HsaINT0072510 @ hg19
Intron Retention
Gene
ENSG00000176884 | GRIN1
Description
glutamate receptor, ionotropic, N-methyl D-aspartate 1 [Source:HGNC Symbol;Acc:4584]
Coordinates
chr9:140056376-140056742:+
Coord C1 exon
chr9:140056376-140056540
Coord A exon
chr9:140056541-140056623
Coord C2 exon
chr9:140056624-140056742
Length
83 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGC
5' ss Score
7.93
3' ss Seq
GACCTCGCGTCCCTCCGCAGGAG
3' ss Score
9.68
Exon sequences
Seq C1 exon
GTGAACAACAGCAACAAGAAGGAGTGGAATGGGATGATGGGCGAGCTGCTCAGCGGGCAGGCAGACATGATCGTGGCGCCGCTAACCATAAACAACGAGCGCGCGCAGTACATCGAGTTTTCCAAGCCCTTCAAGTACCAGGGCCTGACTATTCTGGTCAAGAAG
Seq A exon
GTGGGCAGGGGCCGGGTGGCGGGGTGGCGGCGGGGGGAGTCCCTGGAGGGCCCGGGCCGCGCTGACCTCGCGTCCCTCCGCAG
Seq C2 exon
GAGATTCCCCGGAGCACGCTGGACTCGTTCATGCAGCCGTTCCAGAGCACACTGTGGCTGCTGGTGGGGCTGTCGGTGCACGTGGTGGCCGTGATGCTGTACCTGCTGGACCGCTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000176884-GRIN1:NM_007327:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.055 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0049715=SBP_bac_3=FE(15.8=100)
A:
NA
C2:
PF0049715=SBP_bac_3=FE(11.4=100),PF0006021=Lig_chan=PU(9.4=62.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCGCAGTACATCGAGTTTTC
R:
GTCCAGCAGGTACAGCATCAC
Band lengths:
175-258
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)