MmuINT0163692 @ mm9
Intron Retention
Gene
ENSMUSG00000033327 | Tnxb
Description
tenascin XB [Source:MGI Symbol;Acc:MGI:1932137]
Coordinates
chr17:34851535-34852936:+
Coord C1 exon
chr17:34851535-34851816
Coord A exon
chr17:34851817-34852627
Coord C2 exon
chr17:34852628-34852936
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-Tnxb:NM_031176:28
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
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
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: