MmuINT0164470 @ mm10
Intron Retention
Gene
ENSMUSG00000026875 | Traf1
Description
TNF receptor-associated factor 1 [Source:MGI Symbol;Acc:MGI:101836]
Coordinates
chr2:34957959-34958611:-
Coord C1 exon
chr2:34958513-34958611
Coord A exon
chr2:34958107-34958512
Coord C2 exon
chr2:34957959-34958106
Length
406 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
TCCTCTGCTCTACTTAACAGACC
3' ss Score
8.85
Exon sequences
Seq C1 exon
ACATAGGGTAGCCAAATGACAGTGTGAGAAAGTGACATTTACTCAAGGCCACCCAGATATCCTGGAGGACCCAGAACCCTGGAGATTCCCATCAGAAAG
Seq A exon
GTGAGCCCCATTGTTCCAGAGGTACTGGGGGGGTGGGGGGCACAAAACAGCCTTGGCCTCTCCACCAAGGGTCCGGGAGGAGATAGAGAAGGCAGCCCGTGGTTCTCAGGCGGAGGAATTGTGACTCTGCTGGAGAGCCAGGGCACTACTCTCTTCCTCTGATTCTGTCTCTTGCTCGTTCTCACTCTGAAAAGTGTCTGGACACTCCTTAAAGTTTTTAGCCTCTGTCCAGGGGATTTTTTTAACCACAAAGGGTAATTCCTACTCCACCCTTGCTGTGACTCAGCTATGACGTCGTACCACACAAGCCAGAGAGGAGAAAAAGTCACCAGAAAGGGTGGCCCGGAGCCAGAACCCACCTCTCTCTACAGACTCCACAAGGCTGGTCCTCTGCTCTACTTAACAG
Seq C2 exon
ACCTTCTGGCCACCTGAAACCCCAAGATGGCCTCCAGCTCAGCCCCTGATGAAAACGAGTTTCAATTTGGTTGCCCCCCTGCTCCCTGCCAGGACCCATCGGAGCCCAGAGTTCTCTGCTGCACAGCCTGTCTCTCTGAGAACCTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026875:ENSMUST00000113064:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.169
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Skipping Isoform:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACATAGGGTAGCCAAATGACAGTG
R:
TCAGGTTCTCAGAGAGACAGGC
Band lengths:
246-652
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types