RnoINT0155186 @ rn6
Intron Retention
Gene
ENSRNOG00000006238 | Traf2
Description
Tnf receptor-associated factor 2 [Source:RGD Symbol;Acc:1310457]
Coordinates
chr3:2762544-2764477:-
Coord C1 exon
chr3:2764261-2764477
Coord A exon
chr3:2762623-2764260
Coord C2 exon
chr3:2762544-2762622
Length
1638 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGC
5' ss Score
6.46
3' ss Seq
GTTTCCTCTCTTCCCATCAGCTC
3' ss Score
8.58
Exon sequences
Seq C1 exon
GGCTTTGTGGTGCGTGGGTTATAACTCACATGGCTGCAGCCAGTGTGACTTCCCCTGGCTCCCTAGAACTGCTGCAGCCTGGCTTCTCCAAGACCCTTCTGGGGACAAGGTTAGAAGCCAAGTACCTGTGTTCAGCCTGCAGAAACATCCTGCGGAGGCCATTCCAGGCCCAGTGTGGGCACCGCTACTGCTCCTTCTGCCTGACCAGCATCCTCAG
Seq A exon
GTGTGCATGCCACTCTACCGAGCTGGGCAGGGACAGGTGGGGCTCTGAAGTCAGGTTGCAGTAGAATGGTTGCCAGTATAAATTCTCCATGGATTCTGGAGGCGTAGCCCAAATCAAAAATGTAGAATTTATTGTTTAAAAAACAATGATTGTTTCTGGGTGAGGTGGACATCCTTTAATTTCAGCACTTAGGAGGCAGAAGCAGGAGAACTCTGAGTTCAAGGTCATCCTGGTCTACAACTGAGTTCTAGGGCTAACTAAAAAAGAAAGAATGGAGAATTGATCATAGCAAGGTATGGTAGTCTCTGCCTCTCCCCCTTTCCCTCTCCTCCTCTCCCCTGTCCCCCCCCCCCCCCCGCCCAAATTCTTGTGAAATAGAGACAGGAAGATCAGAAGTTCAGAGTTGTCCTTGACAACCTCAGATCTGTCTCAAAAAATAACAACAGCCATCAGAGAGTTGACTCTGTGTGAAGGCACTCACTGCAAGCCTCACAGGCTGAGTTTGAACCCTGAGCTCCGCACTTAGTGAAGGAGAGAGCTGACTTGTCCTCTGATCTCCACCAACATACCTTCATACATATTTATACACACAGTAAAATTTTAAAATGTAACTAAAAAATTAAAAACAAAACACGGGCAGGGTAGATAAAAGTGCTTCCTGTGAAATCAAGACTTGAGTTTGGGGGTTGGGGAATTAGCTCAGTGGTAGAGCGCTTGCCTAGCAAGCGCAAGGCCCTGGGTTCGGTCCCCAGCTCCGAAAAAAGAAAAGAAAAAAAAAAAAAAGACTTGAGTTTGGTCCTTTCCAGCCATGTAAAAACTTGGGAACTTGGGCATGGTAATGTGTAATTGGAATCACATCATATGCCTAGAGACAGAGGCAGAAGGGTTCCTGGGGCTCATTGTTTAGCCCAATCTGCACATTCTAGGTCCTGGTAAGAGTTCTATCTGCAAAAGGCGGATGGCACCTGAGGAGGAATACCTACATGTGGCCTCTAGCGCCCACATATACATGGTATATGTACCTGTATATTCTCTCCCCCACCCCCTTCTCTCTTACACACACACACACACACACACACACACACACACACACACACACACACACAGAGGTTATCTATTGGAATACTGTTTTTGGACATATGAGATACATATAGCATTGTTGGTTTCATAGGCACTAGTGTGTTAGTGTGAGGATTATGGCTCCCTTAGGCTGTTCTGGGTGGGTAGATTGAACGTTTCACTGCCGCAGTGTGAAAGGGCAGCAGCAGTGCGTGTGGAGAAGCAAACACATCCACATTTTTCTGCCATGTATTTTGGAGGCTGGGGCCTACAGCCAAGGTTCAGTGACAAAGCACTTACCTGTCATTCATGAAACCTTAGCTTGATCCCTGACATCACAAATTCAACAAGAAAGGAGGAGATGGTTGGCCTTGCAAGTCTAGGCCCTGACACCCTTTTCCACATTGAGTCTTCTCATTTGTGAATGTTTATGATTTGTGAAGTTACATACTGTTTGATCAAAGATGAGACAAAGGAAGAAAGAGCAGTGTGGAACCAGGCTGTGGGCTGAGTAGACAGGGCTTGGGTTCCCTGAACAGGCATTTTAGAGGGACTCTGTGTTTCCTCTCTTCCCATCAG
Seq C2 exon
CTCTGGGCCTCAGAACTGTGCTGCCTGTGTTCACGAAGGCCTGTATGAAGAAGGCATTTCTATTTTAGAGAGCAGTTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000006238:ENSRNOT00000008253:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009720=zf-C3HC4=PU(74.4=46.0)
A:
NA
C2:
PF0009720=zf-C3HC4=PD(23.1=33.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTTTGTGGTGCGTGGGTTAT
R:
CGAACTGCTCTCTAAAATAGAAATGC
Band lengths:
295-1933
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]