MmuINT0045978 @ mm9
Intron Retention
Gene
ENSMUSG00000039660 | D2Wsu81e
Description
DNA segment, Chr 2, Wayne State University 81, expressed [Source:MGI Symbol;Acc:MGI:106544]
Coordinates
chr2:30032259-30033002:-
Coord C1 exon
chr2:30032843-30033002
Coord A exon
chr2:30032349-30032842
Coord C2 exon
chr2:30032259-30032348
Length
494 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGA
5' ss Score
5.26
3' ss Seq
GTCTGTCTTAATCTTTCCAGGAG
3' ss Score
8.72
Exon sequences
Seq C1 exon
GACGGCCTTACACTCTGAGTGTGGCCCTGCCAGGCTCCATCCTGGACAATGCCCAGTCACCTGAGCTCCGCACCTACCTGGCTGGCCAGATCGCCAGAGCCTGCACCATCTTCTGTGTGGATGAGATTGTGGTGTTCGATGAGGAGGGCCAAGATACCAA
Seq A exon
GTGAGAGTCTCTGGGGAGTGGGGAGGACCAGCAGGGGTGGCCATGGCTTTGTCCTGCTCCTTGTCACCTGCCTGGCTGCCTGGAAGGAGCTCTCAAAGGCAGCTGCAGACTCACTTTTTCTCACCCTTGGTGCTAGAGAGTGGACTCAGGGTTTTGCCCATGGTCTGTGCTGAGGCTCAGCACTTGGATGGTTTGGGTTGTGTTTAGCATTTCTTTATGGTGCTTGTGTACAAACACCAGTGTGGTTCTGGAGACCAGAAGGCCACTTGAGCTGAGCAGTGGTGGCACACGCCTTTCATCCCAGCACTCAGGAGGCAGAGGCAGGTGGATCTCTGAGAGTTCAGTGCCAGTCTGGTCTACAGAGCAAGGTCTGGGACTGCCAGGGCTATGCCAAGAAACCCTGTCCCCAAAAACAAATGAAAAAGAAAGAAAATAAAAAAAAAAGTATAATAAGCCCAGCACTTGGATCTTGAGGTCTGTCTTAATCTTTCCAG
Seq C2 exon
GAGTGTGGAAGGAGAATTCAGGGGAGTTGGCAAGAAAGGGCAGGCATGTGTCCAGCTGGCCCGCATCCTACAGTACCTGGAGTGTCCACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039660-D2Wsu81e:NM_172660:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.028 A=NA C2=0.129
Domain overlap (PFAM):
C1:
PF0259812=Methyltrn_RNA_3=PU(16.8=90.7)
A:
NA
C2:
PF0259812=Methyltrn_RNA_3=FE(10.3=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:
GACGGCCTTACACTCTGAGT
R:
AGGTACTGTAGGATGCGGGC
Band lengths:
238-732
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: