RnoINT0102398 @ rn6
Intron Retention
Gene
ENSRNOG00000009286 | Noxa1
Description
NADPH oxidase activator 1 [Source:RGD Symbol;Acc:1306687]
Coordinates
chr3:2304493-2306110:-
Coord C1 exon
chr3:2306002-2306110
Coord A exon
chr3:2304628-2306001
Coord C2 exon
chr3:2304493-2304627
Length
1374 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
ATGTCTGTTCGTGGTCCTAGGTC
3' ss Score
9.4
Exon sequences
Seq C1 exon
GCTCCAGGAGGCTGTGTCCGACTTCCAGTTGGCCCTGGCACAGCTGAGGGGCAATGCTGCCATTGACTACACACAACTGGGTCTGGACTTCAAACTGCAAGCCTGGGAG
Seq A exon
GTGAGTGGGCACTGACTCGTGTGAAGGTTGGACGCCAAGCAGTATTGCTGGGGCTTAGAGGTGCGGTCTGTGGCCCTGCGGTTCATGGATGTTCTAAGGTTCCGCCATGGCCCTACATTGCAATAGGGGGCTATAACACAGTCTGAGGTCCTGGCTTGTTCTAGGTCTTGTCTTGTGGAGTCTGCCAGGGCTTTTCTCCTTGATGTTGGTGTTGCTGTCATGGTGGGCCACGTGGAAGGAGGCATTTTGTCCAGCCAAAGATTTTGGAGCCCTGAATCCCCTCGCTCTTTGATTGCCCAAGGAGGCAGTGGAGGGAGTGGAGGGAGTGGAGGCAGTGGAGGGAGTGGAGGGAGTGGAGGGAGTGGAGGGAGTGGAAGCAGTGGAGGGAGTGGAGGCAGTGGAGGGAGTGGAGACAGTGGAGGGAGTGGAGGCAGTGGAGGCAGTGGATGGAGTGGAGGCAGTGGAGGCAGTGGAGGGAGTGGAGGCAGTGGAGGCAGTGGAGGGAGTGGAGGCAGTGGAGGCAGTGGAGGGAGTGGACTCCTCACACTGTGGAGCCAGCCAGCATGGGCTCATGTTGGATAAAGACAGGACGCACTTGAAGACCATGACAAGGTGACAGACAGTTTGGGGGAAGGCGGTTGGCTCAGTATGTACAGCTGGGCCGGAGGAAACAGCAGGAACACAGCCTTAAGAAGAGTAGGTGGGTTTCTCCCCTTGTAGCAAAGTTTTAAGTTTGGTATGTGCTTTCCTCTCCGGGTGAAGGGAGAGTGGGGTCACAGCATTGTGTCAGTTTATCTGCCTGTCACAGAGGGTGTAAGATAGCCTTAACTCTGTCCTCTTTGCCCACGAGAATGCTCTGTTTCATTGCACGTGGGGTTCTGAGTGTCCTTGCATTGACAATGGGAAGGAATCTGTAGACATACAGTACTGACTCAGAGGTGGAGGGAGCAGTTAATGGTGGTGGCAGGGTACAGAATTGGGAGGGTGTCAGCTAAGGGAGACTTTGTGAGCCACCGTGGGAGAGTTAGGAACCTAACCCAAGTCTTCAGAAGAGCAACAAGTACTCTTAACCACTGAGCCATCTCTCTAACTTCCCCCTCAACCCCCTCCCCGTGGGAGACACTTTAAAAGGTAAAGGGAGAGGTACTTCTGCTGCTTCAAGCAGAATAGTCCAAAGCAAAACATGGTCCCCCCAGGACTAAACAGATCCAGGGCATGAGAACTTGGCATCTGAAACCTGAGCTGGTCGGGCAGCAGGTGGCCTGGTAGCATCAGCTGAACATACAGAAGAACCTTCAGCTATTGTAACTGGGGAGCTGGTGTGAGGACCACCTGGGGGTCCTGGCCCCCCGTCATGTCTGTTCGTGGTCCTAG
Seq C2 exon
GTCCTATATAACATGGCATCAGTGCAGTGCCAGGCAGGGCTCTGGACCAAGGCTGCCAATACTCTAGTAGAAGCAATCTCCAAACGGCCAGAGGGGGCCCAAGACACCCTGGAGGCTGCCATGGACAAAGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009286:ENSRNOT00000012375:3
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=0.144
Domain overlap (PFAM):
C1:
PF134141=TPR_11=PD(23.5=43.2)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGAGGCTGTGTCCGACTTC
R:
CTGCACTTTGTCCATGGCAGC
Band lengths:
239-1613
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]