MmuINT0074006 @ mm9
Intron Retention
Gene
ENSMUSG00000026959 | Grin1
Description
glutamate receptor, ionotropic, NMDA1 (zeta 1) [Source:MGI Symbol;Acc:MGI:95819]
Coordinates
chr2:25152397-25152816:-
Coord C1 exon
chr2:25152668-25152816
Coord A exon
chr2:25152555-25152667
Coord C2 exon
chr2:25152397-25152554
Length
113 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGG
5' ss Score
7.13
3' ss Seq
TGAGGTCTCTGTCCCTGCAGCTC
3' ss Score
9.56
Exon sequences
Seq C1 exon
GTGCCCCCCGGAGTTTCTCTGCTCGTATCCTAGGCATGGTGTGGGCTGGTTTTGCCATGATCATCGTGGCTTCCTACACTGCCAACCTGGCAGCCTTCCTGGTGCTGGATAGGCCTGAGGAGCGCATCACAGGCATCAATGACCCCAGG
Seq A exon
GTGAGGCCTCTGGACTGCAGGTTGTGTGTGGGGTATCAAGAGGTTAAGAGGGAGGTGTCTGTTTCTTGTGGTGCTTGGGGAGCAGCCACAAGTTGAGGTCTCTGTCCCTGCAG
Seq C2 exon
CTCAGAAACCCCTCAGACAAGTTCATCTATGCAACTGTAAAACAGAGCTCTGTGGATATCTACTTCCGGAGGCAGGTGGAGTTGAGCACCATGTACCGGCACATGGAGAAGCACAATTATGAGAGTGCAGCTGAGGCCATCCAGGCTGTGCGGGACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026959-Grin1:NM_008169:14
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.040 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0049715=SBP_bac_3=FE(14.3=100),PF0006021=Lig_chan=FE(18.4=100)
A:
NA
C2:
PF0049715=SBP_bac_3=FE(15.2=100),PF0006021=Lig_chan=FE(19.5=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:
CCCGGAGTTTCTCTGCTCGTA
R:
CCGGTACATGGTGCTCAACTC
Band lengths:
242-355
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
Other AS DBs: