MmuINT1033523 @ mm10
Intron Retention
Gene
ENSMUSG00000033327 | Tnxb
Description
tenascin XB [Source:MGI Symbol;Acc:MGI:1932137]
Coordinates
chr17:34717666-34718029:+
Coord C1 exon
chr17:34717666-34717809
Coord A exon
chr17:34717810-34717898
Coord C2 exon
chr17:34717899-34718029
Length
89 bp
Sequences
Splice sites
5' ss Seq
CAGGTATAG
5' ss Score
8.73
3' ss Seq
TTCCATCCTTCTCCTTCCAGGGT
3' ss Score
11.67
Exon sequences
Seq C1 exon
CCCCACCCCTTCAGGCCTCAGCACCTGGCAGCGCTGTGGACTACCCACTGACTGACCTGGCACTCGACACCAATTACACAGCCACCGTGCGTGGTCTCCGGGGTCCTAACTTCACCTCCCCAGCCAGCATAACCTTCACCACAG
Seq A exon
GTATAGCCACGGCTGCGTGTGGGTCACAGGAGATTGAGGAGAATAGACATGGGCCTCATTTTTGTCTCTTTCCATCCTTCTCCTTCCAG
Seq C2 exon
GGTTAAAGCCCCCCCAGGACTTGGAGGCCAAGGAAGTGACTCCTCGCACGGCCCTGCTCACTTGGACTGAGCCTGAAGTCCCACCCACAGGCTACCTGCTCAGCTTTGACACCCCTGGAGGACAGATTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000033327:ENSMUST00000087399:34
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.367 A=NA C2=0.568
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(51.9=85.7)
A:
NA
C2:
PF0004116=fn3=PU(51.9=93.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTCCGGGGTCCTAACTTCAC
R:
CTGAATCTGTCCTCCAGGGGT
Band lengths:
181-270
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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