RnoINT0067642 @ rn6
Intron Retention
Gene
ENSRNOG00000011726 | Grin1
Description
glutamate ionotropic receptor NMDA type subunit 1 [Source:RGD Symbol;Acc:2736]
Coordinates
chr3:2512276-2512614:-
Coord C1 exon
chr3:2512505-2512614
Coord A exon
chr3:2512422-2512504
Coord C2 exon
chr3:2512276-2512421
Length
83 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGC
5' ss Score
6.46
3' ss Seq
CTGAAGGTCCCTTCACACAGGGG
3' ss Score
4.27
Exon sequences
Seq C1 exon
GTCCCATGAGAATGGCTTCATGGAAGATCTGGATAAGACATGGGTTCGGTATCAGGAATGCGACTCCCGCAGCAATGCTCCTGCAACCCTCACTTTTGAGAACATGGCAG
Seq A exon
GTGTGCCTTTCATGCTGCTGTGACCCCGGGATGGATTAGGGGCTTTAATCTCTGGGCAGGCAGCTGAAGGTCCCTTCACACAG
Seq C2 exon
GGGTCTTCATGCTGGTGGCTGGAGGCATCGTAGCTGGGATTTTCCTCATTTTCATTGAGATCGCCTACAAGCGACACAAGGATGCCCGTAGGAAGCAGATGCAGCTGGCTTTTGCAGCCGTGAACGTGTGGAGGAAGAACCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000011726:ENSRNOT00000037725:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.007
Domain overlap (PFAM):
C1:
PF0049715=SBP_bac_3=PD(5.0=44.7),PF0006021=Lig_chan=FE(13.9=100)
A:
NA
C2:
PF0006021=Lig_chan=PD(3.4=18.4),PF105624=CaM_bdg_C0=WD(100=59.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTCCTGCAACCCTCACTTTT
R:
CTGCAGGTTCTTCCTCCACAC
Band lengths:
180-263
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]