HsaINT0072509 @ hg19
Intron Retention
Gene
ENSG00000176884 | GRIN1
Description
glutamate receptor, ionotropic, N-methyl D-aspartate 1 [Source:HGNC Symbol;Acc:4584]
Coordinates
chr9:140055741-140056540:+
Coord C1 exon
chr9:140055741-140055868
Coord A exon
chr9:140055869-140056375
Coord C2 exon
chr9:140056376-140056540
Length
507 bp
Sequences
Splice sites
5' ss Seq
CGGGTAGGC
5' ss Score
7.5
3' ss Seq
CCGGCTCTGTCGCCTCGCAGGTG
3' ss Score
11.3
Exon sequences
Seq C1 exon
CCCGCCACACGGTGCCTCAGTGTTGCTACGGCTTTTGCATCGACCTGCTCATCAAGCTGGCACGGACCATGAACTTCACCTACGAGGTGCACCTGGTGGCAGATGGCAAGTTCGGCACACAGGAGCGG
Seq A exon
GTAGGCTGGACGGCGGGGGTGGGGACCAGCGTGAGAGGGGCCTGCAGGCGCGGTCGGAGTGGGTGGGGCATGGAGTAGGCGGGGCTTGCAGATGGTGGGGGGTCCTGGGGTGAGTGGGGCATGGAGTGAGCGGAGCCTGCGGGCTGGGTCCTGGCGTGGGTAAAGCATGGGGTGGGCGGGGCCTGAGGGCTGGGTGGGGCCTGACATGGGAGGGGCCTGACGTGGGGGTCGGAGTGGGTGGGGCACGGAGTGGGCAGGGCCTGCAGGCGGGGGTCTGGAGTGGGCGGGACGTGGAGTGGGCGGGGCCTGCTGGCTGTGGTGGGGCCCGCCCGGCGTGGGAGGGGTCTGCGAGCCAGGGCGGGGCTGGAGTGGGGTGGGGCCTGCGAGCTGGGTAGGGTCTTGGGGAGAAGACCCCCGGAGTGCTCTAGGGCGGCTTCAGTCGGGGGTACCTGTGGCGGGAGCTGGGAGGACGCTGCCTGCATGCCCGCCGGCTCTGTCGCCTCGCAG
Seq C2 exon
GTGAACAACAGCAACAAGAAGGAGTGGAATGGGATGATGGGCGAGCTGCTCAGCGGGCAGGCAGACATGATCGTGGCGCCGCTAACCATAAACAACGAGCGCGCGCAGTACATCGAGTTTTCCAAGCCCTTCAAGTACCAGGGCCTGACTATTCTGGTCAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000176884-GRIN1:NM_007327:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.023 A=NA C2=0.055
Domain overlap (PFAM):
C1:
PF0049715=SBP_bac_3=PU(10.2=81.4)
A:
NA
C2:
PF0049715=SBP_bac_3=FE(15.8=100)
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:
CCACACGGTGCCTCAGTG
R:
CTTGACCAGAATAGTCAGGCCC
Band lengths:
286-793
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)