MmuINT0074010 @ mm9
Intron Retention
Gene
ENSMUSG00000026959 | Grin1
Description
glutamate receptor, ionotropic, NMDA1 (zeta 1) [Source:MGI Symbol;Acc:MGI:95819]
Coordinates
chr2:25149958-25151457:-
Coord C1 exon
chr2:25151312-25151457
Coord A exon
chr2:25150069-25151311
Coord C2 exon
chr2:25149958-25150068
Length
1243 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
CTTATACATATTCATTTTAGGAT
3' ss Score
8.75
Exon sequences
Seq C1 exon
GGGTCTTCATGCTGGTGGCTGGAGGCATCGTAGCTGGGATCTTCCTCATTTTCATCGAGATCGCCTACAAGCGACACAAGGATGCCCGTAGGAAGCAGATGCAGCTGGCTTTTGCAGCCGTGAACGTGTGGAGGAAGAACCTGCAG
Seq A exon
GTAGGACAGGCCACCCTCCGAGGCCTGGCGTCCAGGGCCCCGCCAGGCCACGGCCCTACTCTATCCCTACAGGCCGTGGCACTGGCTCTGGCTCATGGGCAGGACTGGTGCTAGGAGCCATGGCCAGGGGCAGTGGTGAGTGTTCCCAAGGCACAGGGGCAGCACAGGCAGGGGCTGCCTGCAGGTGGCCACCCACTGCCAAGCTGGGCCAAGGGAAGCCATGCACCCTGCTTCAAGCCTCTGCCCGGCCCCTCTGTCTCCAAGGTCAGCTACTGGCACCCAATCCATAGGAAGGCAAGCAGGCAGGGTAAGACAAGGGCCCTCCTGTGTGAACCTGAGATGCATTATCCTTCTATCATCCAAGCACCTCTGACACCATCTGGGGACCCCTTTTCATGCTGTGTCTTGCTTTGTGATTCCAAATCTAAATGCAGCTGATCTGCCTCAGGCCACATCCGTGTGGATTTGTGGTTAGTGGGGATGAGGCTGCATGTCAGAGCCCACCAGGGAAAGGGACAGGGTGGGCAGTGAGGCTCACACAGGCCTGAAGACTAGTGGCCAATGGTCAGGATCCGATTCACTTGTCTCTTCTCTTTCTCTGGGTGTCTTCCTGGAGCTGTGTCCTGAGCTGGCATTAACATTGCAATGAGGGCTATGGGCGGACGGGGCTATTGGAGCCCCCATACCTCTCATCCACCCATTCTTGCTTTTGGCCCTACAGGTCCCCTGGGGACCTGGCCACAACTGTCCAGGGCCATGCTGGCCATCAGACTCCAGGCCAGCGTCCCCGGATCTGCCTCTGTCTATCACTCCAACTCCAACAGGACATTTCCTCGGGTCCTTGGCCCTTTCCTGGTGTGTGCCCTTTGGGGTCAGCAGCCTCTGAACAGAAAGGCTGGTGTGGCCTGAGGGGAAGCTCTTCCTGTCCTCAGAGGCTCCTCCTCCTCAGGATGCCTCTAAGCCAGGGCCACCCAGGAGCCAGGGAGCCAGGCGGACATCCCAGGAAGAGTGCCGTCAGGACCCCCCAAGCCCAGACCCAGCACAAGCAAGGACAGGCCCAACCCCGGGCAGAAGAGGCCACTCTTGAAAGTCTGGCTGTTGGTCCGTCTTTTCAGCACAGTGAGGCAGGCAGGAGTCAGGGCCTGAGTGACCTGCCAGGCCTGGCAGCGGCCCCAAGGAGCAGGCAAGGGCAGGTGTGGCCGCCACCCTTAGTTGTCTAATCGCTTATACATATTCATTTTAG
Seq C2 exon
GATAGAAAGAGTGGTAGAGCAGAGCCCGACCCTAAAAAGAAAGCCACATTTAGGGCTATCACCTCCACCCTGGCCTCCAGCTTCAAGAGACGTAGGTCCTCCAAAGACACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026959-Grin1:NM_008169:18
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.005 A=NA C2=0.635
Domain overlap (PFAM):
C1:
PF0006021=Lig_chan=PD(3.4=18.4),PF105624=CaM_bdg_C0=WD(100=59.2)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCTTCATGCTGGTGGCTGG
R:
CGTGTCTTTGGAGGACCTACG
Band lengths:
255-1498
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: