MmuINT0163295 @ mm9
Intron Retention
Gene
ENSMUSG00000026725 | Tnn
Description
tenascin N [Source:MGI Symbol;Acc:MGI:2665790]
Coordinates
chr1:162044622-162046464:-
Coord C1 exon
chr1:162046201-162046464
Coord A exon
chr1:162044886-162046200
Coord C2 exon
chr1:162044622-162044885
Length
1315 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATG
5' ss Score
9.43
3' ss Seq
TAAGACTTTTAAACTTGTAGACA
3' ss Score
4.32
Exon sequences
Seq C1 exon
ATATTGATAGTCCCAAAAACCTGGCGATCGACCAGGTGACAGAGACCACTCTCAGTGTCTCCTGGGACCCAGTACAGGCTGACATTGACAGGTATGTGGTGCGCTACACCTCTGCTGATGGGGAATCCAAAGAATTCCTGATTGGGAAGGAACAGAGGAGCACAGTCCTGACAGGCCTGAGGCCAGGTGTGGAGTACAAGGTTGAAGTGTGGGCCCAGAAAGGAGCCCGGGAGAGCAAGAAAGCCAACACCGAAGGTCACACAG
Seq A exon
GTAATGAACAGCATGGGTTAGCAGTATGATGGCTGCCAGGCCAAGCTTAGGGGAAGTCAAGCTTTAATTTCTTCCTGTGATACAGATGGGTATTGATGGATTTTGGAAGAGCAGCTTTATTTCTTGCACGATCAACTTCACATACCATTCCTTACTCCCTGAAACTGGTTTCCTTATGTGCTAGACCAGTGCTTTTCCACCTTCCTAGTGCTGTGACCCTTTAATAAAGTTCCTCATGTTGCAGGGGTCTCCAACCATAAAATTATTTTTGTTGATACTTCATAGATATAATTTTGCTACTGTTATGAATTATAATATAAATATTTGTTATTTTCCAATGGTCCTAGGTGACCCTTATGAAAGAATTAAACCTGCAGGTTGAGAACCACTGGGCTATGTTCTCCAAACAGTCTCCAAACTGCTCAGCTGAATAGTTCCTGATTTCTCTTCCAAGTGCTTGGATTTCTTGCCAGAGATATTATTTTCATGAGTAAGACCGGAAAATGAAAAAAAAATCAAAATTTACTTTAAGATTCTAGATTTTACATCTGCTGTCACAAGTAAAGGCTTGCTTCTCTACATCCAAATCATATTTTAATTATAAAACAAATTTGTCACGGTAAATGATAAGCCCCGTGAGAGAGCTCTATTGTCATGCTAATGGACACAAACTTGTTTGCAAAAGCCAAGGTCTCCAACTTGAATCTCTGTATGTTGCCTGTCGCATGCCTTGCATATAGAGCAAAAGCTTGATAGCTTTACTAAATGAATGAGAAATTAGTGTTTTTTTTGAACTTTTAATAGAAATCATACTTTCGGTTGTCTGATTCTGGTTGTTTGGGGTCTCCATGTGGGTAGGGAAGCATTCCTGGGAAGAGATGTGAATGTATGAAGACAAGTAAGAAACAAACAGCAAATGAACAAACCCCCACCAAAATAGAGTGTCTGAGATAGAAAACAACAGAAAATGAAAACTCACCACTCACCATAGCCAGCAGTGTCTGCACTCTGAGCCTCTTAATGGTATATATCGATTTCTTGTTGTTGCTGCCATCATTATCACCAACATCATCACCACCATCATCACCATCATCATTTTTGTGCATGTGTGTGCAAGTGTGTGTGTGTGTTTACACATAGGCACACATAGGACATGGTACATGTGTGGAGATCAGAGGATAATTTTCTAGAGTTAGTTCTCTCGTACAGTGTCAGGGATGACAGTCAGGTTGCCACATTTGTGCAAGCATCTCTACTGACTGAGCCATCTTGCTGACCCAATAGCACATACTGACTAAGACTTTTAAACTTGTAG
Seq C2 exon
ACATTGACAGCCCCAAAAACCTGGTGACCAATCAGGTGACCGAAAATACAGCCACCATCTCCTGGGACCCGGTGCAGGCTGATATTGACAGATACATGGTGCGCTACACATCTGCTGATGGAGAGACCAGGGAGATTCCAGTGAGGAAGGAGAAGAGCAGCACTGTCCTCACAGGCCTGAGACCGGGTGTGGAGTACACGGTCCAAGTGTGGGCTCAGAAGGGGGCCCGGGAGAGCAAGAAGGCCAAAACCAAGGCCCCCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026725-Tnn:NM_177839:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.315 A=NA C2=0.573
Domain overlap (PFAM):
C1:
PF0004116=fn3=WD(100=88.8)
A:
NA
C2:
PF0004116=fn3=PD(59.5=83.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACAGGTATGTGGTGCGCTAC
R:
GTGAGGACAGTGCTGCTCTTC
Band lengths:
350-1665
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: