RnoINT0067636 @ rn6
Intron Retention
Gene
ENSRNOG00000011726 | Grin1
Description
glutamate ionotropic receptor NMDA type subunit 1 [Source:RGD Symbol;Acc:2736]
Coordinates
chr3:2514073-2514430:-
Coord C1 exon
chr3:2514266-2514430
Coord A exon
chr3:2514192-2514265
Coord C2 exon
chr3:2514073-2514191
Length
74 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGC
5' ss Score
10.08
3' ss Seq
TGACCCTTGGTCACTTGTAGGAG
3' ss Score
7.55
Exon sequences
Seq C1 exon
GTAAACAACAGCAACAAAAAGGAGTGGAACGGAATGATGGGCGAGCTACTCAGTGGCCAAGCGGACATGATTGTGGCACCACTGACCATCAACAATGAGCGTGCGCAGTACATAGAGTTCTCCAAGCCCTTCAAGTACCAGGGCCTGACCATTTTGGTCAAGAAG
Seq A exon
GTAGGCAGGGACCAGGTGGGGATGGGATGGGGCGGTGGATGGCCCTGGTGACACTGACCCTTGGTCACTTGTAG
Seq C2 exon
GAGATTCCCAGGAGCACACTGGACTCATTTATGCAGCCTTTTCAGAGCACACTGTGGTTGCTAGTAGGACTGTCAGTTCATGTGGTGGCTGTGATGCTGTACCTGCTGGACCGCTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000011726:ENSRNOT00000037725:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.073 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0049715=SBP_bac_3=FE(15.8=100)
A:
NA
C2:
PF0049715=SBP_bac_3=FE(11.4=100),PF0006021=Lig_chan=PU(9.4=62.5)
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:
GCGTGCGCAGTACATAGAGTT
R:
GTCCAGCAGGTACAGCATCAC
Band lengths:
178-252
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]