MmuINT0163709 @ mm9
Intron Retention
Gene
ENSMUSG00000033327 | Tnxb
Description
tenascin XB [Source:MGI Symbol;Acc:MGI:1932137]
Coordinates
chr17:34820229-34822156:+
Coord C1 exon
chr17:34820229-34820522
Coord A exon
chr17:34820523-34821865
Coord C2 exon
chr17:34821866-34822156
Length
1343 bp
Sequences
Splice sites
5' ss Seq
TCTGTGAGT
5' ss Score
7
3' ss Seq
TCTCTGCTCCCTTTTCCTAGTGA
3' ss Score
9.04
Exon sequences
Seq C1 exon
ACAGGGCTCAGGAACAGCCTGGGAAGCCATCAGTCCAGCCACGCCTGGGTGAACTGACAGTGACAGGCCTGACCTCTGATTCCCTGCTCCTGCACTGGACTGTCCCAGAGGGGGAGTTTGACTCCTTCCTGATCCAGTACAAGGACAAAGACGGGCCCCAGGCGATATCCGTGGAGGGACCCCAGCGTTCTACACCCATCTCAGGCTTGGAACCAGGACGCAAGTACAAATTTATCCTGTATGGACTCATCGGCAAGAAGAGGCATGGCCCACTTATGGCTGAAGCCAAGATCT
Seq A exon
GTGAGTGACAGCAGGCACCCCTGCCCCACACTCTGTACAGTGCTGAAGCAGGGTGCCCCAGGGAGATTGTCTGTGGCCCGTGGCAGCTGTGTTAAATCCCGAAGGGAAAGCAGTGGGCGGCTCAGAGGCGAGGGTGTAGGTGAGGCAGAGCAGTGGTCCCCAGAGAATGCACAGCTCTCTTTTGGCTAGAGAGCAGAACGACGTGTGGAGCACTGAAAGGCCCAGTCTCGGGGTTCTGTGTGAGCTGGCCTCGACCTGATTTGGGAATCCCAAGGAACCTCTGAGAGCCTTTAAGTGCAATTGTGAAATTATGACCTCTAAAATAGCACACTGTCTGCTGCAGGGGCATGCTAGGGAAGAGAGCCAACAGCTGGTGAGACTGGTGGCTGATGCTGGCCTGGAGTATGGCAGTGGGAGGAGAGCCTCGAAGTCCAGGGTAGCCCAACGTCCCCAGGCCAGCCACTTCTGTCCCCTAAGCAGCAGCAGGTGGGGAACAATGGAGGCTGAGACACTCGGGGAAGTATGTTCTGTGTATTTCCGGAGCCAGTGAGCTCAGAGCTGTGCTCAGAGCATTCTTGAACTAACACAGGTTCTTACAGCAGCTGTGAGTGGCACTGCTATGTCACAGGTGAGAAGAGCTGAGGGACAGACAGAAGGTGCCTGACAGAGGTTGGCAGACCTTGGGGTTACACTGAGTCCCGGTAGCTGTGGGGAGCATCTGAGAGAAGCAGAGGTAGAGAAACAGCAGGGTAGTGTCCCAGATGTTAGGAAACAGGGTGTGGCCAGTGGTGAGTCAGAGTCCTCGGGAGTGGGTTAGGACTCTCAAGTGTTCAGAGGACTTAGTAATGGCAGGCTACCCGGAGCTGCCTGGTGGAGGTTATGGGGTACTCTGGGAACTGTGCCAAGATGGGAGACGGAGACAGATACACTGGGAAAGTGGGTGGAGCCAGGGACAGAGCAGAGGAGGTGTGTGGGTACCCCAAAGAGGAGAACCCAGTGTGGGGCTCTTTCCCACATTGACACACTCCAAGGATGTTCTGTCTTGGGAGAGAAACTGGCTAGAAGTTAAGCTGGAAGCGGGAGGCTGCCTCCGGGAGATTTCCCTGGCTGCATATGTGGAAAGGTTGGAGTGTGTGTGTCAGGGATACCCCTCCCCTTCTGGAGCCTGCTTCCCTTGGCTGGAAGTAGCCACTGCAACAGTACAGTGCTGGGCCATTTAGAAGGTATCACTGCTTCCTGTAACCAGGCACAGCCCCTGATAGAGCTCACAGCCCAGCAGAGCACACCCGCTGCACAGGACGTCCTTTCTCTCGTGACCCCCGTTCTCTGCTCCCTTTTCCTAG
Seq C2 exon
TGATTCAGAGTGACCCTGACCCAGGATCCCCACCCCGCCTGGGAGAGCTATGGGTGACAGACCCCACTCCACACTCATTGCACCTCTCCTGGACTGTTCTCGGAGGCCAGTTCGACTCCTTCGTGGTCCAGTACAGAGACAAGGAAGGCCAGCCCCGTGTGGTACCTGTGGAGGGGCCTGATCGCTCAGTGGTGATCTCCCCACTGGACCCCAATCGCAAGTACAGGTTCACTCTGTTTGGGATTGCCAATAAGAAGCGGTACGGGCCCCTTACTGCTGATGGCACTACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000033327-Tnxb:NM_031176:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.404 A=NA C2=0.398
Domain overlap (PFAM):
C1:
PF0004116=fn3=WD(100=78.8)
A:
NA
C2:
PF0004116=fn3=WD(100=84.7)
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:
GAACTGACAGTGACAGGCCTG
R:
CGAGAACAGTCCAGGAGAGGT
Band lengths:
346-1689
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: