DreINT0075102 @ danRer10
Intron Retention
Gene
ENSDARG00000025728 | grin1b
Description
glutamate receptor, ionotropic, N-methyl D-aspartate 1b [Source:ZFIN;Acc:ZDB-GENE-051202-2]
Coordinates
chr5:29030289-29031108:-
Coord C1 exon
chr5:29030934-29031108
Coord A exon
chr5:29030434-29030933
Coord C2 exon
chr5:29030289-29030433
Length
500 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGG
5' ss Score
9.2
3' ss Seq
ATGCCCCTCTGGTGTACTAGAGT
3' ss Score
5.06
Exon sequences
Seq C1 exon
GCTTGCTCGGCCTCCAGCTAATCAATGGCAAGAACGAGTCTGCGCACATCTACGATGCCGTGGCTGTGGTGGCCCAGTCCATCCAGGAGCTCTTTGAGAAGGAGAATATCACAGAGCCTCCTCGAGGCTGTGTTGGCAATACAAACATCTGGAAGACTGGCCCACTCTTCAAACG
Seq A exon
GTGAGGCCAGGGATGAGCGCTGGCTAGCAGTCGCTAGCTTTCCAACCAACCAACCATCCATTAGCTGTCATGCATTACCATACATTACCACTGGTCTGGCACTGACAAGAGTGGAAGCTTTCACACCGCAAACATTGAAATCCCAAGCATTCGGCTTCTAAAACCATTCCCTGACTCCTCAATTGGAGGAATATTGGAGTGCAAGGACACAACAAGCCTGTTAAGTTGTTGATTACATTGGCCTTGTGAAATCTGGTGGTACCAATTTGAGACCCCTACAGGTGTCATTTCTGTTCTCCTATGTCTGTGCCTGCACAATATGTGCCATCCCACCCTACACAACACCCCATAATCTTCCCTAGTTAGTCGTCATATCTTTACCTGAGACACACCTGCATCTCCCATCTAATCTTCCATTACTTCCAGTCATCGTCAATGTCCTCCTTTGTGTTTAAATGAGCATTTTGTGCCTTTTCTAAAATGCCCCTCTGGTGTACTAG
Seq C2 exon
AGTGCTGATGTCATCCAAGTATCCAGATGGCCTGACAGGCCGCGTGGAGTTTAATGATGACGGAGACAGGAGGTTCGCCCACTACAGCATTCTGAACTACCAGAAAACCCGGCTGGTGCAAGTGGGCGTCTACAATGGCTCGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000025728:ENSDART00000034849:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.068 A=NA C2=0.041
Domain overlap (PFAM):
C1:
PF0109423=ANF_receptor=FE(17.0=100)
A:
NA
C2:
PF0109423=ANF_receptor=PD(10.0=69.4)
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:
TTGCTCGGCCTCCAGCTAATC
R:
TTGCGAGCCATTGTAGACGC
Band lengths:
318-818
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]