RnoINT0067640 @ rn6
Intron Retention
Gene
ENSRNOG00000011726 | Grin1
Description
glutamate ionotropic receptor NMDA type subunit 1 [Source:RGD Symbol;Acc:2736]
Coordinates
chr3:2513023-2513513:-
Coord C1 exon
chr3:2513356-2513513
Coord A exon
chr3:2513185-2513355
Coord C2 exon
chr3:2513023-2513184
Length
171 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGC
5' ss Score
7.47
3' ss Seq
GACTCTGCTCCTGCCGGCAGCAA
3' ss Score
6.62
Exon sequences
Seq C1 exon
CTCAGAAACCCCTCAGACAAGTTCATCTACGCAACTGTAAAGCAGAGCTCCGTGGACATCTACTTCCGGAGGCAGGTGGAGTTGAGTACCATGTACCGGCACATGGAAAAACACAATTACGAGAGCGCAGCTGAGGCCATCCAGGCTGTGCGGGACAA
Seq A exon
GTAAGCAAGCAGACCAAGGGCTGCCCTGGCTGGGGGGGGGGGGACAGTAAAGGGACAGGCAAAGGGGAGCCCATCACCCAGGAAGCACAAGCGAAGACTGTCTACTGCAGTGTGAGCAGGGTGGGGTGAACGGGCTACTCGGGGCTCCTTTGACTCTGCTCCTGCCGGCAG
Seq C2 exon
CAAGCTGCACGCCTTTATCTGGGACTCGGCCGTGCTGGAGTTTGAGGCTTCACAGAAGTGCGATCTGGTGACCACGGGTGAGCTGTTCTTCCGCTCAGGCTTTGGCATCGGCATGCGCAAGGACAGCCCCTGGAAGCAGAACGTTTCCCTGTCCATACTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000011726:ENSRNOT00000037725:16
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(15.2=100),PF0006021=Lig_chan=FE(19.5=100)
A:
NA
C2:
PF0049715=SBP_bac_3=FE(15.8=100),PF0006021=Lig_chan=FE(20.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGGCAGGTGGAGTTGAGTA
R:
ATGGACAGGGAAACGTTCTGC
Band lengths:
247-418
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]