MmuINT0164544 @ mm9
Intron Retention
Gene
ENSMUSG00000026637 | Traf5
Description
TNF receptor-associated factor 5 [Source:MGI Symbol;Acc:MGI:107548]
Coordinates
chr1:193881856-193883040:-
Coord C1 exon
chr1:193882876-193883040
Coord A exon
chr1:193881934-193882875
Coord C2 exon
chr1:193881856-193881933
Length
942 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
CACCCACTTGTCTGTTTCAGGAT
3' ss Score
11.79
Exon sequences
Seq C1 exon
GACCACCTTCAGCACTGTTCCTTCCAAGCCGTGCCCTGCCCTAACGAGAGCTGCCGGGAAGCCATGCTCCGGAAAGACGTGAAAGAGCACCTGAGCGCATACTGCCGGTTCCGAGAGGAGAAGTGCCTTTACTGCAAAAGGGACATAGTGGTGACCAACCTGCAG
Seq A exon
GTGAGAGCAGGAACTGTGGGTGACAATACAGCTCAGATGGAGCCCAGGGGGCGTTCTTTGCTTATTTTTACTGAATTTGAGGGTTTATCTGGACGGGGATGGGCTCGATTATTAGAGTGTCTGTCTTGCATATAGAAAGCTCTGTGTTTGAATCTGAGCACAGCATAAACCAGGCATGGTGGCTCACACCCCTCATCCCAGCACTTGGAGACACTTGGAGGACAAGCAGTTCACCCTTGCCTTCGTAGCACTAAGGCAAGTCTGAGATACATGAGACACTATCTTTAGAAAGAAGTGGCCCTGTATCATCTGGGACTGTAGCTGTAGCTCACTTGGTAACATGCTCGCCTGACGTTCGCAAGGCCATAGGTTTGACCCCCACCACACAAACCAGGTGATGCACACCTATACTCTCAGAGCCTGAAACGTGGAGGCAGATGTGAAGTTCAAAGGTAGTCCATCCGTGGCTCCATAGATAGGTGGTTCTCACCTAGGGAAGAGAGAGGGGGCAGTTTGAGATCCTGCAAAGAGCTCTTTTTCTTGGTGGGGCTCTATTCCTTTATCATTGGTGAAAATAGCACTGTGGCCTCAGTAAGCTTGGGAGGTGAGATGCAAGGTCTGGGTCCCATGGAGGTGATGGCAAGGGCTTCTTAGATTGTTATCTGGCTGGAAAGGCAGGATCAGCTTGGGACCACTGGTGCTTTTACATGTGCAGAGAAGCCTCCCTGGTAGATCCCCAGGCTGCCTGCTTGGGCTCCAAGCCATCTGATTTAGTTGAATTCATTTACATCAAGAAATCAGACACTGCTAATCTCTTTCTGGAACTGGGCTGTAGCTTCCTATGGAGAGCAAGCCATATGACATGTATCTCCAGAGAAACGTGTATGAATACCTTGAGGCAAGCGATCTTGACTTTGTTTCCCACCCACTTGTCTGTTTCAG
Seq C2 exon
GATCATGAGGAAAACTCGTGTCCTGCGTACCCAGTGTCTTGTCCCAACAGGTGTGTGCAGACTATTCCAAGAGCTAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026637-Traf5:NM_011633:5
Average complexity
IR-S
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:
PF0217613=zf-TRAF=PU(94.6=96.4)
A:
NA
C2:
PF0217613=zf-TRAF=PD(1.8=3.8),PF0314511=Sina=PU(4.3=38.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACCACCTTCAGCACTGTTCC
R:
GCTCTTGGAATAGTCTGCACACA
Band lengths:
239-1181
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: