RnoINT0067637 @ rn6
Intron Retention
Gene
ENSRNOG00000011726 | Grin1
Description
glutamate ionotropic receptor NMDA type subunit 1 [Source:RGD Symbol;Acc:2736]
Coordinates
chr3:2513845-2514191:-
Coord C1 exon
chr3:2514073-2514191
Coord A exon
chr3:2513958-2514072
Coord C2 exon
chr3:2513845-2513957
Length
115 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
CTTCTCTTTGCACTCCGCAGTCC
3' ss Score
8.22
Exon sequences
Seq C1 exon
GAGATTCCCAGGAGCACACTGGACTCATTTATGCAGCCTTTTCAGAGCACACTGTGGTTGCTAGTAGGACTGTCAGTTCATGTGGTGGCTGTGATGCTGTACCTGCTGGACCGCTTCAG
Seq A exon
GTGAGCACCATGCAGACAGCCAGACCCCTCCATGTGTAGGGAGGGCAGAACTGGGTAGGGCCGGGCAGAGCTGCCTCTCCTGTCCTCTCTCCCGCCTTCTCTTTGCACTCCGCAG
Seq C2 exon
TCCCTTTGGCCGATTCAAGGTGAACAGTGAGGAGGAGGAGGAAGATGCACTGACCCTGTCCTCTGCCATGTGGTTTTCCTGGGGCGTCCTGCTCAACTCCGGCATTGGGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000011726:ENSRNOT00000037725:13
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=0.000
Domain overlap (PFAM):
C1:
PF0049715=SBP_bac_3=FE(11.4=100),PF0006021=Lig_chan=PU(9.4=62.5)
A:
NA
C2:
PF0049715=SBP_bac_3=FE(11.1=100),PF0006021=Lig_chan=FE(14.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGATTCCCAGGAGCACACTG
R:
CTTCCCCAATGCCGGAGTTG
Band lengths:
232-347
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]