RnoINT0155187 @ rn6
Intron Retention
Gene
ENSRNOG00000006238 | Traf2
Description
Tnf receptor-associated factor 2 [Source:RGD Symbol;Acc:1310457]
Coordinates
chr3:2762162-2762622:-
Coord C1 exon
chr3:2762544-2762622
Coord A exon
chr3:2762261-2762543
Coord C2 exon
chr3:2762162-2762260
Length
283 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
TGAGGGCGTTCCTGTTCCAGGCC
3' ss Score
8.6
Exon sequences
Seq C1 exon
CTCTGGGCCTCAGAACTGTGCTGCCTGTGTTCACGAAGGCCTGTATGAAGAAGGCATTTCTATTTTAGAGAGCAGTTCG
Seq A exon
GTGAGTACACTGTATTGAGCTAAACATGTCAAAACGAATAGAACATGTTTGGCAGTTTTGTTCTGTAACCCTGGTAACAGTGAGAATTGGGAGCTGAAAGTGGCTCTTGATGACTCTTTACGGTTGGAGAGGTGGAGAGGCATGGGTTGACCCATCTGCCCCATGTGCTTGCTGGCGGGGAAGGGTGACCAGGTTGTTTTGGGTAGGATCTCTGGTCTAGGTGATGCTTCATAGACAGTAGGGTACTGGGAGCAGGTGTAACCTGAGGGCGTTCCTGTTCCAG
Seq C2 exon
GCCTTTCCAGATAACGCTGCCCGCAGAGAGGTGGAGAGCCTGCCAGCCGTCTGTCCCAATGATGGATGCACCTGGAAGGGGACCTTGAAAGAATACGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000006238:ENSRNOT00000008253:3
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:
PF0009720=zf-C3HC4=PD(23.1=33.3)
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:
CTGGGCCTCAGAACTGTGCT
R:
CGTATTCTTTCAAGGTCCCCTTCC
Band lengths:
174-457
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]