MmuINT0163697 @ mm9
Intron Retention
Gene
ENSMUSG00000033327 | Tnxb
Description
tenascin XB [Source:MGI Symbol;Acc:MGI:1932137]
Coordinates
chr17:34854068-34854505:+
Coord C1 exon
chr17:34854068-34854211
Coord A exon
chr17:34854212-34854385
Coord C2 exon
chr17:34854386-34854505
Length
174 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
AGCTCCCTGTTCTTGCCCAGTGC
3' ss Score
5.9
Exon sequences
Seq C1 exon
GAGAGCCACAAAGTGTGCAGGTGGATGGCCGGACCCAGACCCAGATCCTCCAAGGGCTGATTCCAGACACTCGCTATGAGGTGACTGTGGTCTCCGTCCGTGGCTTTGAGGAAAGCGAGCCTCTCACAGGCTTCCTCACCACAG
Seq A exon
GTAAGAGAGACAGCCCCCAGCACGAGGAGAGGTAGAGAAAGAGAAAGCAAAAAAGGGGGTAAGGGTGTAATGGGGGCAGAGGATCCCCGGGTTCCAACCTCCAATGAGGGAGGAGCCAGCAGGGTCGGGAGAGTTAGGGCTAGGGATGCCTCTGAGCTCCCTGTTCTTGCCCAG
Seq C2 exon
TGCCTGATGGTCCCACCCAGCTACGGGCATTGAACTTGACTGACGGATCTGCCCTTCTACACTGGAAACCCCCCCACAAACCAGTGGACAAATATGACGTCGAGGTCGAATCCCCTGGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000033327-Tnxb:NM_031176:32
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.490 A=NA C2=0.537
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(50.0=81.6)
A:
NA
C2:
PF0004116=fn3=PU(46.9=92.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAAAGTGTGCAGGTGGATGG
R:
ACCTCGACGTCATATTTGTCCAC
Band lengths:
243-417
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: