MmuINT0163497 @ mm9
Intron Retention
Gene
ENSMUSG00000015829 | Tnr
Description
tenascin R [Source:MGI Symbol;Acc:MGI:99516]
Coordinates
chr1:161842771-161844763:+
Coord C1 exon
chr1:161842771-161842922
Coord A exon
chr1:161842923-161844666
Coord C2 exon
chr1:161844667-161844763
Length
1744 bp
Sequences
Splice sites
5' ss Seq
ATTGTAAGT
5' ss Score
8.54
3' ss Seq
TTTTCTCTTTCTCTTCACAGGTA
3' ss Score
13.74
Exon sequences
Seq C1 exon
GGGGCCGGGTGTTCTCTCATCCTCAAGACTGTGCCCAGCATTTGATGAATGGAGACACTCTGAGTGGCGTTTACACCATCTTCCTCAATGGGGAGCTAAGCCACAAGCTGCAAGTGTACTGTGACATGACCACAGATGGGGGCGGCTGGATT
Seq A exon
GTAAGTATAAGCTGCAGGCGGATGTCTTCAGGCTTCTAGTATACCTGGCTGGGGACCTGGAGTTTACCATGTCGCCATCCTTCCAGATGTTCCCTTATCTAACCACTTCATTTGGATTTGTCTTGTCACTGCCTTCAAGACCCTCATTCAGTAGGCCACTCACAAACAGAGAAAGGAATAACTGTTTCATTCTGTTGCTAGGATAAACACCATGACCAAATGGGACATAGAGGAGAAAAGTGTTTGTTGGCTTATACTTCATAGTACATCACGGAGGAATGTCACAGCTAGAACTCAGAAACTAGGGCTGTGAGCGTGAAAGAAGGGTACTGGCTCACTCATTGGCTTATGCTCAGCTACTTTTCTTATATAGACCAGGCCCACCTCGCTTGGGATGATGCTATACTCACTGAACCCCACTCTCCCACTTCAGTTAAGACAATTCTTCGTAGACATGGCCACAGGCCAATCTATTGGAGGCAATTCTTCAGTTGAGGTTTCCTCTTCCAAGGTGACTCTGTGTTGGGTTAAATTAACAATTAAAAACTAACCAGGACTCATATGAAAGATGTAACGGCCTAGCTGTAAGATGAGACTGGCTCGCTTTGAGCTCCTGCAAACAGACAGGATGCAAGGTGTGCTGCGGAAAGGAAGGAGTGAGGCACATGGATCCTGCTTACCAGGGGCTGTAGCTAAAGTAAAGAGGAGAGGAGGAGGCCACTCTACAGAAGCACATTAGCTTCCCAGAGTGAGGCAGTTAGTAGCCTTGTCTTGGAGAGTCACATATAGTAGATTAGTTATGGGGTAGAATGTGGGTGGGCCTCTAGTTATGAGAGCTACTTGTGTTACATTCTGTTTTAGACCTCCCCCTAGTTCTTCCCTAGAACTGTCATAGCCTTCAGGAGGTAACAGTGGTAGGGAGAGAGACACTACTTGCTGATACCACCTCCTCTCATACATGATAGCTAGCTTACACAGAGCAGAAGAAATAAGCAGCCTGGAGATGCTAACCACTATGCCCATAAGCAACTTCCTGAAGCTGGCTCTAAACCAAGCAACAGGGGTTGAATCAGTGTGAATGAAACTCCGCCCTGCCCACCCTCCTAGCACTGCTCAGATACAGCACCAGAGCTTTCAGGTTCCAAAATGGGAAGGTTTTCTAGAGTTAAATGGTGACTGCACTCGTAATCCTCTCCGGAGACATTTTCTTTTATGTTTCTGACATATTTGTGCCTCCTTCTTAAAGCATAATTGGAAATTGAAGCCAAGGCTGATGTATTGGAGGTTAAATGAAATTAGCACTTAAACAGCTTGGAAAGTGAATGATATGCAATTGCTTTGCCTGCAATAAGATGATGACAGTGAGTAGATGATTTGAAGTTGGTCCCAGTCCTTCGGTGAGAAATGCTTCCAACTACTCTCTGCAGTGCAAAAAGATTAATTTGAGAATCAGGCCCATTTCCCCTGACTATTGGGAGCTTGATATGTATCCTGAATCTTTTCTATATTGCAGGAGTGCAAATTAGTGTCGATATCACACCCCTAGTCTATTTGTCAGATGCATCAGCCCTTCAGAAAGAAGGGTTCTGAGCATGCCCTGCAAAATCTGCCACCAAAACGTGAAACTGACTTCTTAAATGCTTCTGATCCTAGCTGATGCAGAACCCAGACATATTCATATATTAATTATTAATTCTTGCTTTTTTAGACCATATCCTCTCTCTTTTTCTCTTTCTCTTCACAG
Seq C2 exon
GTATTCCAGAGGCGGCAAAATGGACAAACTGATTTTTTCCGGAAATGGGCAGATTATCGTGTTGGCTTTGGGAATCTGGAGGATGAGTTTTGGCTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015829-Tnr:NM_022312:19
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0014713=Fibrinogen_C=PU(21.0=86.3)
A:
NA
C2:
PF0014713=Fibrinogen_C=FE(15.2=100)
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:
GGGCCGGGTGTTCTCTCATC
R:
AGCCAAAACTCATCCTCCAGA
Band lengths:
246-1990
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: