MmuINT0005175 @ mm9
Intron Retention
Gene
ENSMUSG00000040412 | 5330417C22Rik
Description
RIKEN cDNA 5330417C22 gene [Source:MGI Symbol;Acc:MGI:1923930]
Coordinates
chr3:108272446-108272925:-
Coord C1 exon
chr3:108272820-108272925
Coord A exon
chr3:108272584-108272819
Coord C2 exon
chr3:108272446-108272583
Length
236 bp
Sequences
Splice sites
5' ss Seq
GTGGTAGGT
5' ss Score
7.23
3' ss Seq
CTTGCCTCCCCTGGGCTCAGGGC
3' ss Score
7.87
Exon sequences
Seq C1 exon
ACCTCCACAGTCAGTGGTGGCAGACACAGAGAACAAAGAGGTGGCCAGGATCACATTTGTCTTCGAGACCATCTGCTCTGTGAACTGTGAGCTCTACTTCATGGTG
Seq A exon
GTAGGTTTCTTCTCCTAGCCAGATGGGGGCTTCCATGGGAGGGTTGGTCCAGCATGGCCCAGCAGTGAGGCAGTATACTGGACACCCATCATGGTGATCCCACGGATCAAGAGCCTAGAGGGACTGCCAGGGACTCCCTAGTACTTAACACAGGTCTGACCAGTGTGTTAGCCCACAGCATAGTGATTGCCTCACGAAGCAATCCCGCCTTCCTCACTTGCCTCCCCTGGGCTCAG
Seq C2 exon
GGCATGAATTCCAGGACCAATACTCCTGTGGAGACGTGGAAGGGCACCAAAGGCAAGCAGTCCTATACCTACACCATCGAAGAGAATGCTACTGTGAGCTTCACATGGGCCTTCCAGAGGACCACCCTTCATGAAACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040412-5330417C22Rik:NM_001033304:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.065
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CACAGTCAGTGGTGGCAGAC
R:
TGTTTCATGAAGGGTGGTCC
Band lengths:
239-475
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: