MmuINT0163678 @ mm10
Intron Retention
Gene
ENSMUSG00000033327 | Tnxb
Description
tenascin XB [Source:MGI Symbol;Acc:MGI:1932137]
Coordinates
chr17:34694166-34695705:+
Coord C1 exon
chr17:34694166-34694456
Coord A exon
chr17:34694457-34695384
Coord C2 exon
chr17:34695385-34695705
Length
928 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
TCCATGTCTCTCTGAACCAGACC
3' ss Score
7.69
Exon sequences
Seq C1 exon
AGCCCACGAATGCTGCGGACCACACAAAATCTCGACTGGGAGAGGAACTGCGGGTGACTGGTGTGACTCAAAACTCCGTGGACCTCTCCTGGACAGTCTCCGAGGGCCAGTTTGACTCCTTTGTGGTCCAGTACAAGGACAGGGATGGGCAGTCCCAGGTGGTGCCTGTGGACGGAAGCCATAGAGAGGTTAGAGTCTCTGGTCTAGACCCAGGTCGCAGGTATAAGCTGCTACTCTACGGCCTCCGAGACAGCAAGCGTGTGGGTCCCCTTTCAGTCATTGCTGTGACCG
Seq A exon
GTGAGTGTGACAGGCCACCTAACTGGACCACTTCTTTTGGGGGAGGCTTTATCGAGGCAACATTTACATATAGTACCAAATGGGCTTGGCAAATGTATAAGTCACAGAACGATGGCTCAGGGAGGCACAAGAAAGTTCCCTCACCCCTGTATCCAGGATCAGTAGACCAAAGAAACAGATAAGAAGAAAAGAGTGATTTATTCACTGTGGCCATGTTGGGAAGAGGAGCAAAGAGTGAACCCCTCAAGTCCATCTTTGAAGTCTTGGCAGGCATGAGGTTTAGTTTTAAATGGATATACATGTATATATGTATATACATATATATATTATGCACTCACACATAATATACATATACATATATACACACATATATGCACACGCATAACATACACAATACACATATATGCATATATGTGTACATATACATATATATGTAAGCAACCCCTGGCAAGAGGCGGTTCCACCCATCAGCTCCGCTCTCCTGCACGGTGGGCTGATGAATTGTGAAATCTCTTTCCTGAAGACATGTTTCCCCTCTGACTGTACCAAGCTTTATCCCTCCCCCCATGAGATTCCTGCGTAACTTGGCATGGACTGGGTGGAGTTTGTTTCAATGGTCTGACAGTCCATTGGATGGGCACAAGGTTCCATTGGGATGGCTTCATTCCTGCTGGGAGCTTTCGAGGTCCTCTTTGCCCTCACCTCCCCAGGCCCTAGCAGACACTGAGGTGCCTTCTGTCCTTCAGGGTTTGCCTGCCTCTGCATCTCATTTTGGAGCATCTTCTACTTCAAACGCTTTTGCCAACCCTCCGGCCTCTGCCTCCCTCCCTTCTTCCCCACACCCTTTCTCCCTCCTATCCCCCACCACTCTTCAACATATCAATTCTGCAACAGAGCAGCCATTTCTCTCCATGTCTCTCTGAACCAG
Seq C2 exon
ACCCCAGAGAAACAACAGAAGCTTGGACAGAGGTCCCCACAACTTCAACTCCTGCAGCTGTGCCCCGCCTCGGGGAGCTGAGAGTGGAGGAAGCCACGCCTCACAGCCTGCATCTCTCCTGGGTGGTGACTGAGGGAGAATTTAACTCCTTCGAGGTCCAGTACACTGACAGAGATGGGCAACTCAGAGTGGCCAGTACAGAGGGTGACCAGACTGACATTACCCTTACTGGCCTGGAATCGAACCACAGATACCTGATAACCCTATATGGCTTCCATGATGGGCAGCCTGTAGGCTCTGCTCAAATTGAGGCCCTGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000033327:ENSMUST00000087399:15
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=0.519
Domain overlap (PFAM):
C1:
PF0004116=fn3=WD(100=80.6)
A:
NA
C2:
PF0004116=fn3=WD(100=73.1)
Main Inclusion Isoform:
NA
Other Inclusion 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:
TGTGGGTCCCCTTTCAGTCAT
R:
GCCTCAATTTGAGCAGAGCCT
Band lengths:
345-1273
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