RnoINT0067650 @ rn6
Intron Retention
Gene
ENSRNOG00000011726 | Grin1
Description
glutamate ionotropic receptor NMDA type subunit 1 [Source:RGD Symbol;Acc:2736]
Coordinates
chr3:2519462-2520965:-
Coord C1 exon
chr3:2520791-2520965
Coord A exon
chr3:2519607-2520790
Coord C2 exon
chr3:2519462-2519606
Length
1184 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGC
5' ss Score
6.32
3' ss Seq
AAGCTAGCCTCTCTTCCCAGGGT
3' ss Score
3.88
Exon sequences
Seq C1 exon
GCATCATCGGACTTCAGCTCATCAATGGCAAGAATGAGTCAGCCCACATCAGTGACGCCGTGGGCGTGGTGGCACAGGCAGTTCACGAACTCCTAGAGAAGGAGAATATCACTGACCCACCGCGGGGTTGCGTGGGCAACACCAACATCTGGAAGACAGGACCATTGTTCAAGAG
Seq A exon
GTGGGCAGGGTTGCTCTCAGTAGGTGGGGGAATAGGCTGTTCTTAAACAGGGGTGGGGATGGGTAGGGGGTGTTTCACTCTTTCAGGGGTGGTCCAGCCGTTCCCTATCTAGGACATGTTATATGGTTAGTCACCTCCATCGCAGATCCATATTCCCAGTACCACATCTTCTGTCTTTATTAGTACACTGTCGCTGTCTTCAGACACACCAGAAGAGGGCATCAGGGGGGCTGGAGAGATGGCTCAGCGGTTAAGAGCACTGACTGCTCTCCCAGAGGTCCTGAGTTCAATTCCCAGCAACCACATGGTGGCTCACAACCATCTGTAAAGAGATCCGATGCCCTCTTCTGGTGTGTCTGAAGACAGCTACAGTGTACTTATATATAATAAATGAATAAATCTTAAAAAAAAAAACAGTTTAAAAAGAGGGCATCAGATCTCATTACAGATGATTGTAAGCCACCATGTGGTTGCTGGGATTTGAACTCAGGACCTCTGGAAGAGCAATCAGTGCACTGAGCCATCTCTCCAACCCACATCTTCTGTCTTTCCCGTGGGATGTTCTAGGAACTCAGAAATTCAGAGTAGGCATCCATGGACAGTAGAGATTAAGGCTGACCGAGGGAATAATGGCTGCAGGACCCCAGAGCCACTGTCAATGGTTTCCTATGTATCAGTGCGGTTACAGGCTGCATACACATGCCAGTGAATGCACAGGAACTCGGAGGAACATGACATCTGAATGCTACAAGCTCACTCAGAGGAGTGACCCTATACTTCAGTTGCATGCACACAGGCTCTCTGAAATGCTCCACTGAGCAAACATACAGCCAGGCAAGCCACCCAGGGGCTACAGCTAGGTACAGGCTCCGTGTACGTCCCCTATTTGATGGCAAATGGGCCTGAAGTTCTCTGAGCTTCTGCCTTCCCTGTAAAACTGGGATGGCAGCTGTGACAATCACATGTCCCAATCCAGAGAAGACTTTGACATGGCTTCAGATGCAGTAGCTGTCCATCTGGTGCTGGCAGGCACACACCATGTCCTCCACTCAGTGAGGAGCTACCTACCATCTGCTAATCTTTTCCTTTCTCGAGACTGGGGCAGAAGGGATGGGAGCTTGGGCCACTCAGAAGCCAGTAAGGATGGGTGTTCTTGTCAGGTCTAAGCTAGCCTCTCTTCCCAG
Seq C2 exon
GGTGCTGATGTCTTCTAAGTATGCGGACGGAGTGACTGGCCGTGTGGAATTCAATGAGGATGGGGACCGGAAGTTTGCCAACTATAGTATCATGAACCTGCAGAACCGCAAGCTGGTGCAAGTGGGCATCTACAATGGTACCCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000011726:ENSRNOT00000037725:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.068 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0109423=ANF_receptor=FE(17.0=100)
A:
NA
C2:
PF0109423=ANF_receptor=PD(10.0=69.4)
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:
GCATCATCGGACTTCAGCTCA
R:
TTGTAGATGCCCACTTGCACC
Band lengths:
310-1494
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]