MmuINT0074004 @ mm10
Intron Retention
Gene
ENSMUSG00000026959 | Grin1
Description
glutamate receptor, ionotropic, NMDA1 (zeta 1) [Source:MGI Symbol;Acc:MGI:95819]
Coordinates
chr2:25297370-25297714:-
Coord C1 exon
chr2:25297596-25297714
Coord A exon
chr2:25297483-25297595
Coord C2 exon
chr2:25297370-25297482
Length
113 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
CTTCTCTTTGCCCTCCGCAGTCC
3' ss Score
10.26
Exon sequences
Seq C1 exon
GAGATCCCTCGGAGCACACTGGACTCATTCATGCAGCCCTTTCAGAGCACACTGTGGCTGCTGGTGGGGCTGTCAGTTCATGTGGTGGCCGTGATGCTGTACCTGCTGGACCGCTTCAG
Seq A exon
GTGAGCACGTGCAGAGAGCCCGACCCCTGCATGTGTAGGGGGGCAGAACTAAGCAGGGCCGGGCAGAGCTGCCTCTCCTGCCCTCTCTCCCGCCTTCTCTTTGCCCTCCGCAG
Seq C2 exon
TCCCTTTGGCCGATTTAAGGTGAACAGCGAGGAGGAGGAGGAGGATGCACTGACCCTGTCCTCTGCCATGTGGTTTTCCTGGGGCGTCCTGCTCAACTCTGGCATTGGGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026959:ENSMUST00000114312:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0049715=SBP_bac_3=FE(11.4=100),PF0006021=Lig_chan=PU(9.4=62.5)
A:
NA
C2:
PF0049715=SBP_bac_3=FE(11.1=100),PF0006021=Lig_chan=FE(14.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGATCCCTCGGAGCACACT
R:
CAATGCCAGAGTTGAGCAGGA
Band lengths:
226-339
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