MmuINT0164466 @ mm9
Intron Retention
Gene
ENSMUSG00000026875 | Traf1
Description
TNF receptor-associated factor 1 [Source:MGI Symbol;Acc:MGI:101836]
Coordinates
chr2:34816341-34817292:-
Coord C1 exon
chr2:34817044-34817292
Coord A exon
chr2:34816408-34817043
Coord C2 exon
chr2:34816341-34816407
Length
636 bp
Sequences
Splice sites
5' ss Seq
CAGGTTGGT
5' ss Score
8.08
3' ss Seq
CTTTAAACTTTGTATTGCAGTGT
3' ss Score
6.98
Exon sequences
Seq C1 exon
GAGTATCTCAGGAGTGCAGCCACTGATGGAATGCTAGGAGTCAGCTAGCACCAGGACCCCAACAGAAGCACTCCAGTTCTGTTTCCTTGAGGGAGGAGCGATCAGCCCGCCCCCCGGCCAGCCTCCGAAGCCAGCCCAGCTCAGTCCCACCCGCCTGCCCAGCCCAGCTTCCCTTGGCTTCCGCCAGCCCAGCCCGGTTCTCTGCCCCAAGGACGCTACCGCCCGGTGCGAGCAGAAGGCGGCGCACAG
Seq A exon
GTTGGTTGCCCGTCCCCCGCGGGTCCCCAGGGTCCCCAAGTGCGACCATACTCAGCCTCTCTCCCTTCCTGAGCGGTGCTCTGGTCCTTAAGCTGTCACTTCGGTTCTGCCCTCAGCTCTGAGCTCGTTCTGATGTGGCAGGGGACATCACCTGCTGAAGGAAAGGGGGCAGGTAGGCAGGAATTCATAGGTAGGCGACTAGACAGCATGTCCAGGCTAAAGGCAGCATGTAGGCCATGGGATCCCAATCTGGACACTGTCACCGAGATGTTCCAAAGTGTGGGGTGTGGCCCAGGTGGGTCCCCAAAGACTAGAAGGAGGATGAGACGCCTCTGTTCAGCAGATAGATTGTCCATTCTGGGAGCCATGGAGATGAGACTAAGGAAGATGGAGGTGAGAAGGCGGTGAAAGAGACCTGTAAAAAGCCACCGCAGTGTAAAAAATAACTCTGAAGGGTGTGAAGGAAAGTGCTGTCATAGAAAGGAAGGCTAGAAGTCCACTGGCCTGCTTCTGATGGGACTGAAATTAGGGCAGGCCCGGAGCATTTGACAGTGTGTGGGCTTATGACAGGGCTGAGTAGATTCCCTGGAGTTTCAGCAGCTGTGCTGACAATCTTCTTTAAACTTTGTATTGCAG
Seq C2 exon
TGTGAGAAGAGAGAGTGGATATGGGAGAAGAATTTGGGATAATTGCCAAGCTCATTTTAAAGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026875-Traf1:NM_009421:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
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:
AGTATCTCAGGAGTGCAGCCA
R:
TGTGCTTTAAAATGAGCTTGGCA
Band lengths:
314-950
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: