MmuINT0164474 @ mm10
Intron Retention
Gene
ENSMUSG00000026875 | Traf1
Description
TNF receptor-associated factor 1 [Source:MGI Symbol;Acc:MGI:101836]
Coordinates
chr2:34946682-34948551:-
Coord C1 exon
chr2:34948141-34948551
Coord A exon
chr2:34946860-34948140
Coord C2 exon
chr2:34946682-34946859
Length
1281 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
CTGACCAGCCTTCCCTACAGGTG
3' ss Score
7.66
Exon sequences
Seq C1 exon
GGGAGCCCACAATCCATGCAGGAGCATGAGGCTACCTCCCAGTCCTCCCACCTGTACCTGCTGCTGGCGGTCTTAAAGGAGTGGAAATCCTCACCAGGCTCCAACCTAGGGTCTGCACCCATGGCACTGGAGCGGAACCTGTCAGAGCTGCAGCTTCAGGCAGCTGTGGAAGCGACAGGGGACCTGGAGGTAGACTGCTACCGGGCACCTTGCTGTGAGAGCCAGGAAGAACTGGCCCTGCAGCACTTGGTGAAGGAGAAGCTGCTGGCTCAGCTGGAGGAGAAGCTGCGTGTGTTTGCAAACATTGTTGCTGTCCTCAACAAGGAAGTGGAGGCTTCCCACCTGGCACTGGCCGCCTCCATCCACCAGAGCCAGTTGGACCGAGAGCACATCCTGAGCTTGGAGCAGAGG
Seq A exon
GTGAGTGAGATGGGCATGTTTTCAGAGTCAGCTCAGGGAGCCCCTATGCCATCCAGCCTTCTTGCCACTCATCCCTCTCAATGAAGTAGCCTCCATCCAAGACCAACTCCCCTGTGTACCAGGACCTATTATCAAGACCCTGAGTCAGAGGCTTGGGTTAAAAACCAAAGCCCCAGTATCCAGTGCAAATCAAGTCTTCCGCTTTGAATTCACTGGGAACTTTCCCTCCAGGGCTCACTCCCTGGCTGCGCATTCCATCGCTGACGGGTTGTCATTGCTATAGAATTCTTACCACAAAACCGTGTCTTCCCTGTCTTTGTTCCTGGCTGTGCCCTTCGAGGCCTGTGGAACAACCTGAATCGGCTTCCCCACAGCTGCTCTGGACGGATAGTCAGTGTTCACATCCTAGCAGAAGAATTTTCCCTTCGTGCCTTCACCTGCTCATCAGAGCATGGTGGGCGGTGATGTTCTCTTACTCTCCGCCTCAGTCTCTACTTGCAGGCTGTAGTTCCAGACTTACCTGAGCCTGTAGTTCTCAGTCCTCCTCTTCTACTCCAGAGACTGTACTTTCCACAATGTAGCCAGTCACCGAGATCCTGTTACTTTAAAAAAAAAAAAAAACAGCAACATTGTCTCGTTATTATTATTGTCTCCCATAAAACTGCGCCTGACCCTACATAAGTTCCACCCCTACATAAGCTGCTGAGAGGATGTGATCCATTCACCTTCTCTCTCATGACTGGTTTGTTCTTTAAAATTTCTTTGGGGAAAACTATTACAAGGTCCAGGCACTGGGCCAGGCAAAGCCTCAGTCTATACAATTTACACCCTCAACCCAGTTGAAAAGTACATTCCATGGTTTCCATCTCACCAGACTTCTGGCTCCACTTTAGCAGCTGGGCACTATGCAATGGGTGGACAGAGAGGAAAGGAGCCCACCAGGGGGGAAGCAGGGACAGCCTGGACAGGAGGATGGAAATCATCAGAACTGTAAAACACAGTGAGGGAGACCAGCCAGCTAGGGCAATGGCTGGAGGCTTTACAGGAAGGGATATGTGGACTAGGTTCCTGATGGGTGATTAGGAGTTGGTGGCCAGGGGATCAAGAAGAGAAAGGGACTCCAAGCATGGGGCAGCATGCAGTACAAATGCAGTCTCGGGCTCTGGATGATGCTTGGTCAGGAAAACCTCTTTGGGGTGAATGTAGTCCCATGCCTCACTATCCCCAACTGTCCCTCCAAGCTGGGTGCTGGTACCTCTGGCTGACCAGCCTTCCCTACAG
Seq C2 exon
GTGGTGGAATTACAGCAAACCCTGGCTCAAAAAGACCAGGTCCTGGGCAAGCTTGAGCACAGTCTGCGACTCATGGAGGAGGCATCCTTTGATGGTACTTTCCTGTGGAAGATCACCAATGTCACCAAGCGGTGCCACGAGTCAGTGTGTGGCCGGACTGTCAGCCTCTTCTCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026875:ENSMUST00000113064:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.073 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0091721=MATH=PU(15.5=36.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAGCACTTGGTGAAGGAGAA
R:
AGAGAAGAGGCTGACAGTCCG
Band lengths:
346-1627
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