MmuINT0162932 @ mm10
Intron Retention
Gene
ENSMUSG00000028364 | Tnc
Description
tenascin C [Source:MGI Symbol;Acc:MGI:101922]
Coordinates
chr4:64007348-64007867:-
Coord C1 exon
chr4:64007682-64007867
Coord A exon
chr4:64007438-64007681
Coord C2 exon
chr4:64007348-64007437
Length
244 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
ACCTTCACATTCTCTTCCAGGTC
3' ss Score
12.49
Exon sequences
Seq C1 exon
GCCTGGATGCTCCCAGGAATCTCCGCCGTGTCTCACAGACAGACAACAGCATCACCTTGGAGTGGAGGAACGTCAAGGCAGACATCGACAGTTACAGAATTAAGTATGCCCCTATCTCTGGAGGTGACCATGCTGAGATAGATGTTCCAAAGAGCCAGCAAGCCACAACCAAAACCACACTCACAG
Seq A exon
GTGAGCCGTGACCCAGCGGTGCTGTGCCACAGGGGCCCTCGAAAGGACAGGAGCATATGTCCCTATTTTGCAACCCTGTAGAGATTATGAAATAGGCCCAGCTTCTGTCCATTCCTCTCACTGTCACTGCATCATGTGATGAGCATATACAATTCACAGTGGCCAGAAGCCAGTCTGGGGTCACTTTTAAAGTCTTCTGGGAGCCTGCCTTCTACTAGTGCCCAACCTTCACATTCTCTTCCAG
Seq C2 exon
GTCTAAGGCCCGGAACTGAATATGGGATTGGTGTTTCTGCTGTCAAGGGAGACAAGGAGAGTGATCCAGCAACCATCAATGCGGCCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028364:ENSMUST00000030056:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.476 A=NA C2=0.742
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(71.4=95.2)
A:
NA
C2:
PF0004116=fn3=PD(27.4=74.2)
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:
TGGATGCTCCCAGGAATCTCC
R:
CTGTGGCCGCATTGATGGTT
Band lengths:
273-517
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