RnoINT0067643 @ rn6
Intron Retention
Gene
ENSRNOG00000011726 | Grin1
Description
glutamate ionotropic receptor NMDA type subunit 1 [Source:RGD Symbol;Acc:2736]
Coordinates
chr3:2510913-2512421:-
Coord C1 exon
chr3:2512276-2512421
Coord A exon
chr3:2511024-2512275
Coord C2 exon
chr3:2510913-2511023
Length
1252 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
CTTATACATATTCATTTTAGGAT
3' ss Score
8.75
Exon sequences
Seq C1 exon
GGGTCTTCATGCTGGTGGCTGGAGGCATCGTAGCTGGGATTTTCCTCATTTTCATTGAGATCGCCTACAAGCGACACAAGGATGCCCGTAGGAAGCAGATGCAGCTGGCTTTTGCAGCCGTGAACGTGTGGAGGAAGAACCTGCAG
Seq A exon
GTAGGACAGGCCACCCTCCGAGGCCTGGCGTCCAGGGCCCCGCCAGGCCACGGCCCTACTCTATCCCTACAGGCCGTGGCACTGGCTCTGGCTCATGGGCAGGACTGGTGCTAGGAGCCATGGCCAGGGGCAGTGGTGAGTGTTCCCAAGGCACAGGGGCAGCACAGGCAGTGGCTGCCAGCAGGTGGCCACCCACTGCCACGCTGGGTCAAGGGAAGCCATGTACCCTGCTTCAAGCCTCTGCCTGGCCCCTCTGTCTCCAAGGTCAGCTACTGGCACCCAATCCATAGGAAGGCAAACAGGCAGGGTAAGACAAGGGCCCTCCTGTGTATAGCACGTGAATGTGAGATGCACTTAGCCCTCTATCATCCAAGCACCTCTGACACCATTTGGGGACCCCTTTTCATGCTGTGTCTTGCTTTGTGATTCCAAATCTAAATGGGGCTGATCTGCCTCAGGCCACATCCATGTGGATTTGTGGTTTGCAGGAATGAGTCTGCATGTGGGATGGTCAGAGTCCACCAGGGAAAGGGACAGGGTGGGCAGTGAGGCTCAGAGGCCTGAAGACTAGTGGCCAATGATTAGGCTCTGATTCGTCTCTTCTCTTTCTCTGGGTGTCTCCCTGTAGCTGTGTTCTGAGCTGACATTGACATTGAAATGAGGGCTGTGGGCGGACAGGGCTATGGGAGCCCCCACACCTCTCATCCACCCATTCTTGCTTTTGGCCCTACAGGTCCCCTGGGGACCTGGCCACAACTGTTCAGGGCCATGCTGGCCATCTGACTCCAGGCCAGCGTCCCCGGATCTGCCTCTGTCTATCACTCCAATTCCAACTGGACACTTCCTCGGGTCCTTGGCCCTTTCCTGGTGTGCGCCCTTTGGGGTCAGCAGCCTCTGAACAGAAAGGCTGGTGTGGCCTGAGGGGAAGCACTTCCTGTCCTCAGGGGCTCCTCCTCCTCAGGATGCCTTCAAGCTAGGGCCACCCAGGAGCCAGGGAGCAGGCGGACATCCCAGGAAGAGTGCCATCAGGACCCCAAGCCCAGACCCAGCACAAGCAAGGACAGGCCCAACCCCGGGCAGAAGAGGCCACTCTTGAAAGTCTGGCTGTTGGTCCGTCTGTTGAGCACAGTGAGGCAGGCAGGAGTCAGGGCCTGAGTGACCGGCCAGGCCTGGCAGCGGCCCCAAGGAGCAGGCAAGGGCAGGTGTGGCCGCCACGCTTAGCTGTCTAATCGCTTATACATATTCATTTTAG
Seq C2 exon
GATAGAAAGAGTGGTAGAGCAGAGCCCGACCCTAAAAAGAAAGCCACATTTAGGGCTATCACCTCCACCCTGGCCTCCAGCTTCAAGAGACGTAGGTCCTCCAAAGACACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000011726:ENSRNOT00000037725:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.007 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
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCTTCATGCTGGTGGCTGG
R:
CGTGTCTTTGGAGGACCTACG
Band lengths:
255-1507
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]