RnoINT0155199 @ rn6
Intron Retention
Gene
ENSRNOG00000008145 | Traf3
Description
Tnf receptor-associated factor 3 [Source:RGD Symbol;Acc:1304633]
Coordinates
chr6:135690451-135691994:+
Coord C1 exon
chr6:135690451-135690709
Coord A exon
chr6:135690710-135691942
Coord C2 exon
chr6:135691943-135691994
Length
1233 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGT
5' ss Score
7.07
3' ss Seq
ATTTACTTTGTTTCCTTCAGCTC
3' ss Score
9.45
Exon sequences
Seq C1 exon
AATTTCTCCTCCCTAAGATGGAGCCAAGCAAGAAGATGGGTGCTGCTGGCGCAGCGCAGCCCAACCCACCCCTCAAGCTGCAGCCCGATCGCGGCGCAGCGTCAGTGCTCGTGCCGGAGCAAGGAGGCTACAAGGAGAAGTTCGCGAAGACAGTGGAGGACAAGTACAAGTGCGAGAAGTGCCGCCTGGTGCTGTGCAACCCGAAGCAGACGGAGTGTGGGCACCGCTTCTGTGAGAGCTGCATGGCCGCCCTGCTGAG
Seq A exon
GTGGGTGCCGTACATGGCTGCAGGCTGCCTGGGAGGGCACCTGCCCACCCTCACCTGTTCCTCCAAGACTTTGAATTTGAACGATTTTCAGTCCGACATGGGAGGGCACCTGCCCACCCTCACCTGTTCCTCCAAGACTTTGAATTTGAACGATTTTCAGTCCGACATGGGAGGCCTCTAGGGTAACTCAGGCACGGCTCACGCCCTGCCTGCCTCACATCCCACCTGCACAGGCCTCTCCCCTGACGTCTCCTTAGTGGTGTTAGCTCTCCGTCCACAGAGCTCCTGCTCCCCCACCTGCACTGCTGTGTTCTGTGCAAGAAGCTTATGTTTTATGGTGGTCAAATGATCATAAGTCCTTAAAGTTGAAGGGTGCCCCTGGCCAGAGTAGAGGAAGGTCGGGGTCACATGCAGAACTGAACAGGTGCTAATTCTGCATGCTTGCCTAGGGGGTACCCAGAGATCTGGGGTACCGAGACCCCAGAAGCTCATGAGTGTGCTGGGATGCTGTGGTAACATCACAGGGCAGGTTGGGAGTTGGAGGACAGAGGCGGAGCCAGCCGAGGAAGAGTTTCCTCATGCAGCTTTGGGTATTTGCTAGACGTTGTGCTTGGCACTCAGATCACCACAGGACACACTGTACCTCAGGACCCTCAGGACATATTAGCTCGAGAAGGAAGGCCACCCACATCCTTTTCTCACTGGTCACTCACCCCTGGGTGCCTGAGACCAAGGCCGAGGCCAGTACAGCTGTGCACCCCACACCCTCATCCCTCCAACTCACTTGTCCCACACAGCACACTTGGTTTTGCTGAGGGTGAAAGGACAGAGTAGGCTCAACACCCAACTCCTGTGGGACAGGACCTGGAAACCGCTTGTGCTCAGGCCGGGCCTGTGATGGGGTTTCCTGCAGGGTAGTGTGGCTGCCCTGGGCAGGTGCCATTAGTGTTTGCATACACAGTGAGCCCTCAGATAGCCGAAGACTAGTGCATCGAGGCCAGAGGACATCAGTGCCTGTGGTGCACCTCCCAGAGGCTCTCCTCCGAGAACCACTGCGGCACTGACATGTCATTCGCATGTCTTCCCAGTGCGACTGAGTGATGAGCGTATCGCATGTTTTAAAGGCCGGTTGCTGCAAGCTAGAGCAGGCCTGACTAAAGGGAAGCGTTTGGTGCTGGGGGCGTGGAGGAGGGAGCTGCCCCTGCTCTAACATATTTACTTTGTTTCCTTCAG
Seq C2 exon
CTCCTCAAGTCCAAAATGCACAGCCTGCCAAGAAAGCATCATCAAAGACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008145:ENSRNOT00000010906:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.292 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009720=zf-C3HC4=PU(74.4=35.8)
A:
NA
C2:
PF0009720=zf-C3HC4=PD(23.1=50.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATTTCTCCTCCCTAAGATGGAGC
R:
TTGTCTTTGATGATGCTTTCTTGGC
Band lengths:
310-1543
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]