MmuINT0071494 @ mm10
Intron Retention
Gene
ENSMUSG00000073402 | Gm8909
Description
predicted gene 8909 [Source:MGI Symbol;Acc:MGI:3704134]
Coordinates
chr17:36167926-36168537:-
Coord C1 exon
chr17:36168444-36168537
Coord A exon
chr17:36168208-36168443
Coord C2 exon
chr17:36167926-36168207
Length
236 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
GCGGTATTTCACCACCGCAGTGT
3' ss Score
5.33
Exon sequences
Seq C1 exon
TCTCCTGTATCATCATTCCCAGATGGGGCAATGGCACCGCGAACGCTGCTCCTGCTGCTGGCCGCTGCCCTGATACTGACGGAGACACGCGCGG
Seq A exon
GTGAGTGCGGGGGTCGGGAGGGAAACGGCCTCTGCGGGGAGGGGCGGGGACGGCACCGTGGAAGCCGCGTCCCCGTGTCGCTCACAAGACCCTCCGCCCCTTCTACACCCGCATCCCAAACCTTACGCCCTGCTCCGCTTCTGCCCGCGCAGCCACCGAAGGTCCCGGGAGGAGGTCGGGGTCTCACCGCGAGCCGCCCCCAGGCCCACACTCGATGCGGTATTTCACCACCGCAG
Seq C2 exon
TGTCCCGGCCCGGCCCACACTCGATGCGGTATTTCGAGACCGCCGTGTCCCGGCCCGGCCTCGGGGAGCCCTGGTTCATCTCTGTCGGCTACGTGGACGACACGCAGTTCGTGCGCTTCGACGGCGACGCGGAGAATCCGAGGATGGAGCCGCGGGCGCCCTGGATGGAGCAGGAGGGGCCGGAGTATTGGGAGCGGGAGACACAGATCGCCAAGGGCCATGAGCAGGGTTTCCAAGGGAGCCTGAGGAACCTGCTCCACTACTACAACCAGAGCGCGGGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000073402:ENSMUST00000040467:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.055 A=NA C2=0.356
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0012913=MHC_I=PU(50.3=94.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGCCCTGATACTGACGGAGA
R:
CGCGCTCTGGTTGTAGTAGTG
Band lengths:
308-544
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