MmuINT0164491 @ mm9
Intron Retention
Gene
ENSMUSG00000021277 | Traf3
Description
TNF receptor-associated factor 3 [Source:MGI Symbol;Acc:MGI:108041]
Coordinates
chr12:112475773-112477291:+
Coord C1 exon
chr12:112475773-112476031
Coord A exon
chr12:112476032-112477239
Coord C2 exon
chr12:112477240-112477291
Length
1208 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGT
5' ss Score
7.07
3' ss Seq
ACTTACTCTGCTTCCTTCAGCTC
3' ss Score
8.19
Exon sequences
Seq C1 exon
AATTTCAGTTTCCTAAGATGGAGTCAAGCAAAAAGATGGATGCTGCTGGCACACTGCAGCCTAACCCACCCCTAAAGCTGCAGCCTGATCGCGGCGCAGGGTCCGTGCTCGTGCCGGAGCAAGGAGGCTACAAGGAGAAGTTTGTGAAGACGGTGGAAGACAAGTACAAGTGCGAGAAGTGCCGCCTGGTGCTGTGCAACCCGAAGCAGACGGAGTGTGGCCACCGGTTCTGCGAGAGCTGCATGGCCGCCCTGCTGAG
Seq A exon
GTGGGTGCCCTCCAGGGCTCAACCCCCACTCACCTGCTTCTTCCAAGACCTCCAGCGTGGGGGGCCTTTAGAGCAACTCAGGCACATCTCATGCTTGAGTGCCTGAGACCTCCATACCTTGCCCTGCCTGCCTCACATCCCACTTGCCCAGGCCTCTCCGCCCACAAAGCTTCTGTGCCTCCCATCTGCCTTGCTGTACTCTGTGCAAGAAGCTTATGTTTTATGGTGGTCATGTCAAATGATCCTAAGTCCTTAAAATTGAAGAGTGCCCTGGGCCAGGAGAGAGGAAGGTCAGGGTCACATGCAGAACAGAGCATGTGGCAAGGCTGCATGCTTGCCTGGGGGATCCACAGAGATCTGGGGTACCAAGACTCTAGAAGCTCATGAGTCTAGTAATTGCTATGGTAAAGTCACAAGGGCAAGTTGGGATTTGGAGGACAGAGTTGAGTCAGCTGGGAAGAGCATCATCGTGCAGCTTTTTATATTTGCCAGGCACTGTGCTTGACACTCAGACCACTGCAAGACACACTGTGCCGTCAGTGCCCTCAGGACACATTAGCTTCAGAAGGCCACAGAGTTTTTCTCATCTGGTCACTCACACCTGGGTGCCTGAGACCGAGGCCGAGCCCAGTAGCCAGGCTCCTGTGCGTCCCACACCCTCAGCACATCCATTCACGTGTCCCACACAGGCCACTTGGTTTTGCTGAGAGTGAAAGGACCCAGGTTGAAATTGCTGATGACACAATAGGTTCAGCACCCAATTTGCATGGAAGAGGACCTGGAAACCACCTGGGCTCAGGAGAGGCCTGTAGTGGGGTTTCCTGGAGGATAGATGCAGCTCCCCTGTGCAGGTGAGTTTGTAGATAGCCCAAGACCAGAGCATCAGAAGGACTTCAGTATTTGTGGGTGCACCTTCCAGAGGCTCCCCTCCGAGAACCACTGTGGCACCAAATGTCACTCTCGTGGTCATTAACTCATAGTCATTAAGTCTTCCCAATGGGACTGAGCTACTGAATGTAGTCGCATGTTTTAAAGTTCAGTGCTTTTTCTCCTGTGGATTACTATTTAAACTCAGTTTTCAACAGCCCTGGAGCCCTGCCTGTTGCTGCAAGCTCGAGCAGGCCTGACTACAAAGGAAAGCATTCTGTGCTGTGAGCCTGGGGGAGGGGCTGACTCCTGCTCTGACATACTTACTCTGCTTCCTTCAG
Seq C2 exon
CTCCTCCAGTCCAAAATGCACAGCGTGCCAAGAAAGCATCATCAAAGACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021277-Traf3:NM_011632:3
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=0.325 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF127342=CYSTM=WD(100=82.7),PF0009720=zf-C3HC4=PU(77.8=43.2)
A:
NA
C2:
PF0009720=zf-C3HC4=PD(23.1=50.0)
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:
AATTTCAGTTTCCTAAGATGGAGTCA
R:
TTGTCTTTGATGATGCTTTCTTGGC
Band lengths:
310-1518
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: