RnoINT0131735 @ rn6
Intron Retention
Gene
ENSRNOG00000006639 | Scn9a
Description
sodium voltage-gated channel alpha subunit 9 [Source:RGD Symbol;Acc:69368]
Coordinates
chr3:52644306-52645636:-
Coord C1 exon
chr3:52645573-52645636
Coord A exon
chr3:52644448-52645572
Coord C2 exon
chr3:52644306-52644447
Length
1125 bp
Sequences
Splice sites
5' ss Seq
AGGGTATGT
5' ss Score
8.34
3' ss Seq
AGTTTCTTGTTCATCTGTAGGCA
3' ss Score
8.48
Exon sequences
Seq C1 exon
AATATTTTTATTACTTGGAGGGATCCAAAGATGCTCTACTCTGCGGCTTCAGCACAGATTCAGG
Seq A exon
GTATGTAATATTTGCTTTCAGTTTAAGTTTGTTACAAAAGAAAAAAATTATGCTGAAGAGCAAATCTACATGAATTTTCACAACTTTCATAGCATTGACTTTGTTCATTTTATCTAACAATGAGAACACAGACTTTAAAATGTTAATAGTTGATGCGTATTCTGGAAAGCAAGACTGACCGTGAGCTAAGGCTTCAATCAAAACAAAATACCAGTCACGGGAATCTTGAGATATAAAAAAAAAGTATTCATGAAAGCTCGTTCAAAGTTAGTTAGCTAGTTTAAGGGTTTTCTTCTTGGAAAGGAGAGTAACAAAATATCGATCTCTTTCCATCTCCAAGTTCTCCATTGCTTAAGACAGTATGGTAACCGAGTGTACTGCTCTGAGCTCTCGGCACAGGATCCAGTAGATAGGGCAAAGGTATTTTGAGACCCTCTTGTTTATGCAAATGCCATGCTGCTATTCCTCCAAACACCACCTTCAGTTTCCAGGGGAGCTTTGCTCCTGCTCTCCCTCCCATCAAAAAATCTCTTCATCAGGCTCTGAGAACTCTACCAACTTCCGAATCAACAGTGTTGCCCCTCCCCCAAGCCCATGGGACACGATGTTCATCTAAAGAAACTAAAAGCCCATCTGGGCAGTTTTAGGAAGTAAAAAGGTTTAAAGCCACAGATCTTTATGAACATTCACAAATGTTCTATCATTGCTGTTCTTGGGTCTAATTCATTCCAAGAATAACGTTCAGAGAAGCCATTTTGTCAGAGGCCCTCATATCAAACCCTATTGATTTGAGATGAACATAATGTGACTTATGCCATCCACCATTTACTAAATGTTGCTATGGACAGATTTTTCAGTTCAAAATCAATCTTAAGTCTTTGAGGTAAATTATTCTGTGGATTCCACTGGAGGAAAGCATGCCTTTGAGAATTTAAGTAATTTGACAAAATAGTCAATTAGTAAATAGTAGAATGGGATCTTATACCCTCTCTTTCTGATCCCAGATTACGTGCTCTTAGCTTTTACACAGTACTGAGCCTCAGAAATGGTCCTCAGGCTTAAACCTCTGCTCCTTAGCTACATGCCCAGGATATTCTGACCTAGAAGTTTCTTGTTCATCTGTAG
Seq C2 exon
GCAGTGTCCAGAAGGCTACATCTGTGTGAAGGCTGGCAGAAACCCGGATTATGGCTACACGAGCTTTGACACATTCAGCTGGGCCTTCTTGGCCTTGTTTCGGCTAATGACTCAGGACTACTGGGAGAACCTTTACCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000006639:ENSRNOT00000065126:8
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:
PF0052026=Ion_trans=FE(8.5=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(19.0=100),PF0253517=Zip=PU(10.1=39.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGAGGGATCCAAAGATGCTCT
R:
TGTTGGTAAAGGTTCTCCCAGT
Band lengths:
190-1315
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]