BtaINT0069125 @ bosTau6
Intron Retention
Gene
ENSBTAG00000047202 | GRIN1
Description
glutamate receptor, ionotropic, N-methyl D-aspartate 1 [Source:HGNC Symbol;Acc:HGNC:4584]
Coordinates
chr11:105928284-105928705:-
Coord C1 exon
chr11:105928557-105928705
Coord A exon
chr11:105928442-105928556
Coord C2 exon
chr11:105928284-105928441
Length
115 bp
Sequences
Splice sites
5' ss Seq
CGAGTGAGG
5' ss Score
4.44
3' ss Seq
CTGGCTCTCTGGCCCCGCAGCTG
3' ss Score
9.61
Exon sequences
Seq C1 exon
GCGCCCCCAGAAGCTTCTCGGCGCGCATCCTGGGCATGGTGTGGGCGGGGTTCGCCATGATCATTGTGGCCTCTTACACCGCCAACCTGGCAGCCTTCCTGGTGCTGGACCGGCCCGAAGAGCGCATTACCGGCATCAACGACCCGCGA
Seq A exon
GTGAGGCCGGGCCCGTCTGGGGGCTGGGGAGGGAGGCGCTCAGGCCCTCCGCCCCGTGGGGCGGGGTGGGGTGGGGCCGGGGAGCAGCCACGAGCCTGGCTCTCTGGCCCCGCAG
Seq C2 exon
CTGAGGAATCCCTCGGACAAGTTCATCTACGCGACGGTGAAGCAGAGCTCGGTGGACATCTACTTCCGGCGGCAGGTGGAGCTGAGCACCATGTACCGGCATATGGAGAAGCACAACTACGAGAGCGCGGCGGAGGCCATCCAGGCCGTGCGCGACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000047202:ENSBTAT00000065439:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.060 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0049715=SBP_bac_3=FE(14.8=100),PF0006021=Lig_chan=FE(17.4=100)
A:
NA
C2:
PF0049715=SBP_bac_3=FE(15.7=100),PF0006021=Lig_chan=FE(18.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATCCTGGGCATGGTGTGG
R:
CGCTCTCGTAGTTGTGCTTCT
Band lengths:
251-366
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development