MmuINT0163490 @ mm9
Intron Retention
Gene
ENSMUSG00000015829 | Tnr
Description
tenascin R [Source:MGI Symbol;Acc:MGI:99516]
Coordinates
chr1:161817001-161818507:+
Coord C1 exon
chr1:161817001-161817270
Coord A exon
chr1:161817271-161818387
Coord C2 exon
chr1:161818388-161818507
Length
1117 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CAACTCTCTGATCTTTGTAGGAA
3' ss Score
8.09
Exon sequences
Seq C1 exon
GCTTCCGCCCTATCTCCCATTTGCACTTTTCTCATGTGACCTCCTCCAGTGTCAATATCACCTGGAGTGACCCATCTCCCCCAGCAGACAGACTCATTCTGAACTACAGCCCCAGGGACAAAGAGGAAGACATGTTGGAGGTCCTCTTGGATGCCACCAAGAGGCACGCTGTCTTGATGGGTCTACAGCCAGCCACTGAATATATAGTGAACCTTGTAGCTGTCCATGGGACGGTAACCTCTGAACCCATAGTGGGTTCTATCACTACAG
Seq A exon
GTGAGGCTGGAGATGTTGATCAAGAGGGTTCTCACTTCAGCTTTTGACAAGCCAATGCAATCTAAAATGACAAACTTTCAAGAAATAGCAGAATGAGCCTATAGCTAGAGACTTCTGTGAGTTATTCTGTAGCAGGTACTTCTTTCAGCATTGCATAAGAGACATATGATGAGAAACATCCATTTGCAAAGTAGGACAGGCCCAGTGCTCTGCATGCCCAAGTCTTGAATGCATTGGTTCTAGATTTGCCAATCTAGGAAAAAGGCCCGGAAAAAGCTTGTCTCCAAGGGATTCTTTCTAAGTAAAAAGATGATATTTCTATTCTGGAGAGCCATCTCTTGACAGCCTAATAAATGATTCTTCCTCAGAATCAACATAGAGCTAGCATGTAACCATGTAGCTACCTGGCATTCAGAGATAGGAGCTGATTTGCACATTGGAAGACATAGAACTTTGAGATGAATTGGGCCATTTCCCTTTGGTCATTTGCAAATGCAATCCCAAATATGATACATTTGTATATAAAAACACCTATAATTAGATAGTTCCCTACATACTGACAAGAACTCACAAACTGGAAAAGTATGTTAAGTAGTCAGCGAATTTGACCCCACAGTTTAAATGCACCATAATTATGCACCATAAATAAAATATAACTTAGGAAAGTATATTCGTTTAGGATTTGTGCTCTGAAATCTCTCTACAGTTAATGGGCAGTTTTTTTCCAAGTTGAACCAAAAGTAGCTGCTAAAAACTAAGAAAGAGTAGCAGAGTTAGGTCTTTGCAAGAGAAGTTTCCCTTAGAGAAGATAATTATATGATCCTCTATTTGAAATAAAACACACAAACTTAAAAGGAAGTTTCTGGTTGGTCTAGATGGTAGTAGCTGTGGCACAGAAGTGTAGATCTTGCCAATTTAGCTTCCTGACTTTGGCCATAGCTACAATGTTATAAGTGTGACATCACACAGACTGTCATGTTAGGGATGCCCAGTTAGTTATGTAGGGTCATGCCTGCCTGAGGGACACTAGTGGATCAACAGAAATCTAGAAATAGATAGATATTCCACTTTCAAACTGTGCTTCTGTCTTTTCCCCACAACTCTCTGATCTTTGTAG
Seq C2 exon
GAATTGATCCTCCCAAAAACATCACAATTAGCAACGTGACTAAGGACTCCCTGACGGTGTCCTGGAGCTCTCCTGTTGCGCCTTTTGATTACTACCGAGTATCGTACCGACCCACCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015829-Tnr:NM_022312:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.088 A=NA C2=0.012
Domain overlap (PFAM):
C1:
PF0004116=fn3=WD(100=89.0)
A:
NA
C2:
PF0004116=fn3=PU(47.5=92.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCCCTATCTCCCATTTGCAC
R:
TCAAAAGGCGCAACAGGAGAG
Band lengths:
353-1470
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: