MmuINT0164471 @ mm10
Intron Retention
Gene
ENSMUSG00000026875 | Traf1
Description
TNF receptor-associated factor 1 [Source:MGI Symbol;Acc:MGI:101836]
Coordinates
chr2:34956196-34958106:-
Coord C1 exon
chr2:34957959-34958106
Coord A exon
chr2:34956281-34957958
Coord C2 exon
chr2:34956196-34956280
Length
1678 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
ACTTATTCGTGTTTCCCCAGAGA
3' ss Score
8.82
Exon sequences
Seq C1 exon
ACCTTCTGGCCACCTGAAACCCCAAGATGGCCTCCAGCTCAGCCCCTGATGAAAACGAGTTTCAATTTGGTTGCCCCCCTGCTCCCTGCCAGGACCCATCGGAGCCCAGAGTTCTCTGCTGCACAGCCTGTCTCTCTGAGAACCTGAG
Seq A exon
GTGAGGGGACAAAGCCAAGGGCCGGTGGGAAAGACTGCCAGGGAGGAACCCCTGATGGGATTCGGGGCTGAAGGGAACTGGTGACTGTGAGCAGATAACTTCACCTCTCTGGGCCTAAATTTCCACACTCTTTTCTTCTGAATACTGCCCATGCCCTGGGCTGTGGGTGGATGGATCAGTAGCCACAGGAAGCTGTCAGTCAGTTCAACTACTGTTAAGATGGAACTTTAAGCATCACTCAGCCACTTACTGGGTGACCTGATGTGGACCTTGGATGTCTCCAAGCCCCAATGTCTTATCTGTGGAGCTGTTTTCTGCCTCACAGAATTGTTCCAAGACTCCATCAATAACGTTCCCAGAACTTCTTACAGTAATTAATGTGTCTCCCCTTGGCAAACATCAAACTGTGATTAAAAAAAAAAAAAGAACAACACAATTTTGTTCCATTAGACCCAGTTAAAGGGGCAAAGATACAGTAAGGTATACATTTATGCTTAAGGAGTAAATAATTGGATCAATAGCAGCATTAATAGCCTGCCTTGAGCAATTGTTATGCACCTGCTGTGTGTCACATACCCAGCCAGTGCCTGTGTCCTCAGACCAGCTTCCAGAAGGCAGTACAATCGCTCCCCTATTGCATAGATGAGAACTGCAAAGTCCCCCAGAGAGATCAAGCCTCCTTGCCTCCTGTGAGTTTCCTGCTGAGGATACTCCTAAGTGGCCTTGGGCCCTGAGCACGGTCTTTTCTTTGGGACTTTACAACGGTAAGAATGTGGGGAAACTGAATCAGCCAAATGAGAAGTCCGAATTTGGTGACTGAAGGGGAGGAGGCTGCAGGAGCAGGGCCAGAGGTTGTGGCTGTGGAAAGGCCAGGAAGAGGGTAGAGGCCGCAGTTGTTGGGCTTCCTGGACAGCTGATGCTCTGAGCTTATATGGGGTTCTCCAACCCCCCACCTCACTGAAAACCTGGCAGAAGAATAAGCAGAGCTGACTGGAGCATGCAGGCAGGGGCCCAGCCTGAGGTGCTGTGCTCTGGATTTGCCTTGCTATCCTATGGCCTCGGTCTCCTCACCTAGAAAGCAATTTGCACACTTGCTGTCAGTCAGAGCTATGTGCACAGATATCCTATAGAGCACCCTTGTCTGAACCTGATGCCCATTTCCAGTAGACAGACTCTGAGGTCTCTTCTTGTCAAGATAGGTCAACATCCCCTGGCCAAAAAAGGAGAGACCAGAAGCATATACAGGGTACTGAGAAAAACATACAGAGTTCCAAGCCCAGAACCCCTTGCCTAATCCCTTGGGATTGGACATATTGGGGGAGATCCAAAATTTTTGCAAATTTGGGAAAGGCAATAGATAATTCTTCCAAAAGAGACCCTGTAACCAGGCGCTTGCATGGGTATTTCTACAGTGGGACAATCATAACCACACCACATAGATAAGGAAGGGAACATCAGGTGAAGGCAAGTGGAACTGCAAAAGCAGCTAACAGCAAGCTTCAGGTAACAGTGTACACCCATGGTTTCGAAGACCTTAGCAGCAGGCCTCTAGGATCGTGGAGTTACTGCAAGAGGCAAGGTCCGGGCTTTGAAGTCTGTCAGGAAGGTACGAGTGACCGATGGCAGGTGCCAGCAAGGTGTGGTGCCTTATATGAGACACTTATTCGTGTTTCCCCAG
Seq C2 exon
AGATGATGAGGATCGGATCTGTCCTAAATGCAGAGCAGACAACCTCCATCCTGTGAGCCCAGGAAGCCCTCTGACTCAGGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026875:ENSMUST00000113064:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.169 A=NA C2=0.351
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion 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:
CTTCTGGCCACCTGAAACCC
R:
CTTCTCCTGAGTCAGAGGGCT
Band lengths:
231-1909
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