RnoINT0067639 @ rn6
Intron Retention
Gene
ENSRNOG00000011726 | Grin1
Description
glutamate ionotropic receptor NMDA type subunit 1 [Source:RGD Symbol;Acc:2736]
Coordinates
chr3:2513356-2513768:-
Coord C1 exon
chr3:2513620-2513768
Coord A exon
chr3:2513514-2513619
Coord C2 exon
chr3:2513356-2513513
Length
106 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGG
5' ss Score
7.13
3' ss Seq
TGAGGTCTCTGTCCCTGCAGCTC
3' ss Score
9.56
Exon sequences
Seq C1 exon
GTGCCCCCCGGAGTTTCTCTGCACGTATCCTAGGCATGGTGTGGGCTGGTTTCGCCATGATCATAGTGGCTTCCTACACTGCCAACTTGGCAGCTTTCCTGGTGCTGGATCGGCCTGAGGAGCGCATCACGGGCATCAATGACCCCAGG
Seq A exon
GTGAGGCCCCTGGGCTGGGGGTTGGGGGAAGGGAGGGGCGAGAGGGAGTGCCTGTTTCTTGTGAGGCTTGGGGAGCAGCCATGAGCTGAGGTCTCTGTCCCTGCAG
Seq C2 exon
CTCAGAAACCCCTCAGACAAGTTCATCTACGCAACTGTAAAGCAGAGCTCCGTGGACATCTACTTCCGGAGGCAGGTGGAGTTGAGTACCATGTACCGGCACATGGAAAAACACAATTACGAGAGCGCAGCTGAGGCCATCCAGGCTGTGCGGGACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000011726:ENSRNOT00000037725:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.040 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0049715=SBP_bac_3=FE(14.3=100),PF0006021=Lig_chan=FE(18.4=100)
A:
NA
C2:
PF0049715=SBP_bac_3=FE(15.2=100),PF0006021=Lig_chan=FE(19.5=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:
GCACGTATCCTAGGCATGGTG
R:
TGTGTTTTTCCATGTGCCGGT
Band lengths:
244-350
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]