RnoINT0131712 @ rn6
Intron Retention
Gene
ENSRNOG00000005309 | Scn8a
Description
sodium voltage-gated channel alpha subunit 8 [Source:RGD Symbol;Acc:3638]
Coordinates
chr7:142611538-142613615:+
Coord C1 exon
chr7:142611538-142611744
Coord A exon
chr7:142611745-142613321
Coord C2 exon
chr7:142613322-142613615
Length
1577 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TGCTGTGGTCTCTTTCCTAGGCT
3' ss Score
9.7
Exon sequences
Seq C1 exon
ACCTTACGAGCCGCTGGGAAAACGTACATGATCTTCTTTGTCTTGGTCATCTTCGTGGGTTCTTTCTATCTGGTGAACTTGATCTTGGCTGTGGTGGCCATGGCTTATGAGGAACAGAACCAGGCAACACTGGAGGAGGCAGAGCAAAAAGAGGCCGAGTTCAAGGCAATGCTGGAGCAACTCAAGAAGCAGCAGGAGGAGGCACAG
Seq A exon
GTGAGGGAGCGGCAGTCCTGTGCACTGCGCACGCGCAAGCCGCCTTCTTCCGGGTCCTGGAGGCTAAGTCCCAACCATTGCCTGTGCAAGCGCTCTTTTCCTGACTTTCTTAGCTCAGCGCTAAGTGGTGACTGGAAGGGGGCAGTAGCAGTTTCTGGTGCAGCACGGTCTGATTTGTTTGTTGATTCAGTGTTGGAGACTGAACACAGGGCTTTGTTCATCTACGGCTGGACGGTACTCCACACCTACCTATTTTTTGATTAGAACATTGGGATATACTTGATAGGTTCACTACAGCCAGAGAATATTAAAACAAAATGCAGGGAACTGGGGAGAGAACATAGTCAGTAAAGCACTTGCCACAGAAGCATGAGGACCCGAGTTTATCCCTAGAACCCACACAAAAAGCCAGACATGGCAGCTCCCTGAAGTGGTGGGGATGAGTGGGTCCCAGGGGTCCCTGGCCTGCCAGCCTAGCATACTTGGTGAGTTCCAGGCTAGTGAGAGGCTCACCTCAAAAAAAACAAAAACAAAAAAACAACCAAGGTGGGTCAAATCCTGGGTTGACCTCTGGGTTCAAATATATACACTTGTCCATAAGAGCATACACGCACACATACATGTGCACACACACACACACACGTACACATATTCACACATACACGTACAAATGCACACACACACATATACTCACACATACACTTACATGCACATACATATACTCACACAAACAAACAAATAAACACATACATGCACACACACTCTCACATACACACAAGCACACATACATGCACACATGTGCACAAAACACACACAGAAATGCACATACAGATACACACAGACACACATATTCTCACAATACACACACACACACACACACACACACACACAAAGGAGGTGGGAGACACAGTGAGATGGCTCAGTGGGGGGAAAAAAGCTTGCCACAAAAGCCTGGTGACCCGAGTTTGATCCCCAGAATGCAAAAACTGGCTTCATGAAAGTTGTCCCTTTGATATCTGTACACACACACATATGCACCCCCCATGCATAGACATGCATAATAGTTTTGAAACACTTAAAATGAAGATATTGGCAAAAAATAAAATTTAGAAACAATTGTGATTCTATTACTGTTAATATTTAGCCTCCTACTCATATATATGCCTCATATATATGAGTTATCTGAGTCACGCACGCACGCGCGCACACACACGCACACACACACACACACACACACACACACACACACACACACACTGCAGTGTTTGCTGGGTAATGTGTAATATAGTTTCCAAGCATTCTTTTCCATCGTTGCTCACTAAGAAATCCTTTGGTAGGAAGCAGCCAGGCCCTCATCTGGGATACTCAGAGTAAATCCCCAGCATCCTCACCACGAGGTACGCTGGTCGTTTTGGTCTGAGCACCGGGATGCAACTTCACAGAGAGTGGGAACAGCCAGTGCTGACCTCAGGCTCCTCCAGTAGGGTGGGCTCCCCCATGTCCCTGTCTGTCAGTGACTGACTGTGTGGCCCCGGATTCTGCTTCTGACCGTGCCTTTGCTGTGGTCTCTTTCCTAG
Seq C2 exon
GCTGCTGCAATGGCCACCTCAGCGGGCACTGTCTCGGAAGACGCCATTGAAGAAGAAGGGGAAGATGGGGTAGGCTCTCCGAGGAGCTCATCTGAACTGTCTAAACTCAGTTCCAAGAGCGCGAAGGAGCGGCGGAACCGACGGAAGAAGAGGAAGCAGAAGGAGCTCTCTGAAGGCGAGGAGAAAGGGGACCCAGAGAAGGTGTTTAAGTCAGAGTCGGAAGACGGTATGAGAAGGAAGGCCTTCCGGCTGCCAGACAACAGGATAGGGAGGAAGTTTTCCATCATGAATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005309:ENSRNOT00000008160:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.072 A=NA C2=0.857
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(12.4=44.9),PF057587=Ycf1=FE(24.4=100),PF0043013=ATP-synt_B=PU(72.1=89.9)
A:
NA
C2:
PF057587=Ycf1=PD(30.8=87.8),PF0043013=ATP-synt_B=PD(25.6=22.4),PF119333=DUF3451=PU(35.1=68.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGCTGGGAAAACGTACATGA
R:
CTGCTTCCTCTTCTTCCGTCG
Band lengths:
356-1933
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]