RnoINT0131697 @ rn6
Intron Retention
Gene
ENSRNOG00000005309 | Scn8a
Description
sodium voltage-gated channel alpha subunit 8 [Source:RGD Symbol;Acc:3638]
Coordinates
chr7:142659170-142661530:+
Coord C1 exon
chr7:142659170-142659324
Coord A exon
chr7:142659325-142661356
Coord C2 exon
chr7:142661357-142661530
Length
2032 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGA
5' ss Score
7.54
3' ss Seq
AGCCGCTGCATCTCTTGCAGGCC
3' ss Score
8.25
Exon sequences
Seq C1 exon
GTTGCGTCCAGCGGTTCAAGTGCTGCCAGGTCAACATCGAGGAAGGACTAGGCAAGTCGTGGTGGATCTTGCGGAAAACCTGCTTCCTCATTGTGGAGCACAATTGGTTTGAGACCTTCATCATCTTCATGATTCTGCTCAGCAGTGGCGCCCTG
Seq A exon
GTGAGAGTCAAGGGAGAATGACTAGCAGCTGGTGGGGGAAGGGTACAAAGAAACAGGGAACCGAGGCTGGGTGAGGTTACCAGTCTTTGAAGGGGTAGAGAGCTCCCAAGAACAGGAATTTGTTCAAGAGATTTGAGCTGGCCAGGATATATATAGTGCTCTTGAGTCTAGAATCCACCCTTCTTCACATCTGACCTTAAGATAACCCCCACCCCCGAACCTGCAGTGCTCTTTGCATGGGATTGAAGACAAACCTGCCACTGCCAGCTTTGCCCTACCCCAGACAGCCTCCTGAGATGGGCCAGTATCCCTCTCCACATCCAGACTGCTCACTCTTCATTTCTCCCCTAGAACTGCTCTCACTGACACACCTACAGGTGTGCCTTTCTACTCTCCCAACCACAGGTAACCATCATGCTCCCTCCAAGCACCACAACTACATAGTCCACCATCATGCAATAGGAGGGACTACCTCCTTCATGAGTTCCCTAGAGAGAGAAGACTCTCCCAACCCAGGCCGCCCCCTGCCCCATATCTGTGGCATAGAGGAGCTAACAGAAAGGATCTTGTCAAATCTGATAAACAATGGGCAAGGGTGTGAGCATCTGGAACTCTCACACCCTCCTGATGTCCTGCATGTGAAGTCCTGTGGCCATGTTGGTAAACAGTTCCTAGTTCCTCCCAATGTTAAGGACTTAGCAGCAAGTTCTGTTCCTAATCACACACCCTAAAGGATTGAAAACACATTGCCAATCAAACACAAACACTCATAGCAGAGTTATTCATACTAGCTTAAAAGTAGAAACAGCCCGTGTCCATCAAGTAATGATCGTTAAACAGACCACAGTGTTTCCATACCTTGGAGTCGTGTTCCTCCTTGAAGAGTGAATCATCCACACACGCTGAACTATGAGATAGATTGAGAACTTTGAGAAGCCAGGCTTTGGGGTCAGGAGGTGGCTCGGCCATTAAGAATGCAAGCTATTCTTCCTGAGGACCTGAGTTCGGTTCCTAGCACCCATATCAGGTAGTTCACAACTGCCTGTAACTCAGGTACAGGCAATACAACATAGCCTTCATGGGCACCTGCACTCCTGCACACATACCCTTACACAAACACACATGCAGACACATGATTGGAAAGAAAATAATTTTTTTATAAAAATAAGAAGCCCTGGGGCTGGGGATTTAGCTCAGTGGTAGAGCGCTTACCTAGGAAGTGCAAGGCCCTGGGTTCGGTCCCCAGCTCCGAAAAAAAGAACCAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGCCCTGAGGCTGGAGAGATGGCTCAGCGGTTAAGAGCATTAACTGCTCTTCCAGAGGTGCTGAGTTCAAATCCTAGCAACCACATGGTGGCTCACAACCATGCATAATGAGATCCAATGCCCTCTTCTGGTGTGTCTGAAGACAGCTACAGTGTACATACATACATACATACATACATACATACATACATACATACATCTTTAAAAAATAAGAAGCAGCCAGGCACACACAAAAAAAGTATTGGATCGGGGGTTGGGGATTTAGCTCAGTGGTAGAGCGCTTGCCTAGGAAGCACCAAGGCCCTGGGTTCGGTCCCCAGCTCCGAAAAAAAGAACCAAAAAAAAAAGTATTGGATCGTTTTACTTGTATGAAATGCCCCCAAAAAGGCAGATTAGTATACTGAGGACCAACAGAATGAGGGGTCCAGAAGGTAACAGCTGGAAGATGTGGGATAATGAAAATGTTATAAATGTATATGATGAATATGTAATATCCTAAAAGCCACTGAATTTAAATATGGGATATAAATTATTTCTCAATAAAATACTTTCCTGGACTTAGTGGTTAGCCTGCATATACCCGGCCCTGGGTTCAGTCCCCTGCATCACTAACCAATAAGCAAGGAGGGGAAGCGGGGGATCAGAGTGGAGGAGTGGGAACCTGATGGCGGACAGCTTGTGTGAGGAGCTGCGACGCTGGCACACTGCCCTGATTCGGCAGCCGCTGCATCTCTTGCAG
Seq C2 exon
GCCTTTGAGGACATCTACATTGAGCAGAGGAAGACCATCCGCACCATCCTGGAGTATGCGGACAAGGTCTTCACCTACATCTTCATCCTGGAGATGTTGCTCAAGTGGACAGCCTACGGCTTCGTCAAGTTCTTCACCAATGCCTGGTGCTGGTTGGACTTCCTCATTGTGGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005309:ENSRNOT00000008160:19
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:
PF065128=Na_trans_assoc=PD(20.2=84.6)
A:
NA
C2:
PF0052026=Ion_trans=PU(17.0=67.2)
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]