MmuINT0164475 @ mm9
Intron Retention
Gene
ENSMUSG00000026875 | Traf1
Description
TNF receptor-associated factor 1 [Source:MGI Symbol;Acc:MGI:101836]
Coordinates
chr2:34800918-34802379:-
Coord C1 exon
chr2:34802202-34802379
Coord A exon
chr2:34801067-34802201
Coord C2 exon
chr2:34800918-34801066
Length
1135 bp
Sequences
Splice sites
5' ss Seq
CAGGTGACT
5' ss Score
6.6
3' ss Seq
ACACTGGCTTCACCTTGCAGCTT
3' ss Score
8.98
Exon sequences
Seq C1 exon
GTGGTGGAATTACAGCAAACCCTGGCTCAAAAAGACCAGGTCCTGGGCAAGCTTGAGCACAGTCTGCGACTCATGGAGGAGGCATCCTTTGATGGTACTTTCCTGTGGAAGATCACCAATGTCACCAAGCGGTGCCACGAGTCAGTGTGTGGCCGGACTGTCAGCCTCTTCTCTCCAG
Seq A exon
GTGACTCCTCCTCGCGGCCACAGAGACTGGTAGGAGAGGGAAGGCATGGAGTGAAAACAGCCATGCTAGGTCAGCTGGGGTCCCTGACAGTGATTAGAGGGAGACAGACACCGTGCTCTGACCCATGGCTCTCTCCTCCTGAATGTCACCTGCACTCTGTAAAGAGGAACAAAAGTCAGGTTCTTCTTGAGGCTGTGGGATGAGAAGGGGCCTTGGGAGCCTACGTTCAATGGTGAGAGTGGAGCAAATGAGGAACTCTCCAGGAAGCAATCTTCAGTAGGAGGCAGAGGAGCGAGTCAGGCACTGGGGAGCTGTGTGCACGATGGGCAAACCATGGCAACGGTAAATGGGTGGCTCTTTGTTTCTGGGTCCCTTGCTCAAAACAATGATTTTACAGAGTAGTGACTTGGTAGGACCTTGCCATCCCTGAATGTGACCTTTGAGAGCCTTGCCAAGTGCTTGTCCTCCCAGCCTCATTTTACATAAAAATAAACTGAAGCCAAAGAGGTGGGGTCCCCAGCAGGGGCTGCTTAGAGCTGTGCAGAGCCCTTCCCAAGAATGTGCCATCAGGGAAAGAGCTCCATAGGACCCCAGGCTTGGTCACTGGCGATGTCTTGCCTCTTGGAGCCATTCCTAAGGATTTTTAGCAAAACCAAAAAGTACCCTTCTCATACCAGCCTCCAGGGAGGGCCCAACCTTTGGGTAACAGAGAAGACTCAATGCCAAGATTTGGTAGGCCTGGGCCTTAACCCGAATTCTGTTCTGGGTCATAAAACAATACCCAGCCACTTCCTCAGTCTCTAGCTATTTGATGGTTCGTTAAAATGGTAGCTCCCAAGTGTAACTGGGAGGCAAGCCTCAAGGCACCCCATGGAAGAATTAAAACCACAAATGCTAGCTCACCCCCACTGCTGAGTCAGCACTGTCAAATATGGGGCCTTCCCTGTGATCAGAAGGGCAGGTGCCAGCCCCAGGGCTAGGCAATTAGAGCATGACCTACCTCAGCACTTTCCTAGAGAAGAGGGCTGGGCCCCAAACCCCGATATCCTCAGGGTTCCTGCTGAACCCCACCCCCTCATCCTCACTGCCCAGTGCCGCCCTGCTGCCCTGTACTGACACTGGCTTCACCTTGCAG
Seq C2 exon
CTTTCTACACTGCCAAGTATGGTTACAAGTTGTGCCTGCGCTTGTACCTGAACGGGGATGGCTCAGGCAAGAAGACCCACCTGTCCCTCTTCATCGTGATCATGAGAGGAGAATACGATGCTCTCCTGCCCTGGCCTTTCAGGAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026875-Traf1:NM_009421:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0091721=MATH=PU(15.5=36.7)
A:
NA
C2:
PF0091721=MATH=FE(34.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGTGGAATTACAGCAAACCCT
R:
CTGAAAGGCCAGGGCAGGAG
Band lengths:
319-1454
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: