MmuINT0163488 @ mm9
Intron Retention
Gene
ENSMUSG00000015829 | Tnr
Description
tenascin R [Source:MGI Symbol;Acc:MGI:99516]
Coordinates
chr1:161814902-161816451:+
Coord C1 exon
chr1:161814902-161814991
Coord A exon
chr1:161814992-161816187
Coord C2 exon
chr1:161816188-161816451
Length
1196 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
AACCTTATTTTAATCCTCAGAAC
3' ss Score
7.5
Exon sequences
Seq C1 exon
ATCTGGTTCCAGGCACAGAGTATGGAGTTGGAATATCTGCAGTAATGAACTCAAAACAAAGCATTCCTGCCACTATGAATGCCAGGACTG
Seq A exon
GTAAGTAGGAGAATGGTTAAGAGGATGACTAGGCTGTAAGCATGTAAGACTTGGTGTATGAAGGCTTGTACTGTCAGGATCACTATGGGGCACCCCTCCCAGTGAACAAGTCCCTGTTGATAATTCTCCCCTAGTGACAGCATCTACCCTATGCTTGACCTGACGTCAGAAGTTTGATCTACAACCAAAAGGACTGCAGAGTAGATGTGAAAACTCCCCAACAGGCTGATGCTGTAGCAGATTGTCTTTCTGTTTAATCTACTTCATAGCAGGCAGAGTGTGTGTCCTCAAGTTTGCAACACAGGGGCTCTCAAAAAGGTCACTGGAAGAAAGGTCTAGACTTGGAAACATTCTGTACAATCCCAGAGCAGCAGAAAAGATTCCACATAAGATTCTTACTGCTCTGAATCTAACAGTTTCCCTTCCAAATCCTTGGGAAATTTCAAAGTCACTTCAGTAAGCTTAGATATAAACATCTTGGACTGAGCAGGGGTTGGGGTTGGGGATTGGATCAGTCCCTGTCCCCAGGGTTCATCCTAGCATAAACAAACATGCTGGAAGAGCACACCAACAATTGTCTCCGTTAGTCCTCAGACCTGTACACCCGAGGTTAGGACAAGCCAAAGAAACCTCCGAGTCAGGGGGGTGGGGGTGGGGACAGGAAACTTACTTGCCATGAACACCTTATCTTATGTGGTAGTGGCTCCTCTTTCCCCATTTGGCTAACCAAGGGAGGATGAATGAAAACAAGTCTGGAGCTCTAGCAAATCAGCAGTTAGATCTATCCCAGTGGGGGATGCATGCGAGTGTCACTGCTAATAATGGCTTTCTGCAGATTGCCCATCTGTTTGCCCTATCACTGGCCATCTTTCAAAGGGAAGCCGTTAAACAAAATGTGAGAAAAGTACCAGCTATGACAAGCTGGGGCTCATGGTCATTAGGTCTACTTGACAGCCTGGAGATACAAAGGGTAGTCCAATAACTAATGACTGTCCTATGGAGTCAGTGTGAAATAGGCCAATTGCCAAGTGAGGCAGTATATGCCTGTAATCTCACACTTAGGAGGTAGAGGAAAGGGGATCACAAGTTCAAGGTCATCCTTGGATACATAATGAATTCAAGACCTGTCTCATCTAAATAAGACTTTGAATGAATGAATGAATAAATGAATGAATGAACCTTATTTTAATCCTCAG
Seq C2 exon
AACTTGACAGTCCCCGAGACCTCATGGTAACAGCCTCCTCAGAGACCTCTATCTCTCTCATCTGGACCAAGGCCAGTGGTCCCATTGATCACTACAGAATTACTTTTACCCCATCTTCTGGGATCTCCTCCGAAGTCACTGTGCCCAGGGATAGGACTTCATACACACTAACAGATCTAGAGCCTGGAGCAGAATACATTATCTCCATCACTGCTGAGAGGGGTCGGCAGCAGAGCCTGGAGTCTACTGTGGATGCCTTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015829-Tnr:NM_022312:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.419 A=NA C2=0.281
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(26.5=71.0),PF120283=DUF3515=PD(12.5=29.0)
A:
NA
C2:
PF0004116=fn3=WD(100=89.9)
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:
ATCTGGTTCCAGGCACAGAGT
R:
CCACAGTAGACTCCAGGCTCT
Band lengths:
342-1538
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: