RnoINT0131517 @ rn6
Intron Retention
Gene
ENSRNOG00000032884 | Scn11a
Description
sodium voltage-gated channel alpha subunit 11 [Source:RGD Symbol;Acc:3630]
Coordinates
chr8:128509306-128510641:-
Coord C1 exon
chr8:128510523-128510641
Coord A exon
chr8:128509399-128510522
Coord C2 exon
chr8:128509306-128509398
Length
1124 bp
Sequences
Splice sites
5' ss Seq
TTCATATCC
5' ss Score
-14.87
3' ss Seq
GCCTTAACGGGTCCTGGCACAGT
3' ss Score
-3.76
Exon sequences
Seq C1 exon
ACATTCATGGTGTTGAACAAGAAGAGAACAATTTATCGCTTCAGCGCCAAGCGGGCCTTGTTCATTCTGGGGCCTTTTAATCCCCTCAGAAGCTTAATGATTCGTATCTCTGTCCATTC
Seq A exon
ATATCCTTTCTCCAAGTCCATGCCGGGAAACCAGTGTGAGCCCCAGGGGTCCGTGTGTGCTCTGTTGCCACTATTACTGTTAGTTTGAGTCAGGGTCTCGTAGCTCAGGCTATCCTTGAAAGCCCCATGTAGCAGATAACCTCAAACTTTTGATCTTCCCACCTCTGCCTCCCAAGTTCTGGGATTATAGGAACATGCCGCCACACACCGTTTATGCAGTGCTGGGGGTTGAACACGGCTTCAGTATGCTAGACCAGCCCTTGACCAGCTCCATTTTCAGTGGAAGCAAATAGTCTTTGTTCTCAAGGTGCTCCTGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTACATGTGTGTGAGCGCGTGTGAGTGTGTGAGCAGCCGTAGCCCAGGAGCACCAGCTTCAGGAGACATGCCCAGAGGCATTTGAGTCTAAGTGAGCACAGAAGAGGCTAGGCCATTTTAGACCTGAGAGGGAAGCCAATGTGTAACCCGTACACCTAGTTCCTGGAAACAGGGTCTGTGGTAGGAACTCTTAATTCAGGAGTACAGTAGAGAAGAACTCTCTGGAGAAGGAGGAAAGGAAGCAGGAAGGCGAAGAGGAGGGCCCAGCAGGTAGTGCTCCTGCTTAGCGTGCATCAAGTTCTGGGCTTTGCCCTCTCATGCTGCCACGGCCGCCGCAGGGGATGGGATGAGGATAAACCAGTGATGGCTGCAGTTTCAGCTAAGTCTGCCTGAGTCTGACTCTGTGGGGAGTCCCTAGATCACACGGCACCTGGATCTCAAAAGTCCAGGCTGGCCTCAGACTCTCTCTGACCCAAGAATGATGTAGAACTATTGCTGTTCAAGGTGCTGAGGTGTGAGCTGCCATGACTGGTTCCTGCAGTGCTGAGGACCCGCTGTGCATGCTGGGTAAATGCTCTTCCAACTGAGCTACAAACATTCCCGACCCAGGGACTCAGGGCGGGTTAAATCTACCTCCGAGCCTTCTTTAGAGGTCCAGAGGCTGCTCTCACAGAGAACAGATGTGTTTGTGCGCAAGCTCAGAGATCCCCACCACAATGGCAGTCTGTCGCCTCCTGCGGTGTCTCGCCTTAACGGGTCCTGGCAC
Seq C2 exon
AGTCTTTAGCATGTTCATCATCTGCACGGTGATCATCAACTGTATGTTCATGGCGAATTCTATGGAGAGAAGTTTCGACAACGACATTCCCGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000032884:ENSRNOT00000034025:3
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:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(0.8=6.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCATGGTGTTGAACAAGAAGAGA
R:
TCGGGAATGTCGTTGTCGA
Band lengths:
208-1332
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]