MmuINT0162917 @ mm10
Intron Retention
Gene
ENSMUSG00000028364 | Tnc
Description
tenascin C [Source:MGI Symbol;Acc:MGI:101922]
Coordinates
chr4:63975202-63976568:-
Coord C1 exon
chr4:63976446-63976568
Coord A exon
chr4:63975346-63976445
Coord C2 exon
chr4:63975202-63975345
Length
1100 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGG
5' ss Score
7.81
3' ss Seq
TTGCTTTCGCTAATCTCCAGGTG
3' ss Score
8.57
Exon sequences
Seq C1 exon
CCATGGGTTCTCCGAAGGAAATCATGTTCTCAGACATCACTGAAAATGCAGCCACAGTCAGCTGGAGGGCACCTACTGCTCAGGTGGAGAGTTTCCGGATCACTTATGTACCTATGACAGGAG
Seq A exon
GTAGGGAACCTGGAGGTGGAAGACGGTGGGGAGAACATGCAACATTAGGGTTAAATGGCAAATGAGACCCTGGGTGTTCTTATCAGACTTTCTTCAAGCATTATGGCTAATGAAAATCACTTCCCTCCTTCTGAGATCATCTAGAAAGATGCCCTTTGTAAAGACATTTTGGAAACTTGGAAAAAGTCACCTTATTAACACTCTCTGTGACCTTGATATTGTAAAATATTTTCAAGGAAATGGTTCCCTAGTACTTTTGAACACAAACACAAGGGAATTTATATAAACAATCTTTTTTTTTCCCCTTTGATCACAGTCATCTGGAAAGCTGAGATATGTGTGAGGTTTTACCCTTAGGGACCATATCCTATCTCACTACAGGATAGAGAACTGAGTCTTAGCAATGTTAGAACTTGGAACACATAGACTTTAATGAAGACCTCAGGGAAGTATAGTTCGAACACAGCCTAGCAGGTAGTGAGCTGCCTCTTGTTGGAGGTTTGAAAAGACAGGCTGGTTGGTAACGGCAACACTGTAGCATCTCCATTTGGGCGTTTGGCCAGCTGGATTGCAAATCCTTCACTCTTCCTGAAATTCTAAGAAATATAAATTCCAGACTTCCTAATAAATTTAAGAGCACACATTTAACTGGGACCATCTTTTTTATCATGACTAAAATCTCTCCAAGTAAGGGGGTCTATAGCATCTTAAGTCAACCCAATGAGTTACATAGCTTGGATCTATGCTACATTGTGAGCTTCCCATATAGTGCATGGAGGGACAAGAATAAGGAAAATAAAATTTGTGCAACATGCCAACTCCTTCCCGAAAGGAAACTTGCCATTTTTAGTATACTGTGACTTCATGATTTTTTCCTTTCCTGACTGGGTTTTTGGCATCTGCACCAATGGAAAAAAACATTATACAAAAAGTAAGGTCTTGTCCTTCATGCCAGAGGGTGGGATGAGAGGAGAGGAACTCCAGAGAATGAAATTGAATAAAGATATAATTTAATTTCCAAGTTGCATCCACCCGGTTTGGAGGCTATGACAAGGAAGTGTGGAAGAGGCTCCCCTGATCTTGCTTTCGCTAATCTCCAG
Seq C2 exon
GTGCCCCGTCCATGGTGACTGTGGATGGAACAGATACTGAGACCAGGCTGGTGAAGCTTACCCCGGGTGTAGAGTACCGCGTCAGTGTGATTGCCATGAAGGGATTCGAAGAAAGCGATCCAGTCTCGGGGACTCTAATCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028364:ENSMUST00000030056:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.048 A=NA C2=0.245
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(48.8=92.9)
A:
NA
C2:
PF0004116=fn3=PD(50.0=81.6)
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:
CGAAGGAAATCATGTTCTCAGACA
R:
CTGTGATTAGAGTCCCCGAGAC
Band lengths:
255-1355
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types