DreINT0075087 @ danRer10
Intron Retention
Gene
ENSDARG00000025728 | grin1b
Description
glutamate receptor, ionotropic, N-methyl D-aspartate 1b [Source:ZFIN;Acc:ZDB-GENE-051202-2]
Coordinates
chr5:29027899-29028380:-
Coord C1 exon
chr5:29028253-29028380
Coord A exon
chr5:29028064-29028252
Coord C2 exon
chr5:29027899-29028063
Length
189 bp
Sequences
Splice sites
5' ss Seq
CGTGTGAGT
5' ss Score
7.42
3' ss Seq
TGTTATCTTCCTGATACCAGGTA
3' ss Score
7.11
Exon sequences
Seq C1 exon
GTCGCCCCATAGTGCCTCAGTGCTGCTATGGGTTCTGCATTGACCTTTTGATCAAACTTGCATTCACAATGAACTTCACCTATGAAGTGCATCTTGTGGCTGATGGCAAATTTGGCACTCAGGAGCGT
Seq A exon
GTGAGTAATATGATAACTTTATTGATTTTTCACCTGCCTGAAGCTTTGCATGTCTTTTTGTTTTCAAGGTCATGCCATAGCCTTTCCCAGCTCTTCTTCACAGAGGCTGTTGAGAATCTGCTGAAATTTACATGAAGTAAAGGCCATTGATGCATGACAAATTGCTTAGTGTTATCTTCCTGATACCAG
Seq C2 exon
GTAAATAACAGCAACAAGAAAGAGTGGAATGGCATGATGGGAGAGCTTCTGAGTGGCCTGGCAGACATGATCGTGGCTCCACTTACAATCAACAATGAACGAGCCCAGTACATAGAGTTCTCTAAACCGTTCAAATACCAGGGGCTCACAATACTTGTCAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000025728:ENSDART00000034849:11
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=0.055
Domain overlap (PFAM):
C1:
PF0049715=SBP_bac_3=PU(10.0=79.1)
A:
NA
C2:
PF0049715=SBP_bac_3=FE(15.8=100)
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:
GTGCTGCTATGGGTTCTGCAT
R:
GAGCCCCTGGTATTTGAACGG
Band lengths:
256-445
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]