HsaINT0072516 @ hg19
Intron Retention
Gene
ENSG00000176884 | GRIN1
Description
glutamate receptor, ionotropic, N-methyl D-aspartate 1 [Source:HGNC Symbol;Acc:4584]
Coordinates
chr9:140058011-140058356:+
Coord C1 exon
chr9:140058011-140058120
Coord A exon
chr9:140058121-140058210
Coord C2 exon
chr9:140058211-140058356
Length
90 bp
Sequences
Splice sites
5' ss Seq
CCGGTGCGT
5' ss Score
9.74
3' ss Seq
CTCTGGGTCCCGGCACACAGGGG
3' ss Score
4.43
Exon sequences
Seq C1 exon
GTCCCACGAGAATGGCTTCATGGAAGACCTGGACAAGACGTGGGTTCGGTATCAGGAATGTGACTCGCGCAGCAACGCCCCTGCGACCCTTACTTTTGAGAACATGGCCG
Seq A exon
GTGCGTTCTCCTTCATCCATTCTCGGGTGGGTTCTCCGTGGGCTGCGGCCTCCCTGGCCAGCAACTGAGGCTCTGGGTCCCGGCACACAG
Seq C2 exon
GGGTCTTCATGCTGGTAGCTGGGGGCATCGTGGCCGGGATCTTCCTGATTTTCATCGAGATTGCCTACAAGCGGCACAAGGATGCTCGCCGGAAGCAGATGCAGCTGGCCTTTGCCGCCGTTAACGTGTGGCGGAAGAACCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000176884-GRIN1:NM_007327:17
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=0.017
Domain overlap (PFAM):
C1:
PF0049715=SBP_bac_3=PD(5.0=44.7),PF0006021=Lig_chan=FE(13.9=100)
A:
NA
C2:
PF0006021=Lig_chan=PD(3.4=18.4),PF105624=CaM_bdg_C0=WD(100=59.2)
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:
CCCCTGCGACCCTTACTTTTG
R:
GGTTCTTCCGCCACACGTTAA
Band lengths:
174-264
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)