RnoINT0131598 @ rn6
Intron Retention
Gene
ENSRNOG00000005007 | Scn3a
Description
sodium voltage-gated channel alpha subunit 3 [Source:RGD Symbol;Acc:3635]
Coordinates
chr3:51532627-51536817:-
Coord C1 exon
chr3:51536547-51536817
Coord A exon
chr3:51534377-51536546
Coord C2 exon
chr3:51532627-51534376
Length
2170 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGA
5' ss Score
9.14
3' ss Seq
GCTTCTATAATTTTCCGTAGGAA
3' ss Score
8.21
Exon sequences
Seq C1 exon
AACAAATTTCAAGGGATGGTCTTTGATTTTGTAACCAGACAAGTGTTTGACATCAGCATCATGATCCTCATCTGCCTCAACATGGTGACCATGATGGTGGAAACGGATGACCAGAGCAAATACATGACCCTGGTTTTGTCCCGAATCAACCTAGTGTTCATTGTCCTCTTCACTGGGGAGTTTCTGCTGAAGCTCATCTCCCTCAGATACTACTACTTCACGATAGGGTGGAACATCTTTGACTTTGTGGTGGTGATTCTCTCGATTGTAG
Seq A exon
GTAAGAACAGTTCAGTTACAGAGACATGTTCTTCAAGAGAGCCCATGGGAATGGCTTCTACTCAAGCCACAACATTCTGCTAGTGGTAAACAGAGCCAGGTTAGGGACAAGGTGTATGTTTTTAAAATACATCATGATGACACAGTGGTGTTAGTACTTTTCTTGGTCATGGTCTTACTGTTGTGAAGACCCTATGCTTATAAGAGAAAGAAAGCATTTAATTAGGGATTTGCTTACAGTTTTAGAGGGTTAGCTCATGATCATCATGGTGGGAAGAAGAGAGGCACAGCACTGGAACAGCAGCTGAGGGCTTTAAATCCTGATCCACAGGCAACAGGAAAGGGGTGCAATATTGGGCCTTGTATGGGCTTTTAGAAACCTCAAAGCCTTAGATAGGACTGGCAAAAACAGTCAATGAAATGATTCCTGATAATATTCTACTATACGTATAGACTGGAACCCTAGCACAATCATCATCAGAGAGTCTTTTTAAAAATAATTATTTATTTTTATTTTATGTACATTGTTTCTTTGCCTGCATGTCTGTCTGTATGTATGAGGGTGTCAGATCTTGGAATTAGAGACCATTGTTAACTGCCATGTGGGTGCTAGGAATTGAACTCTGGTCCTCTGGAAGAACAGTCAGTGCTCTTAGCTGCTGACCCACCTCTACCATTCCCATCAGAGACACTTTATCCAGCAACTGATAGGAGCAGATATAGAGACACGCAGTCACACATTGTGCAGAGCACTAGGGATCCTGTGGAAGAGGAGGAGGAAGGATTATAGAAGCCCAAGGGTTCAAGGACAGCACAAAAATACTATCCTCAGAATTAACTAACCAGGGCACATAGGGGCTCAAAGAGACTGGAACAACAATCAGGGAGCATGCATGAGTCTGAACTAGGTCCTACACACATATGTGATGGTTTTGTAGTATTCTTGTGGGACTCCTAACACTGTGACAGGGGGCTGTCTTTCACTCCTTTGCCTGCTTTGAGGATCTGTATCCTCCTACAGATCCTCATCCTGCCTTGACATGAGGGTATGCAGGTAGCTTTATTGTAACTTGTTGTGGAATGATAGGTTGATATCCCTGCTCTTTTCTGAAGGGAAACAGAGGAGTAGTTGAGTCTGGGGGACAGGGTAGGTAGGGGAAAGGAGCTGGGAGGAAGGGAAGCTGTGATTGACATGTAAGATGTGAGAGAAGAATAAATTATCTACTTTTTTTAAAAAAAAGAAACCTCAAAGCCTACTCTCAGCAACATACTAAATCTAAAAAAGCTATATCTACTCCAAAAGCCACACCCACTCCAACAAAGCCACACCCACTCAACAAAGCTACATGTCCAACAAAGCAACACTACTCCGACAAGGCCCTACCTCCTAACCCTCCCAAAACGGTTCCACTAACAGGAGACCAAGCATTCAAGCTTATGAGCCAATGAGAACCATTCTCATTCAAACAGTTCTATATATAACTCAGAGAGAGAGAGAGAGAGAGACAGAGAGACAGAGAGAGACAGAGAGAGAGACAGAGACAGAGAGAGAGAGAGACACAGAGAGAGAGAGACAGACAGACAGACACACACACAGACACAGACACAGACACAGACACAGAACAAGAAAGAGAAAAATCAAGAGGAGATAGCCAGCACTGCACAAAGCATTAAACAGTCTTTCATAACAAAGAGCAAAGGCATTTGACATGAGTCTTGTAAGAAGGATGGGGTTTTTAACAAGAGGAAAAGAAAAATGAGACTATTACAAAGCTCCAAATGTAGAAACTAGTTCAGATGTGGTCCACTTTCTCAAACTAAAGAACGTCACTCTCATTGAGAACAACGAATTAACTTATTTCAGAAATAATCTTTACTTTCATTGCCATATTTTATGTAGAGTGGTGAAGTATATAAGGGTAAACTTGAATTGTCACAGTAATATTTTAGATTACTTTGGATTTTACAAAAAAAATCACATTCCTTTATAAAACCATGTCATAGAATCATTTTATTAAAACTCTTAAACATTTAAATCTCAATATTAGAGTAGATTCAAATGTGAGGCTCAGTTTTTTGTTATTTTATTTTTTAAAAGGAGGAATAGACATACGGCACTCCTATAACATCGATATACTCACTGTCCATCTGGCTTCTATAATTTTCCGTAG
Seq C2 exon
GAATGTTTCTCGCGGAGCTGATAGAGAAGTATTTCGTGTCCCCTACCCTGTTCCGAGTCATCCGCCTGGCCAGGATTGGACGAATCCTACGCCTGATCAAAGGCGCCAAGGGGATCCGCACTCTGCTCTTTGCTTTGATGATGTCCCTTCCTGCGCTGTTCAACATCGGCCTCCTGCTTTTCCTGGTCATGTTCATCTACGCCATCTTTGGGATGTCCAACTTTGCCTACGTTAAAAAAGAGGCTGGAATTGATGACATGTTCAACTTTGAGACTTTTGGCAACAGCATGATCTGCTTGTTCCAAATCACCACCTCTGCCGGCTGGGACGGACTGCTGGCCCCCATCCTCAACAGCGCACCTCCCGACTGTGACCCCGATGCAATTCACCCTGGAAGCTCGGTGAAGGGGGACTGTGGGAACCCATCCGTGGGGATTTTCTTTTTTGTCAGCTACATCATCATATCCTTCCTGGTGGTGGTGAACATGTACATCGCTGTCATCCTGGAGAACTTCAGCGTCGCCACCGAAGAAAGTGCAGAGCCCCTGAGTGAGGACGACTTTGAGATGTTCTACGAGGTCTGGGAGAAGTTCGACCCTGACGCCACTCAGTTCATAGAGTTCTGCAAGCTCTCTGACTTTGCAGCTGCCCTGGATCCTCCCCTCCTCATCGCAAAGCCAAACAAAGTCCAGCTCATTGCCATGGACCTGCCCATGGTGAGTGGAGACCGCATCCACTGCCTGGACATCTTGTTTGCTTTTACAAAGCGGGTCCTGGGCGAGAGTGGAGAGATGGACGCTCTTCGAATCCAGATGGAAGAAAGGTTCATGGCTTCCAACCCCTCCAAGGTCTCTTATGAGCCCATTACCACCACCCTGAAACGGAAACAAGAGGAGGTGTCTGCTGCTATCATTCAGCGTAATTATAGATGTTATCTTTTAAAGCAACGGTTAAAAAACATATCGAGTAAATACGACAAAGAGACAATCAAGGGAAGGATTGACTTGCCTATAAAAGGAGATATGGTTATTGACAAATTGAATGGGAATTCCACCCCAGAAAAGACGGATGGGAGTTCCTCCACAACCTCTCCTCCTTCCTATGACAGTGTAACAAAACCAGATAAGGAAAAGTTTGAGAAAGACAAACCAGAAAAAGAAATCAAAGGGAAAGAGGTCCGAGAGAATCAAAAGTAAAAAGAGACAAAGAAATGTCTTTGTAATCAATTGTTTACAGCCTCTGAAGGTAAAGTATCCGTGTCAACTGGACTCTAAGGAGAGGTCCATGCCAAACTGACTGTTTCAACAAATACTCAAGGTCAGTGCCTATACCAGACAGTGACCTCTGTCACTGCCACTCTGTGAGACAGGGTATCAACATTGACAAGAGGTTGCTGCTTCCATTACCAGCTGACACTGCTGAGGAGAACTCCATTGTGCAAGTGACCCGTCATCACGCCCCCAAACTCCATTAGTACAACGCTCCTGTCATCTATTTTTAACATTCACATTTGCCATATTTTTACAAAATCTGTCCCAGTGTATCTTCCTGGTCCCCACTTCATAGTCTGTTCATAATACTATGTCACTATTTTTGTAAATGAAGTTTACGTTAAGGGAAAATATATATATAAGAATCCCATGTTGCTAAGTCCACAAGTTTCTCCAGTAATCATAAAAAAATATTTTGCCTGAGAGATGAAATTATTGCTCAAAACAAAAAAAAAATAAATTCTAATGTTAACAGTTTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005007:ENSRNOT00000006646:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.146
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.4=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.1=41.9)
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]