCAAAGATGGAAACGGGACGACCAGTGGCATAGGCAGCAGTGTGGAGAAGTATGTGGTAGATGAGAGTGATTACATGTCGTTCATAAACAACCCCAGCCTCACCGTGACTGTGCCCATCGCCCTTGGAGAGTCTGACTTTGAAAACTTAAACACGGAAGAATTCAGTAGTGAGTCAGATATGGAAGAAAGCAAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005018:ENSRNOT00000007069:15
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=0.115
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(62.1=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(4.2=5.0),PF065128=Na_trans_assoc=PU(61.3=85.0)
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]