HsaINT0072514 @ hg38
Intron Retention
Gene
ENSG00000176884 | GRIN1
Description
glutamate ionotropic receptor NMDA type subunit 1 [Source:HGNC Symbol;Acc:HGNC:4584]
Coordinates
chr9:137162846-137163330:+
Coord C1 exon
chr9:137162846-137163003
Coord A exon
chr9:137163004-137163168
Coord C2 exon
chr9:137163169-137163330
Length
165 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGG
5' ss Score
5.85
3' ss Seq
GACTCCGCCTCTGCCGGCAGCAA
3' ss Score
6.01
Exon sequences
Seq C1 exon
CTGAGGAACCCCTCGGACAAGTTTATCTACGCCACGGTGAAGCAGAGCTCCGTGGATATCTACTTCCGGCGCCAGGTGGAGCTGAGCACCATGTACCGGCATATGGAGAAGCACAACTACGAGAGTGCGGCGGAGGCCATCCAGGCCGTGAGAGACAA
Seq A exon
GTGAGGCGCGGGCGGCCACCCTGGCGGGGCGGGACAGGTGCGGGGAGGGGGAGGGTGGCCTCCACCGGGCAGGAGAGCGTCCGGGCCGGGCACCCCGGAGGGCGCGGGCGTGGGGCTTCCAGGCTGGCAGGACCAAGGCCCCCGTGACTCCGCCTCTGCCGGCAG
Seq C2 exon
CAAGCTGCATGCCTTCATCTGGGACTCGGCGGTGCTGGAGTTCGAGGCCTCGCAGAAGTGCGACCTGGTGACGACTGGAGAGCTGTTTTTCCGCTCGGGCTTCGGCATAGGCATGCGCAAAGACAGCCCCTGGAAGCAGAACGTCTCCCTGTCCATCCTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000176884:ENST00000460273:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
In the CDS, with uncertain impact
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0049715=SBP_bac_3=FE(15.2=100),PF0006021=Lig_chan=FE(19.5=100)
A:
NA
C2:
PF0049715=SBP_bac_3=FE(15.7=100),PF0006021=Lig_chan=FE(20.3=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:
AGGAACCCCTCGGACAAGTTT
R:
AGCGGAAAAACAGCTCTCCAG
Band lengths:
250-415
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development