RnoINT0131678 @ rn6
Intron Retention
Gene
ENSRNOG00000029342 | Scn7a
Description
sodium voltage-gated channel alpha subunit 7 [Source:RGD Symbol;Acc:61922]
Coordinates
chr3:52782292-52783358:-
Coord C1 exon
chr3:52783221-52783358
Coord A exon
chr3:52782397-52783220
Coord C2 exon
chr3:52782292-52782396
Length
824 bp
Sequences
Splice sites
5' ss Seq
AAGATAAGT
5' ss Score
2.82
3' ss Seq
ATTTATTTATTTTTTTTTACCAG
3' ss Score
-1.12
Exon sequences
Seq C1 exon
GTGTACATGCAGCCTAGTTTTGAGCACAGCCTCCACATGTACACTTACTTTATCATCTTTGTTGTGTTTGGATTATTTCTTCCCTTGTGTATGCTGATTGGTGTTATTATCAGGAATTTCAACAAGCAGAAAATTAAG
Seq A exon
ATAAGTATAAATATTCTTTCTACTTGCTTAACAATTAGACTTAACAAAAATATTTCTAGGATTGTCCTCTTGGTTTGATGTCAGGTATACATGGCACAAATGTAATAGAACAATAATTAGTGTTCTTGTACATTATAAATATTATGAAAATGCCCAGCCTTATTGTATCTCCAATAGACAAAGGACACTCAGGCAAGAGGTACAGTTTAAAAGTTCCTGCACTTATATATGTTTGCTGGTAAATGATAGTGTAATGAAAACCAAATAACAAAATTCTACTATGTTCTTACACATATGTATGTGTTCAGAAAAAAGTTTTATTTATTAAATAATGTCTCGCTATTCTTTGAATTAGGCACGTGATAAATCCAGGGCATTATTAAGTTATAATTACAGTAGGTTTTTGCAGTTAGGCAGAGGAACATAAATGATATATACTTCCAGAATTATTTTTTTAAAAGTGTTTTGATTGCATTTGTAAAATTAGGCCATATTTTAAATTTATAAAAATGCAAAACTATTCGATCCTAATTTTAATTACTTCTGCTTTAGACACAAACCATATCGATTAAATTTAATTTGTCACAGTGGGCTTCTCATGTCTTCCGCTGTGTCGCCTTGTCTCGCTAACTGAAAAGGAAAACCTGAAATAAAGATGGTTGATTATCATATATTCTGTGTATTTTATATGGATTTTATATAGAAATACCTAAACTTGATTGTGCAAAGAATGAAATCTAATTTTCTAAAGCATACCTCCGAAAAGGGAAGATTTTGGGTGAACTGCAATTTTCATATCTTTTTATTTATTTATTTTTTTTTAC
Seq C2 exon
CAGGGAGGATCAAATATCTTTATAACGGTAAAGCAGAAGAAACAGTACCGGGCACTGAAGAAGCTCTTGTATGCAGACTCTCAGAAACCAGCAGCCCGCCCTAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000029342:ENSRNOT00000041096:23
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=PD(15.7=76.1)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACATGCAGCCTAGTTTTGAGCA
R:
GGCTGCTGGTTTCTGAGAGTC
Band lengths:
230-1054
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]