MmuINT0164478 @ mm9
Intron Retention
Gene
ENSMUSG00000026942 | Traf2
Description
TNF receptor-associated factor 2 [Source:MGI Symbol;Acc:MGI:101835]
Coordinates
chr2:25392591-25394604:-
Coord C1 exon
chr2:25394386-25394604
Coord A exon
chr2:25392670-25394385
Coord C2 exon
chr2:25392591-25392669
Length
1716 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGC
5' ss Score
6.46
3' ss Seq
GTTTCCTGTGTTCCCACCAGCTC
3' ss Score
8.69
Exon sequences
Seq C1 exon
GGCTTTGTGGTGTGTGGGGGTTGTAACTCACATGGCTGCAGCCAGTGTGACTTCCCCTGGCTCCCTAGAACTGCTACAGCCTGGCTTCTCCAAGACCCTCCTGGGGACCAGGTTAGAAGCCAAGTACCTCTGTTCAGCCTGCAAAAACATCCTGCGGAGGCCTTTCCAGGCCCAGTGTGGGCACCGCTACTGCTCCTTCTGCCTGACCAGCATCCTCAG
Seq A exon
GTGTGCATCCATTCTCTCCAGGTGGGTGGGGCAGCTGGGTGGCTCTGAAGTCAGATTGCACACTGTCCTGTAGAGTGGATGCCAGTACAAATTCTTCATGGATTCTGGAGGCTTAGCTCAAATCAAGAATGTAAAATTTATTGGGCTGGAGAGATGCCTCAGCGGTTAGGAACACTGACTCCAGAGGTTCTGAGTTCAATTCCCAGCAATTACATGGTGGCTTACAACCATCTGTAAAGTGATCAGATGCCTTCTTCTGGTGTGTCTGAAGACAGCTACAGTGTACTTATATACGTAAAATAAATAAATTATTCTTTTTAAAAAATATAAAAAACATTGATTGTTTCTGGGTGAGGTGAAACATCCCTTAATTTCAGCACTCAGGAAGCGGAAGCAGGAGACCTCTGAGTTCAAGGTCATCCTGGCCTACAACTGAGTTCTAGGGCTACCTAAAAAAAGAAAGAATGGAGAACTGATCATAGCAATGTATGGTAGTATATTCCCCCCCCCCCCCCCCCCCCGTGTGTGTGTCTGGTGTCTCTGTCTCTGTCTCTCTCTAAATTTTTGTTCCCAACTCTTGGGAGGTAGAGACTGGAAGATCAGAAGTTCAGGTCATCCTTGGCTATGTAGAAAGTTCAAAACCAACCTCAGCTCTGTCTCAAAAAATAAGACATCAGAGAACTGGCTCAGTGCATGAAAGCACTTGCTGCAGGTTTGACAGGCTGAGTGTGAGCCCTGTGATCCACACTTAATGAAGGAGAGAGCTGACTTGTCCTCTGACCTCCATCAGCACACCTTGGTACATGTTTATACACACACAGTAAATTTTAAAAATGTAACTAAAAAATTAAAGAGGCAGGGTAGATAAAGTGCTTCCTATGAAATCAAGGCTTGAGTTTGGTCCTCTCCACCCATGTAAAAACCTGGCATGGAAATATGCACTTGAAATCACATCAAATGCCTGGACATAGAGTCAGGAGGGGTCTTGGGGCTCATTGTTTAGCCTAATCTGCATGTTGTAGGTCCCGGTAAGAGTTCTATCTGAAAAAGGTAGATGGCACCTAAGGAGCAGTACCTGATATGTGACCTTGAGCTTTCTCAGATACATGTATATGCACCCATATTCATTTTCTCCCCCCCCCCCCACACACACATTGGCTATATATTGGAACACTATTTTTGGACATGTAGATTAAATATTGCATGTTGGTTTCACAGGCACTAGAAAGCTAGTGTGAGGATTATAGCTCCCTTAGGCTGCTCTGGGTGGGTAGATTGAATGTCACACGAGTGGGTGGCTGACATGTGTCACTGCTATAGTCTGAAAGGGCAGCAGCAGTGCACATGGAGAAATAAACACACCCACATTTTTCTACCATGTAGTTTGGAGGCCAGGGCCTACAGTCAAGGCTCAGTGACAAAGCACTTACCTGGCATTCATGAAGCTTTAGCTAGATCCCTGACATCACAAATTCAAAAAGAAAAAGGAGGAGATGGTTAGCCTTACAAGTTCAGGCCCCGATACCCTTTTCTATATTGAAGCTTCTCATTTGTGGGTTTTCATGATATTGTACAGTTGATATACTAGTTTGTTCAAAGATGAGAAAAACAAAGAATGAACAGTGTGGAGCCGGGTTGTGGGCTGAGCAGGCAGTGCTCAGAGATTCTCCAGAGCGGGCATTTGAGCGGACTTTGTGTTTCCTGTGTTCCCACCAG
Seq C2 exon
CTCTGGGCCCCAGAACTGTGCTGCCTGTGTCTATGAAGGCCTGTATGAAGAAGGCATTTCTATTTTAGAGAGTAGTTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026942-Traf2:NM_009422:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009720=zf-C3HC4=PU(74.4=46.0)
A:
NA
C2:
PF0009720=zf-C3HC4=PD(23.1=33.3)
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:
CTTTGTGGTGTGTGGGGGTTG
R:
AGAAATGCCTTCTTCATACAGGCC
Band lengths:
278-1994
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: