DreINT0075091 @ danRer10
Intron Retention
Gene
ENSDARG00000025728 | grin1b
Description
glutamate receptor, ionotropic, N-methyl D-aspartate 1b [Source:ZFIN;Acc:ZDB-GENE-051202-2]
Coordinates
chr5:29017307-29019123:-
Coord C1 exon
chr5:29018975-29019123
Coord A exon
chr5:29017465-29018974
Coord C2 exon
chr5:29017307-29017464
Length
1510 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGC
5' ss Score
7.75
3' ss Seq
ACTGTTTCTTTGTGTTTCAGCTG
3' ss Score
11.04
Exon sequences
Seq C1 exon
GTGCCCCTCGGAGCTTTTCGGCGAGGATTTTAGGTATGGTGTGGGCTGGTTTTGCTATGATTATAGTTGCATCTTATACTGCCAATTTGGCAGCCTTCCTAGTGCTGGATCGGCCTGAGGAGCGCATTACCGGCATCAACGACCCTAGG
Seq A exon
GTGAGCAGGAAATATGAAGCAGTACTACATGTTATACAACAGAATATCAAATAAGGCTGAAAATTAGCACGTTTAGAGATTGCACATTTCACACAGCATAAAATCAACGCATATAATTAAGCTTGTCAAGGACATGTAATTACGGGTCATTTTGTTCACAAAGGTTATTTTTATGTGGCTTTTTTCATCATAACAGCCTACAGTATGTCAGTTCTGGGATGTGGGCTGAAAATTGGCAAAGAAATAAATGTAAACATTTGATGTAAAATAGCAAGTAATTGTATTTTTTTAATGAGTCTGTAGGTTTTTGAGAAGCAGTGCTGTGTAATACCTGATCCAGAATTGTAATTAGATTAAATTGCATTTTAAAATGCTAATATTTACATGTTTATCTTTTTAATTAATCACACAATAACATTATTTACATTGTAAATTATTAATGGTTTATGGATTTTCCGCAGTTTTTTAATATAATTGTCTTTCCATTGGCATGTAGGTAAATATATAAAATGTACAGTTTTATCAAATGTTTTTATTTTTATAATTAAAAAAAAAAACATTAGCTGTAGATCACAACTCCAGGTTGGAGTTCTTTAATGCACTTCAAGTTATTGAAAGCAGAGTAGGAAATGTATTTCCTTTTTATTATTTAGATCATCCCGGTACTAAATATTTTAATTTAAATCTCTTTGAAAAACAGGGTGGGTAAAAATGATTCTAATGTAACCAAAAAGTCATTAAAAAATGTGTAATCTAATAAATAATTACAACTCCGGTCATGTTATTTGTAATCAGCAACAGACAATTATAAGTAATCTACTATACACCTGCTGTAATTCAGTACTGAATGTAATTTTTAAACTATAATTAGTGACCCTGGACCACAGTCTTAGGTTACTAGACCCAAAAAATCTTTGTATGGGTCACAATTATAGATTTTTTATTTTATGCCAAAAATCATTACAATATTAATTAAAGATCAAGATTCTTGGAAATAGTTTTGAAATTTCCAGCTGTAAATATATCAAAACCTAATATTTGGCTGGTAATATGCACATTCAATTTATTTGGACAACTTTAAAAAGGTTTAGAACTTTAAAATATTTAGTTGTTTGTGAACATCTCAGCCAAATATTGTCACTTTCTAAAAAAACATACATCAGTGAAAAGCCTATTTATTCAGTTTACACGGGATGTATACATCTCATTTTAAAAATCTGGTTTTATAGTTCCTTGTCACACATAAGTTACTTATTTTCTAGCTTTCTTCTTAGACACACAGCAATATGACTTCACTGAACATTTTTAGGTCACACTCAATTCCCACCACTATTTTCATCTTTAATATTTAATGTTATTACAGAGACAAAAAAAAACTTCCAAATTTTGGAATTGCAGACACCAAACACCATTTTACTTGAATTATTCAGCATGTTGTGAATCAACAGTCACTTCACTACATCTACAAGCAGTTCGTCAAGACCATCCAAACTGTTTCTTTGTGTTTCAG
Seq C2 exon
CTGCGAAACCCATCAGATAAGTTCATCTACGCCACAGTGAAGCAGAGCTCTGTGGACATTTATTTCCGGCGCCAAGTTGAGCTTAGCACCATGTACCGCCACATGGAAAAGCACAACTACGAGAGCGCCGCTGAAGCCATCCAGGCTGTGCGAGACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000025728:ENSDART00000034849:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.040 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0049715=SBP_bac_3=FE(14.4=100),PF0006021=Lig_chan=FE(18.4=100)
A:
NA
C2:
PF0049715=SBP_bac_3=FE(15.2=100),PF0006021=Lig_chan=FE(19.5=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:
GTGCCCCTCGGAGCTTTTC
R:
TTGTCTCGCACAGCCTGGAT
Band lengths:
307-1817
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]