MmuINT0163705 @ mm9
Intron Retention
Gene
ENSMUSG00000033327 | Tnxb
Description
tenascin XB [Source:MGI Symbol;Acc:MGI:1932137]
Coordinates
chr17:34815517-34816064:+
Coord C1 exon
chr17:34815517-34815673
Coord A exon
chr17:34815674-34815800
Coord C2 exon
chr17:34815801-34816064
Length
127 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGA
5' ss Score
3.73
3' ss Seq
CTTCTGTCTGATTCCACTAGTGA
3' ss Score
5.77
Exon sequences
Seq C1 exon
ACCGAGGGGGTGAGTCCACCATTCACAGCTCGGGTGCCCAGCTCTGCCTCAGCCTATGACCAGCGAGGACTGGCGCCTGGACAGGACTACCAGGTCACTGTTCGTGCTCTACGAGGGACCAGCTGGGGTCCTCCTGCCTCTAAGACCATCACTACCA
Seq A exon
GTGAGAGCTGGGGCTGGAGGGGCAAGATTTCTGGATTTGACAGGCAGCTGGGAGTCAGCTTGGGGTGGGGACTATACCAGAGCAAAGAGGACTCACTACTGAGCCCTCTTCTGTCTGATTCCACTAG
Seq C2 exon
TGATCGATGGTCCTCAGGACCTCCGGGTGGTAGCTGTGACCCCGACCACACTGGATCTTAGCTGGCTGCGCCCCCAGGCTGAGGTGGACCGATTTGTGGTGTCCTATGTCAGTGCTGGAAACCAAAGGGTGCGACTGGAAGTTCCCCCTGAGGCAGACAGGACTCAGCTAACCGATCTGATGCCTGGTGTGGAGTATGTGGTGACTGTCACTGCAGAAAGAGGCCATGCAGTCAGCTACCCAGCTTCTATCAGGGCGAATACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000033327-Tnxb:NM_031176:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.396 A=NA C2=0.296
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(54.2=84.9)
A:
NA
C2:
PF0004116=fn3=WD(100=89.9)
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:
GAGTCCACCATTCACAGCTCG
R:
CCACAAATCGGTCCACCTCAG
Band lengths:
245-372
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: