RnoINT0155180 @ rn6
Intron Retention
Gene
ENSRNOG00000048914 | Traf1
Description
TNF receptor-associated factor 1 [Source:RGD Symbol;Acc:1596290]
Coordinates
chr3:14008642-14009619:-
Coord C1 exon
chr3:14009554-14009619
Coord A exon
chr3:14009053-14009553
Coord C2 exon
chr3:14008642-14009052
Length
501 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
GACCCTCACTCTCTCACCAGGGG
3' ss Score
11.21
Exon sequences
Seq C1 exon
GTTCTCCCTGATGTGGCTGAGGCTGGAATCGTGTGTCCCTTTGCAGGTGTTGGCTGTTCCTTCAAG
Seq A exon
GTAAGTGACAGTGGCAAATCTGTCCATGGTCCCAGACCCTGTGTCTCTCACTTCACCAAAGCTTCCCAAAACACAAGCTACTCCTCCGTGCGGCTCCTACACGAGTGAGCTACCAAGCAACAAATCCCGCCATTATGTCATTGTTGCACAATGTGCACAATGGGAAGTGGCTCTTAAGGCCTCACCTGAGCTCTCGCTGAAGCATCACTCAAGTCTCTCCCACTCACACCCCTCTCCATGGTCCTGAATTGTCATTACACTGATGGGCGGGGCAGAATGGTCACACTAGAGACCGAGATGCATGATGGATGCTCTCTGTGGGCATATCTAAGGACTGTATTCCTGTTTATGGCTCCACTCCACCTCTACCCTATACTGACAGCTACTTCCCCTTTGCTGAGAGAGTGGATCTGGCTTGGTGGCTTTTGGTGCCACGTCTCCTTGCTGGTACCCAGGGTCTCCTACTTCACTGTTTAATAAAGACCCTCACTCTCTCACCAG
Seq C2 exon
GGGAGCCCACAGTCCGTGCAGGAGCATGAGGCCACCTCGCAGTCCTCACACCTGTACCTGCTTCTGGGGGTCCTAAAGGAGTGGAAATCCTCACCAGGTCCCAACCTGGGCTCTGCACCCATGGCACTGGAGCAGAACCTGTCGGAGCTGCAGCTTCAGGAAGCTGTGGAAGTGACAGGGGACCTGGAGGTAGACTGCTACCGGGCACCTTGCTGTGAGAGCCAGGAAGAACTGGCTTTGCAGCACCTCCTGAAGGAGAAGCTGCTGGCTCAGCTGGAGGAGAAGCTGCGTGTGTTCGCGAACATAGTTGCTGTCCTCAACAAGGAAGTGGAGGCTTCCCACCTGGCGCTGGCCGCCTCCATCCACCAGAGTCAGTTGGACCGAGAGCACGTCCTGAACTTGGAGCAGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000048914:ENSRNOT00000072400:3
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=0.072
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAATCGTGTGTCCCTTTGCA
R:
GGACAGCAACTATGTTCGCGA
Band lengths:
358-859
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]