MmuINT0164493 @ mm10
Intron Retention
Gene
ENSMUSG00000021277 | Traf3
Description
TNF receptor-associated factor 3 [Source:MGI Symbol;Acc:MGI:108041]
Coordinates
chr12:111242443-111243538:+
Coord C1 exon
chr12:111242443-111242547
Coord A exon
chr12:111242548-111243370
Coord C2 exon
chr12:111243371-111243538
Length
823 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGC
5' ss Score
8.69
3' ss Seq
GACGTTGCTTTCTTCTACAGGTG
3' ss Score
12.27
Exon sequences
Seq C1 exon
GTGTTTAAGGATAATTGCTGCAAGAGAGAGATTCTGGCCCTTCAGGTCTACTGTCGGAATGAAGGCAGAGGTTGTGCGGAGCAGCTGACTCTGGGACATCTGCTG
Seq A exon
GTAAGCACCAAACAGCACCAGGGTGTCTCTGTTCAGAGGGCCACTGCCTCACCTCACCAGCTGCCTGCCTGCCAGGGAGATGTAGCATGTGTGCACCGTAGTGCTGTGTTTACCCTTTAAAGCAGCACCGTGCAGGGTATGGGTTTTTATTTTTCCAAGACACTTTAGAACTTTATCCCTACCCTGAAACGCCATAAAACTTAAGGATTTGGGTTGTTTTTTTTTTTTTTTTTTTTTTTTTTCCGAGACCGGGTTTCTCTGTGTAGCCCTGGCTGTCCTAGAACTCACTTCTTAGACCAGGCTGGCCTCAAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAATGACGTGCGCCACCACCACCTGGCTAAAACTTAAGGTTTTTTTATTTGTATACTTTATTTAGAATGGATGATTGAATTAGCATAAAGGGTTTGTGTGTCTGTGTGTCTCTCTGTGTGTATGTGTCTGTGTGTGTACACTTTTTGACATAGTTCAGGATGGCCTGGAACTCAGCATCCCCCTGTCTCAGCCTATTCTGCTAGGATTACAGGTCTGCATAGCCATATCTTGCTAGAATCGTTGTTTCCAGAGACCTGCCACCCCAGGTATGGGAACAGAGAGGCAGTCCATGATCCCTTGCTCTTGTGCTGAGGACACAGTGAGCCTATGTCTCTGCGCTTGCCTCTCTGTTGCCCAGAACTGTCCCAAGAGCAAGGTCACAGTGTTCTGCAGACCTCAGTACAAAGCAGGTACAGTCTGCCATTTCACACTTACATTTCTGCCAGCTAAGACGTTGCTTTCTTCTACAG
Seq C2 exon
GTGCACCTAAAAAATGAATGTCAGTTTGAGGAACTTCCCTGTCTGCGTGCCGACTGCAAAGAAAAAGTACTGAGAAAAGACTTGCGGGATCACGTGGAAAAGGCCTGTAAATACCGCGAGGCCACGTGCAGTCACTGCAAGAGCCAAGTGCCCATGATCAAACTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021277:ENSMUST00000021706:5
Average complexity
IR
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:
NO
A:
NA
C2:
PF0217613=zf-TRAF=PU(94.7=96.4)
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:
GTGTTTAAGGATAATTGCTGCAAGA
R:
TGCAGTTTGATCATGGGCACT
Band lengths:
272-1095
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