HsaINT0072517 @ hg19
Intron Retention
Gene
ENSG00000176884 | GRIN1
Description
glutamate receptor, ionotropic, N-methyl D-aspartate 1 [Source:HGNC Symbol;Acc:4584]
Coordinates
chr9:140058211-140059748:+
Coord C1 exon
chr9:140058211-140058356
Coord A exon
chr9:140058357-140059637
Coord C2 exon
chr9:140059638-140059748
Length
1281 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
CTTATACATATTCATTTTAGGAT
3' ss Score
8.75
Exon sequences
Seq C1 exon
GGGTCTTCATGCTGGTAGCTGGGGGCATCGTGGCCGGGATCTTCCTGATTTTCATCGAGATTGCCTACAAGCGGCACAAGGATGCTCGCCGGAAGCAGATGCAGCTGGCCTTTGCCGCCGTTAACGTGTGGCGGAAGAACCTGCAG
Seq A exon
GTAGGGCAGGCCACCCTCCGAGGCCTGGTGCCCAGGGCCCGGCCTGGCCACGGCCCTCCTCCATCCCCGAAGGCCGTGGCACTGGCTCTGGCTCTGGTGGGCAGGACTGGAGCTAGGAGCCATGGCCAGGGGCAGTGGTGAGTGCTCCCAGGGCACGGGGGCAGCACCGGTGGGGGGCTGCCTGCAGGTGGCTGCCCACTGCAAAGCCGGGGCCGAGGGAGGCCACGCACCCTGCTCCAAGCCTCCGCCTGGCCCCTCTGTCTCCAGAGTCGCCCGCCGGTACCCATTCCATAGGAAGGCAATCAGGCAGGGTAAGACAGGGGCCCGCCTGTGTATGGCACGTGAGTCCAAGATGCATTTTGCCCTCCGCCGACCCAAGCCCCTTGACACCCTTCGGAGACCCCCCCCTTTCCTGCTATGTCCTTGTGCTCCGTGACTCTAATCCGAATTGGGCCAGGTCCGGTCCTGCCTGGTGCCCAGGTTGTATCCATGAGAATTTGCCACCAGCAAGGGCAGCCACGGCCCACCTGGGACAGGGTGGGCAGTGGGCCTGTACAGGCCTAAGGGCTCGTGGCCCGCGGTCGAGTTCCGGTTCACTCCGTCTCTTCTCTTTCTCTGGGTGCCGTCCTGGAGCCTGTGTCCTGAGATGAAGCCGACAGTGCGGCCAGGGCTGCTGGGGGATGGGGGTTGCTGGAGGCTCCACACCTCTCATCCGCCCGCTCTTGCTCTTGGCCCCCACAGGTCCCCTGGGGACCTGGCCGCTGCCAGCACTGGCGGGCACAGGCCACCTGGCCATCAGACCTGAGGCCAGAGTCCCGGGAGCTGCCTCTGTCACTCCAATTCCACCTCGACACCTGCCTCCAGCCCTCGGCCCCTTCCTGAATCTTGGTGTGTGCCCCTTGGGGGTCAGTGGCCTCCACGCAGACAGCTGGTGTGGCCTGAGGGGCAACTCCTCCAGTCCTCAGAGGACTCCTCCTCCTCGGGACGCCTGTAAGCCAGGGCCACCCAGGAGCCAGGGAGCCAGGCGGACCTCCCAGGAAGAGCCAGCCGAGAGCCCCCAAGCCCAGCCCCAGCACGAGCAAGGTCAGGCCCGAGACCCCGGGCAGGAGAAGAGGCCACCCTCGAACGTCCGCTGTCGGCCCGTCTGTCCAGCACAGGGAGGCAGGCAGGAGCGAGGGCCCAAGTGGCCGGCCAGGCTGGGCAGCGGCCCATGCAGGAGCAGGCGAGGGCAGGTGTGGCCACCACCCTAGCCATCTAATCACTTATACATATTCATTTTAG
Seq C2 exon
GATAGAAAGAGTGGTAGAGCAGAGCCTGACCCTAAAAAGAAAGCCACATTTAGGGCTATCACCTCCACCCTGGCTTCCAGCTTCAAGAGGCGTAGGTCCTCCAAAGACACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000176884-GRIN1:NM_007327:18
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.017 A=NA C2=0.635
Domain overlap (PFAM):
C1:
PF0006021=Lig_chan=PD(3.4=18.4),PF105624=CaM_bdg_C0=WD(100=59.2)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCTTCATGCTGGTAGCTGGG
R:
GTGTCTTTGGAGGACCTACGC
Band lengths:
254-1535
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)