MmuINT0045975 @ mm9
Intron Retention
Gene
ENSMUSG00000039660 | D2Wsu81e
Description
DNA segment, Chr 2, Wayne State University 81, expressed [Source:MGI Symbol;Acc:MGI:106544]
Coordinates
chr2:30028967-30030589:-
Coord C1 exon
chr2:30030442-30030589
Coord A exon
chr2:30029706-30030441
Coord C2 exon
chr2:30028967-30029705
Length
736 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
ACCAACTTCTTTTCTTCCAGGAG
3' ss Score
10.26
Exon sequences
Seq C1 exon
GCATGCCCTTGTGGTGTTTGGAGGCCTCCAAGGGCTAGAAGCTGCAGTGGATGCTGACCCGAACCTTGAAGTGGCTGACCCCAGTGTCCTCTTCGACTTCTATGTCAACACATGCCTTAGCCAGGGCAGCCGTACCATCCGCACCGAG
Seq A exon
GTGAGCCGCAGCCCGAGTTCTTGCAGCCCACCTTGCGTGCCTTTTCTAAAATTTACTTATGAATGTTTTGTCTGCGTGTGCTTGTGCACATGAGGAGAGGGCATCGGATCCCATGAGACTACAGGTGTCAATAGTTATGAACTGTTATGTGGATTCTGAGAATTGAACTCAAGACTTCCCGGAGAGCAGCCAGTACTCCTAACCCATCTCTCCAGCCCCAGCCTAAAGAGCTTTTCTGAAGCTGGGATCTTTACCACAGCCAACTAGTAGCAGGGACTGAACACAAGAGCAATTAAGAGTTGCAGTCCTGGCCCTGTGCCCTGTGGTAGCCCTGTGTTCTTAGGTTGAGGGACCCAGGTGATCTGTCTGTCTGTCCCTCTGCAGGGCTTCTTGCTTCCGCTTCCTTGGTTGTATCCTAGGTCCCTCTGGGTGTTGGGGGAAAGTGTGCCACAAGCTCTGAGCATCCACAGGATCTATGCACCCATCCTGGAGACTAGCATGGGATTCAGTGCCTGTGGATATTATGGGGGAGGCTCTGTTGCTGTCAGCCTCAGGGGCAGTGACTATGCAGACGGGCAGCCCCAGTCTCCCTGTCTCTGAAGTCTTGCCCATATCACTAATTACTGTTCCACCAGTATCCCTCCTGACCCTGAGGTAGGTCTCACATGGGGCCTGAAAACAAGCAGCTGGGAAGGCTGCCTGGCTTCCTGGTCCCAACCAACTTCTTTTCTTCCAG
Seq C2 exon
GAGGCCATACTCATCTCGCTGGCTGCTCTGCAGCCTGGTCTCACCCAGGTGGGATCGAGGCCCGCCTCCCCGCTTTCTGGACCCAGGATGTAGAGGAAGCAGCAGGACAGGAGGATCATGGGAGTAGAGATGGTCAAGTCTTCTCTCCAAAAATAACTGCCTTTAATGTGAGTCAGCCCATCTCCCCAGGGGCTCCAGTGAGTCCTCCACCATCACTTGCTGCCAGCAGTGATAGCCTTGAGGTTTCCAGCTCGAGCCAGAATATTGGGCACGAAGAGCAATCCCGAGGCCCGCTCGATGCTCTCGATGGGCACCAGGAACCGCTCCAGAGGGATGGTCTCATCCACGGGGGCATTGGGCATCACGTAGGAACGTAGCTCGATCTGCCCACCGGCTGCCTCCAGGATCAGCACCTTGAAGAAGTGTGTGGGCACTGCCACGTGGTTCTTCCCAATAACCTGGTACTTCACATAGGACTTCCCATCAGCCTCGGTCCTGTGGATAGACCCGGGCGCATGGCCAAGAGGCCTGGTTACATACAAGGTCACCTCTTCCAGGAAGCCTTCCTAACTTCCAACAAGCAAGAAGTTTGTGCTGGGCCTGGTGCCTCCTTGGGTCTGGGAACTATGTAAGGTGGGGACCAATGCTTAACCTCTGCTTTTCTGCCCAATACTGCTTCAGACAGAATGGGAGGCAATAAACGCAGCTAGAGGAATGAGCTCTCTAGACCCTGATGCTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039660-D2Wsu81e:NM_172660:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.433
Domain overlap (PFAM):
C1:
PF0259812=Methyltrn_RNA_3=FE(16.8=100)
A:
NA
C2:
PF0259812=Methyltrn_RNA_3=PD(3.4=32.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCTAGAAGCTGCAGTGGATG
R:
CTCAAGGCTATCACTGCTGGC
Band lengths:
358-1094
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: