HsaINT0072526 @ hg19
Intron Retention
Gene
ENSG00000176884 | GRIN1
Description
glutamate receptor, ionotropic, N-methyl D-aspartate 1 [Source:HGNC Symbol;Acc:4584]
Coordinates
chr9:140055508-140055868:+
Coord C1 exon
chr9:140055508-140055649
Coord A exon
chr9:140055650-140055740
Coord C2 exon
chr9:140055741-140055868
Length
91 bp
Sequences
Splice sites
5' ss Seq
GCCGTGAGT
5' ss Score
8.56
3' ss Seq
TACCGCCCGCACCTACCCAGCCC
3' ss Score
2.49
Exon sequences
Seq C1 exon
ATTGTGACGATCCACCAGGAGCCCTTCGTGTACGTCAAGCCCACGCTGAGTGATGGGACATGCAAGGAGGAGTTCACAGTCAACGGCGACCCAGTCAAGAAGGTGATCTGCACCGGGCCCAACGACACGTCGCCGGGCAGCC
Seq A exon
GTGAGTGCGCGGGGCAGGGCGCGGGGCGCGGGGCAGGGCGCGGGGCGTGGGGCGGTCTGGAGCCCAGCAGTTACCGCCCGCACCTACCCAG
Seq C2 exon
CCCGCCACACGGTGCCTCAGTGTTGCTACGGCTTTTGCATCGACCTGCTCATCAAGCTGGCACGGACCATGAACTTCACCTACGAGGTGCACCTGGTGGCAGATGGCAAGTTCGGCACACAGGAGCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000176884-GRIN1:NM_007327:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.250 A=NA C2=0.023
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0049715=SBP_bac_3=PU(10.2=81.4)
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:
GAGCCCTTCGTGTACGTCAAG
R:
AGGTCGATGCAAAAGCCGTAG
Band lengths:
170-261
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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)