DreINT0075090 @ danRer10
Intron Retention
Gene
ENSDARG00000025728 | grin1b
Description
glutamate receptor, ionotropic, N-methyl D-aspartate 1b [Source:ZFIN;Acc:ZDB-GENE-051202-2]
Coordinates
chr5:29018975-29019374:-
Coord C1 exon
chr5:29019262-29019374
Coord A exon
chr5:29019124-29019261
Coord C2 exon
chr5:29018975-29019123
Length
138 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGAA
5' ss Score
6.33
3' ss Seq
CTCCACGCTTCCATTCACAGGTG
3' ss Score
9.83
Exon sequences
Seq C1 exon
CCCATTTGGAAGGTTTAAAGTGAATAGTGAAGAGGAAGAAGAAGACGCCCTCACCTTATCCTCCGCTATGTGGTTCTCCTGGGGTGTACTTCTGAACTCCGGCATTGGAGAAG
Seq A exon
GTAGAAAAATCAGCAAGCAAATTATTATTCGCTCCATTTCCCCCTGTGAGGTGCAGATATTGCTGACTCAGTGTTTGATTGATTGTGCAGTAAGCATAATATTCATTATCGCTCTCACCTCCACGCTTCCATTCACAG
Seq C2 exon
GTGCCCCTCGGAGCTTTTCGGCGAGGATTTTAGGTATGGTGTGGGCTGGTTTTGCTATGATTATAGTTGCATCTTATACTGCCAATTTGGCAGCCTTCCTAGTGCTGGATCGGCCTGAGGAGCGCATTACCGGCATCAACGACCCTAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000025728:ENSDART00000034849:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.040
Domain overlap (PFAM):
C1:
PF0049715=SBP_bac_3=FE(11.1=100),PF0006021=Lig_chan=FE(14.3=100)
A:
NA
C2:
PF0049715=SBP_bac_3=FE(14.4=100),PF0006021=Lig_chan=FE(18.4=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:
CCCATTTGGAAGGTTTAAAGTGA
R:
GGGTCGTTGATGCCGGTAATG
Band lengths:
258-396
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]