DreINT0075086 @ danRer10
Intron Retention
Gene
ENSDARG00000025728 | grin1b
Description
glutamate receptor, ionotropic, N-methyl D-aspartate 1b [Source:ZFIN;Acc:ZDB-GENE-051202-2]
Coordinates
chr5:29028253-29028606:-
Coord C1 exon
chr5:29028471-29028606
Coord A exon
chr5:29028381-29028470
Coord C2 exon
chr5:29028253-29028380
Length
90 bp
Sequences
Splice sites
5' ss Seq
CAGGTATTT
5' ss Score
7.51
3' ss Seq
ACTGGCTTGTATAAATACAGGTC
3' ss Score
5.48
Exon sequences
Seq C1 exon
ATTGTAACAATTCATCAAGAGCCCTTTGTCTACGTGAAGCCGACTTTACGAGATGGAACCTGTAAGGAAGAGCACACTGTAAATGGAGTCAAAATCAAAAAAGTGATCTGCACCGGCCCAAACGAGACCATTCCAG
Seq A exon
GTATTTATTATGTGTTATATCATAGTGTATGCTATTGTTTTGGATTGCACTTGTGCTTTGTCTGGATCTGACTGGCTTGTATAAATACAG
Seq C2 exon
GTCGCCCCATAGTGCCTCAGTGCTGCTATGGGTTCTGCATTGACCTTTTGATCAAACTTGCATTCACAATGAACTTCACCTATGAAGTGCATCTTGTGGCTGATGGCAAATTTGGCACTCAGGAGCGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000025728:ENSDART00000034849:10
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:
NO
A:
NA
C2:
PF0049715=SBP_bac_3=PU(10.0=79.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCCCTTTGTCTACGTGAAGC
R:
TCAAAAGGTCAATGCAGAACCCA
Band lengths:
168-258
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]