HsaINT0072523 @ hg19
Intron Retention
Gene
ENSG00000176884 | GRIN1
Description
glutamate receptor, ionotropic, N-methyl D-aspartate 1 [Source:HGNC Symbol;Acc:4584]
Coordinates
chr9:140051315-140052975:+
Coord C1 exon
chr9:140051315-140051489
Coord A exon
chr9:140051490-140052830
Coord C2 exon
chr9:140052831-140052975
Length
1341 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGC
5' ss Score
6.32
3' ss Seq
AGCTATGCTTCCTTCCCTAGAGT
3' ss Score
8.72
Exon sequences
Seq C1 exon
GCATCCTCGGGCTGCAGCTCATCAACGGCAAGAACGAGTCGGCCCACATCAGCGACGCCGTGGGCGTGGTGGCCCAGGCCGTGCACGAGCTCCTCGAGAAGGAGAACATCACCGACCCGCCGCGGGGCTGCGTGGGCAACACCAACATCTGGAAGACCGGGCCGCTCTTCAAGAG
Seq A exon
GTGGGCGGGGCCTCCCCGGAGCTGGGCGGGGCTGCTCTTGGGGAGGTGGGCGGGGTCACTCCAGAGATGGGCGGGGCCGCTCTTGGGGAGGTGGGCGGGGCCACTCTCCAGAGCTGGGCGGAGCAGCTCTCAGGACTAGGCGGGGCCGCTCTTAGGGAGCTGGGGGAGCGCTCCTCAAGAGATGGGTGGGGGCACTCTCGGGGAGGTGGGCGGGGTCGCTTCCAGGAGGTGGGCGGCGTCGCTCTCAGGGGTACTGCAGTGGAGCCTGCTGCCAACATCCTCTGGACACTGTTACTTCTCTCCTCTCCCCCCACACCCCCAGCACCACCACATCTAATGGCACAATCATCTGCCCTCTTCTCAACACTGACACCAGTACCTGGGCCGTCACTGGAGTGGGGACTGGCTCCACTGCCTCCGCCCCTACTTTCCACACTGCAGCCCACCCTGAAACAGCACCCCTCTCCCTGTGTGGCTGGCAGCCTTTGGGAGGAGGCTCTTGATGCAGATGGGGACTGAAAGCTTCCAGGGACCCAGGAGGCCAGACAAGCAGCCCAAGAACAGCACACGAGCCTTAGACAGCCAGGGTTGGCCAAGGCCCAGAGACCCAAGTGAACATCTGCAGTGTGGCAGGAGTTAGCTCACAGCACGCCTGGACACCATGCCATGCCAGCTCACCCCCAGATCCCCAACCACTGAGTAGCACGTGCAGAGCCACCATCCACAACGCCCACATAAGTGCAGATGTAGGCAGCACGTGTGCACACACACGACACACATACACAGAACCATGTGTGCACACAGACTCAGGCACATGACACACATGTGACACAAGCACATGCATGGGGTGCACCCCACATAGGGATCACGTGTGCACACAGGTTCACTGATGTGGCCCGATGGGTACAATGCACACGTGCACACACAGCCGGACAGGACAGCCTGGTGGTTAGAGCTGGCTCAACCTCGCCTTCACTTGCTGGCAAGAGGGCAGGCATCCTTCTGAGCTTCTGCCTCCGTCTCTGTAAGGCAGGATGGTTCTGAGGACAACGTCCTAACCCACAGAAAGCCGGGTCTGGCACCCATAAACCACTCAGCTGTCATGAACCACACCGTCCATCTGGTGCAGGCAGATACCACGGTGTCCAGGGTCTGGCGTCTGCTGATCTTTCCGTTCTTGGGACTGGGACAAGGGAAAAGCCCAAGCTGCTCAGCCGGCAGGAGAAGGAGCAGGGAGAAGGAGCAGGGGGAAGGAGCAGGGAGAAGCAGCAGGGGGAAGGAGCAGGGAGGAGCAGGAGAAGGAGCATCTCTGAGAAGCCTCAGCTATGCTTCCTTCCCTAG
Seq C2 exon
AGTGCTGATGTCTTCCAAGTATGCGGATGGGGTGACTGGTCGCGTGGAGTTCAATGAGGATGGGGACCGGAAGTTCGCCAACTACAGCATCATGAACCTGCAGAACCGCAAGCTGGTGCAAGTGGGCATCTACAATGGCACCCAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000176884-GRIN1:NM_007327:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.068 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0109423=ANF_receptor=FE(18.1=100)
A:
NA
C2:
PF0109423=ANF_receptor=PD(10.6=69.4)
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:
ATCCTCGGGCTGCAGCTC
R:
GTGGGTGCCATTGTAGATGCC
Band lengths:
318-1659
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)