RnoINT0131592 @ rn6
Intron Retention
Gene
ENSRNOG00000005007 | Scn3a
Description
sodium voltage-gated channel alpha subunit 3 [Source:RGD Symbol;Acc:3635]
Coordinates
chr3:51555319-51556330:-
Coord C1 exon
chr3:51556176-51556330
Coord A exon
chr3:51555493-51556175
Coord C2 exon
chr3:51555319-51555492
Length
683 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
AAAGTTTCCTTGATTCACAGGCC
3' ss Score
6.22
Exon sequences
Seq C1 exon
GGTGCATTAAAAAATTCCCCTTCTGTCAAGTAAGTACAGAAGAAGGTAAAGGAAAAATATGGTGGAATCTTAGGAAGACATGCTACAGCATTGTGGAGCACAACTGGTTTGAAACGTTCATTGTGTTCATGATTCTCCTCAGTAGTGGCGCTTTG
Seq A exon
GTAAGTGATTGTGTCCTGGCATGAACCAAGTTCTGCCGAAGAAGCCAACTCTCTGGTGACACTAGGAGTGCCCACTCAGTTTAGAAATCAAAAGAATAGGTGTATCTGTGCCGTGCAGAGCTGAGAACTCTGCAAATTTTTGTTCAAAGCAAGTCAGGAACAGGCTGAATTTCACGTCTGGTGACTGATTGCCCACCAGGTGTTTTCCTCACTTGACAAGCCATCTGCAGACATTCCTCTGGCTGTGCTAGCATGCCTGTCAAATGTCACCCGGTCTACCTTAATAATTGCGTTTCCGGATTATCTGTGGATCTTGCTTTCTTTAAATACCGTGAACTTATTCTTTGAAAATAAGAGATGGAATCACAGAAGATACTGTTGGAAGGAGCCGGTTCTAGCTCTTATGAACTGGATGTCTTTAGTTCATCTTCCATGAGTGGAAGCATGCCTTTTGGTAGTGATTGACGTAGATACTTTTCGGGGAGACGTAAAGATGTCAGCACATATAAAATCAATATAGATGTCAACAGTCCTGTGCCAATATTCCCTCAGCTAGCTTTGGTCTTTAGCTTCAGCCTGATAGAAAATATTTGAGTGATTTAAGTAGGTTGGTTCTTAGACTAGAAATATTCATAAATGTTTTGGGAAGCCATTAAAGTAAGTAAAGTTTCCTTGATTCACAG
Seq C2 exon
GCCTTTGAGGATATATACATTGAGCAACGAAAGACGATCAAGACCATGCTGGAGTATGCAGACAAGGTCTTCACGTACATCTTCATCCTGGAGATGCTCCTCAAATGGGTGGCCTATGGATTTCAAACCTATTTCACCAATGCCTGGTGCTGGTTGGACTTCCTGATCGTTGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005007:ENSRNOT00000006646:20
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(20.1=84.6)
A:
NA
C2:
PF0052026=Ion_trans=PU(17.3=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:
AAAATTCCCCTTCTGTCAAGTAAGT
R:
TCAACGATCAGGAAGTCCAACC
Band lengths:
318-1001
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]