HsaINT0072514 @ hg19
Intron Retention
Gene
ENSG00000176884 | GRIN1
Description
glutamate receptor, ionotropic, N-methyl D-aspartate 1 [Source:HGNC Symbol;Acc:4584]
Coordinates
chr9:140057298-140057782:+
Coord C1 exon
chr9:140057298-140057455
Coord A exon
chr9:140057456-140057620
Coord C2 exon
chr9:140057621-140057782
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-GRIN1:NM_007327:15
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=0.000
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(15.8=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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)