MmuINT1033519 @ mm10
Intron Retention
Gene
ENSMUSG00000033327 | Tnxb
Description
tenascin XB [Source:MGI Symbol;Acc:MGI:1932137]
Coordinates
chr17:34714590-34715991:+
Coord C1 exon
chr17:34714590-34714871
Coord A exon
chr17:34714872-34715682
Coord C2 exon
chr17:34715683-34715991
Length
811 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CTCTGGTTTCTCCCATGCAGCCT
3' ss Score
8.81
Exon sequences
Seq C1 exon
CTCCCGTGGAGAAGACACCACAGCCCCGCCTCGGTGAACTGTCAGTGACAGAGGAGACCTCTGACTCCATGCACCTCTCTTGGTCTGTGGCCCAGGGTCCCTTTGACTCCTTCCTGGTCCAGTACAAGGACAGGGATGGGCAGCTCCAGACGGTGTCCTTGGCTGCAGACCAGCGAGAGGTCACCATAGAGGGTCTACAGCCAGGCAGGAAATACAAGTTCCTGCTCTATGGGCTCACTGGAGGGAAGCGCCTGGGACCCATCTCTGCCTTGGGAGTGACAG
Seq A exon
GTGAGGCTGTCCTGCCTGGTCTGAAGACCACGGAACTGACTGGAGTGGACAGGAGGGAGGGGGAGAGGCCTGGCCAGAGCCAGAGAAGGGAGAGTTTGTGCCCACCCCACCCCAGGTGTTAATCAGTCATTTGAAAGAACAGGAGAAGCCAGGCCAAGCAGGAAGGAAAGGCCTTGAGGATTCCCTGCTTTCTCTCTCAAGCCCAGCCATCCCCTCAAGGGCTGCTTCCCACCGCCCTGTTGGAGCAACTTTAGCTCCTCACAATGTAGGCTTGCCACATCAGCACACACCTCCCATGCTAGTGAGCCAGAGATGTTTTCTGAAAGGGAAAACCACCGAGAAAGCCAGTGGGCAGAGGCCACTGACACCCACCTCAGAAGGGCACATGGCTAGTGTGTCTTGCCAGGCACGTACACCAGTCGGTGCCACCTTCAGCTGCTTTCAAAAGGCTCTATGGGTGGGGCCACTGCTGAGGCGGGCTTGATGTGCCCAAGGCTGGGAGAGCAGAAGTGAGTCTCAGGTCCAGATACATTGAGAGGTAGAGGAAAGACCAACAGCTTCCCAGACAGGAGACAGACCCTGGGGCTCTTCTCAGAGAGGTCTCCTGGGGCACACTGCTGAAATGAGTTCAAGAACTGGAAGGTTCTAGATGATCTCCTCCCTCCCTTTCCTCTCGTGGGCTGCTCTGCCAGGACTATGAGGTGTCACCAGTCTCAAGCCAGCCTTGCCAGCTTTCCTCTGAAGGGCAAGATGGGAAGGGAGGGCCCCATGGCACCCCCGCGTAGATTCTGCTCTGGTTTCTCCCATGCAG
Seq C2 exon
CCTCAGAAGTTGACATATCAGCCCCAGACCACACTGAGCCCCCTCATGCTCCCGGCCTGGGGACGCTGGCAGTGACAGAGGCAACCCCAGACTCCCTGCGACTCTCCTGGGCTGTGGCTCGTGGCCCCTTTGACTCCTTTGTGGTCCAGTACCAGGACACAGAGAATGAAACCCAGGCCCTGCTTGTTGATGGAGACCAGGACAAAGTCCTCATCTCAGGCCTGGAACCCAAAACTTCCTACAAGTTCTTCCTCTATGGCCTCCGTGAAGGGACACGCCACGGACCTGTGTCTGTAGAGGGCACCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000033327:ENSMUST00000087399:28
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.211 A=NA C2=0.385
Domain overlap (PFAM):
C1:
PF0004116=fn3=WD(100=86.3)
A:
NA
C2:
PF0004116=fn3=WD(100=77.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGCGAGAGGTCACCATAGA
R:
AAGTTTTGGGTTCCAGGCCTG
Band lengths:
350-1161
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