DreINT0075101 @ danRer10
Intron Retention
Gene
ENSDARG00000025728 | grin1b
Description
glutamate receptor, ionotropic, N-methyl D-aspartate 1b [Source:ZFIN;Acc:ZDB-GENE-051202-2]
Coordinates
chr5:29030934-29031937:-
Coord C1 exon
chr5:29031816-29031937
Coord A exon
chr5:29031109-29031815
Coord C2 exon
chr5:29030934-29031108
Length
707 bp
Sequences
Splice sites
5' ss Seq
ATGGTATGT
5' ss Score
8.35
3' ss Seq
TAATGTTGTCAACTGGGCAGGCT
3' ss Score
1.68
Exon sequences
Seq C1 exon
TGAAGACGAAGCCGCGGCCATTTATAAAGTGGCACGCCAGCTCAATATGACAGGCTCTGGTTACGTGTGGCTGGTTGGAGAAAGGGAGATGTCTGGTAAAGCACTGAGTGAAGCCCCAGATG
Seq A exon
GTATGTACTTTTCATCCTCTCCATTTTCATTCTCTTGCTCTTTCTCTCTCTCTCCCAGGCTGTTTAACAATTTGAACATGTTTGCCTTTTAAGCTTTTTATACGATTACAATTTGCAATCCCCACCGACGAATCAGTGTCTGTGCTGTACTTGCGTGTTTAAACGTTTAAACAGCTGCGTGTTTAAAGGTTTTAAACACAGTGACTCTTTACTCATTGTACTGTGCTTTATGTCTAATGTTTAATTTGTTTCATTTTTGAGTGTTTGTCCTTTCTTTCAGTAGACAACAATTGATGCAATAGAGAGTTGTGGTAATCCATATTGGTTTGAGTGTGCATACATTTTTTAAGGTTTGGCTTTCATGAGTTTATTTGTAAGTGACGCTTTGCTACTTCCACATTGAGGTGTGGATACGATGGTAAGCGACAATCGCATTTCTTTGTTCCTGGCTTCTTTATATACACATCCGTGTTCAACTTCACGTCATTCTGCTCAGTGCTGACCCTGTCCTAACCCCCCATGACTTTCACAGTCCTTCTGTCTGTCTTGAGACAATTCGTTGCTCATATGCAATGCACGTTTTTTGTTTCTCTCTCTGCCAATGTGTGCGTTTCTTTATTATTATTATTATTATGAGTATGAGTATGCCTCTTAAAGTCTTGTTGTGAGGCACTGGCCAACACCATGTAATGTTGTCAACTGGGCAG
Seq C2 exon
GCTTGCTCGGCCTCCAGCTAATCAATGGCAAGAACGAGTCTGCGCACATCTACGATGCCGTGGCTGTGGTGGCCCAGTCCATCCAGGAGCTCTTTGAGAAGGAGAATATCACAGAGCCTCCTCGAGGCTGTGTTGGCAATACAAACATCTGGAAGACTGGCCCACTCTTCAAACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000025728:ENSDART00000034849:6
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=0.068
Domain overlap (PFAM):
C1:
PF0109423=ANF_receptor=FE(12.0=100)
A:
NA
C2:
PF0109423=ANF_receptor=FE(17.0=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:
AGCCGCGGCCATTTATAAAGT
R:
CGTTTGAAGAGTGGGCCAGTC
Band lengths:
288-995
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]