MmuINT0164496 @ mm10
Intron Retention
Gene
ENSMUSG00000021277 | Traf3
Description
TNF receptor-associated factor 3 [Source:MGI Symbol;Acc:MGI:108041]
Coordinates
chr12:111251130-111252756:+
Coord C1 exon
chr12:111251130-111251204
Coord A exon
chr12:111251205-111252663
Coord C2 exon
chr12:111252664-111252756
Length
1459 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGT
5' ss Score
8.94
3' ss Seq
CCCCACTGTTGCTCTTGCAGGGT
3' ss Score
10.36
Exon sequences
Seq C1 exon
TTGAGTGCACACTTGTCCGAGTGTGTCAATGCCCCCAGCACCTGTAGTTTTAAGCGCTATGGCTGCGTTTTTCAG
Seq A exon
GTCAGTATCCAACATTTGTCCTTCCCAGTTACTGACATCTGCCATTGAAGCAAGTTCTCATAATATTTCAGCATTTGAGTTCTCGCTCTTTTAGTCTTCCTCATGAAATCATAACACCTGCTGCATGAGTGCAAAAGGCCACATGCGTGCAGCTGGTGCGGGGCTCACTTGTCAGGCCAGGGTGTTCTAAGACTCAGGCGAACAGCGTGGGTGCCCTGCTGACAGCGCCTGCGACAGTAAGAACCAGCGCAGTGACACCTGCTGGAGTCTGTGGCTGCTTTAACTGTATCATTACCAAGTATCAGTGACTGTAAACTAGATGGAGCTTTGACATCATTTGTCAGACCTTAGTGAAAGAGAATCACACATGGGTGTCCATAATGCTTTGCTTACACGTGTGTGCTGACCCTGACCCCTGCCAGGGGTGGATTTGACTGAGCAAGTCTGCAGAAAGCCTGCTTCTCGGGAAATGGCGTTATCCTCACAAACCTGTATCTGGTTTTCTATTTTTTTTTAATTGTACCTGAGAATTTCTAGGGAGTCAAGATTGAGTTTTTATTCAAATATATATATCCTAATATTTATCTACCAAAAGGCAAAATACGTCACACAGAAAGTATTGTATGTTTAGTTTTATGTATCGACGGTGTGTTGTTATGGAGTCGGTACAGAAACAGTGAACCTCACTGTCGTATCTTTTACTGAGGAGACGCAGAGAGTGAGCGTGGTGAGGTCCTCCCTTGCTGATGTTAGTCCAGGAGGCGCCTGCACCTCCCTGTTGTGTTGTGCGTGGTTCCATCCATCCTGTGTGTGTGCGCGTATGTATGCTGATGCGGAGCCGCGCTCAGATCAGCATAGATAGAGACAGACTATGTACAGAGTATGTGTTTTGGAGATCATGAAAACGCTTTCTCTGATTTCTTAATTTTCTGGTATCAAAACAAATTATATTCTCGTTCTAATTGTTTCCTTGAATATGCAAAGTACTACTTAATGTGCTTGCTCTTGGCTTGAATGGTCTGCATCTTATGTACTCTGTAGATTATTTATGTTTTGTATGTAAATTTCTCAGCACACTCAGCCTGCTGAGGCGGTGCCTTTTTGGTTACAGTGCTGTATCATAGCTCACTGGACCGCTGTAGCAGCAACTGGCTGCAGCTTCAGGTTCCAGAACATTCTCTTTGTATATCTTCATGAAAATGATGTGTAAAGGAACACGTTAGGTTTCAGATTTAATTCCGTGGTTTTGTAAGTGTGAAGCAAGGTGAGAAGCGTGAGCTTGAGGTCAGCTCTTGGTGAGCTCCCCGCACTGCAGCCCAGGAAGGCCTTGGGTGAGGGCCCTGGGATCCCTGCACATGCACAAACCCTTCCTGTGTGGCTCCGTCTAGAGCTGTGTGCTAGGTTTCCTGTTCTTTGAGTGGCGTGACTGGTTTAGAGTCCCCCACTGTTGCTCTTGCAG
Seq C2 exon
GGTACAAACCAGCAGATCAAGGCCCATGAGGCCAGCTCCGCGGTACAGCACGTGAACCTGCTGAAGGAGTGGAGCAACTCCCTGGAGAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021277:ENSMUST00000021706:8
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=0.052
Domain overlap (PFAM):
C1:
PF101744=Cast=PU(0.7=4.0)
A:
NA
C2:
PF101744=Cast=FE(19.6=100),PF0205011=FliJ=PU(13.3=58.1),PF0149614=V_ATPase_I=PU(4.5=25.8)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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