MmuINT0162925 @ mm10
Intron Retention
Gene
ENSMUSG00000028364 | Tnc
Description
tenascin C [Source:MGI Symbol;Acc:MGI:101922]
Coordinates
chr4:63964598-63965680:-
Coord C1 exon
chr4:63965584-63965680
Coord A exon
chr4:63964760-63965583
Coord C2 exon
chr4:63964598-63964759
Length
824 bp
Sequences
Splice sites
5' ss Seq
TTGGTAATG
5' ss Score
4.83
3' ss Seq
ACATTGCCCGTCATCCACAGGAC
3' ss Score
9.6
Exon sequences
Seq C1 exon
GTTTTCCTGAGACGCAAAAATGGACGTGAGGACTTCTATCGCAACTGGAAGGCCTATGCTGCTGGGTTTGGAGACCGCAGAGAAGAATTTTGGCTTG
Seq A exon
GTAATGCAGCTCTGAAAGTTTGTGACAGATATGCCTATTTCTGTCCTCTTGGTCACTTACCCTCCTGTCGTGAGCAACAGGGAGAGGAAAGGATCAAAAGGAAAGAAGTTTGGTAGGAGCCACATAGTGTTGAATTAATTAAATATTCCAGGTCACAAAAATAAAGCATTATCAAGCCAGACCTGTGGACAAACCTTGCATTAAGTCAGACACTAAAACCAATTATGGAGCCAACCTCAGTGCTGTCGTGAACTGCTTTCCTCTTAAGCTCAAACACTGAGATGGGTCTCCTGGTTGTAATCTTTCACCTAGAACATCCCTGCAAAGAGCAGAATTCCCATCTTACTCATGAGAAAACAGACCCTCAAGGACGTTGTATGGTTTGTCTATGGCAATCTAGCCAATTGACAAATACACTGTCCTTCAAATTTTCCCAAACTAGTATAACAGGGCCATCATTCATCATGGACACTTTGCAGCAAACCACATGGACAAAGCATTGTTATCTGCTCCACTGTCCGAGCCTAAGACACCCCATCCCAAAGTTATCCTTTGCTTCACATTGGTTATAAATTTTAGAGTGTACAAGTCACGTCCCTGGATTATCACCTTTGACCTTCACAATACAATAGGAAGCTGATAAGCAAAGGTGTTGAACTGTTTTCTTCTGAGGCTCAGAAACATGAGATTTGTTTTGTCTGCCTTCATACCAGCAAACAGAGAATGTTTCAAGCCCAAGTTTTCAGGATATGTCCCACTGTTGAGTGGTAGGGACCTCCTCAGTCACCTGTGATTGCTTACCAGACATTGCCCGTCATCCACAG
Seq C2 exon
GACTGGATAACCTGAGCAAAATCACAGCCCAAGGGCAGTATGAGCTCCGGGTGGACCTACAAGACCATGGGGAGTCTGCCTATGCTGTGTACGACAGATTCAGTGTTGGAGATGCCAAGAGTCGCTACAAGCTGAAGGTAGAAGGATACAGTGGAACAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028364:ENSMUST00000030056:22
Average complexity
IR
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=FE(15.2=100)
A:
NA
C2:
PF0014713=Fibrinogen_C=FE(25.7=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:
CCTGAGACGCAAAAATGGACG
R:
CTGCTGTTCCACTGTATCCTTCT
Band lengths:
254-1078
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