DreINT0075104 @ danRer10
Intron Retention
Gene
ENSDARG00000025728 | grin1b
Description
glutamate receptor, ionotropic, N-methyl D-aspartate 1b [Source:ZFIN;Acc:ZDB-GENE-051202-2]
Coordinates
chr5:29028471-29028780:-
Coord C1 exon
chr5:29028694-29028780
Coord A exon
chr5:29028607-29028693
Coord C2 exon
chr5:29028471-29028606
Length
87 bp
Sequences
Splice sites
5' ss Seq
AAGGTACGT
5' ss Score
10.75
3' ss Seq
CTTATTTTTCCCACTGATAGATT
3' ss Score
7.65
Exon sequences
Seq C1 exon
GTTGTAATGAACGCTCAGAGGAAGATTATTTGGCCAGGAGGAGAGACTGAAAAGCCGAAAGGCTATCAGATGTCAACTAGATTAAAG
Seq A exon
GTACGTCTCATTGCAGCAATTTTAATACATCTTTGTTTTAGGAGGAGGGGGTGTTACATTGCATTTACTTATTTTTCCCACTGATAG
Seq C2 exon
ATTGTAACAATTCATCAAGAGCCCTTTGTCTACGTGAAGCCGACTTTACGAGATGGAACCTGTAAGGAAGAGCACACTGTAAATGGAGTCAAAATCAAAAAAGTGATCTGCACCGGCCCAAACGAGACCATTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000025728:ENSDART00000034849:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.034 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCCAGGAGGAGAGACTGAAA
R:
GGCCGGTGCAGATCACTTTTT
Band lengths:
174-261
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]