BtaINT0069129 @ bosTau6
Intron Retention
Gene
ENSBTAG00000047202 | GRIN1
Description
glutamate receptor, ionotropic, N-methyl D-aspartate 1 [Source:HGNC Symbol;Acc:HGNC:4584]
Coordinates
chr11:105925760-105927216:-
Coord C1 exon
chr11:105927071-105927216
Coord A exon
chr11:105925871-105927070
Coord C2 exon
chr11:105925760-105925870
Length
1200 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
CTTATACATATTCATTTTAGGAT
3' ss Score
8.75
Exon sequences
Seq C1 exon
GGGTCTTCATGCTGGTGGCTGGGGGCATCGTGGCCGGGATCTTCCTGATCTTCATCGAGATCGCCTATAAACGGCACAAGGACGCTCGGCGGAAGCAGATGCAGCTGGCGTTTGCGGCCGTGAACGTGTGGAGGAAGAACCTGCAG
Seq A exon
GTAGGGCAGGCCGCCCTCCGAGGCCTGGTGCCCATGGCCCGGCCCGGCCCGGCCCTCCTCCATCCCCGCAGGCGGAAGCGCTGGCTCTGGCTCCCAGGAGCCCAAGAGGCAAGGACTGGAGCTGGGAGCCACAGCCAAGGCCGCAGTGCTGGGGGCCGCCTGTGGGTGGCTGCCTCTGCGAAGCCAGGCTCCAAGCGTCCACCTGGCCCCTCTGTCTCCAGAGTCGCCCACCGAGGCCCATTCCGTAGGAAGGCAGACTGAGGCAGGGTAAGACAGGGACCCAGCTGGGTGTAGCATGTGAGTCCAAGGTGCAGTCCGCCATCCCTCGCCGCCCCGTGCCCCTCCAAGGACCCGGTTCCCTGCCACCCTGCTGTGCTCCATGTAACTGCAGTCTGAGCTGGTCAGCTGGTCCCGCCGGGCACCCCAGGCTGTGCTCGTGGGGCTTTGCTGGCAGCAGGGGACGGGCTGCCCACAGCCCACCTGGGCCGGGCTCGTGCCCCATGGTCCAGCCCCAGGCTGCCCCATCTCTTCTCTTTCTCTGGGTGCCTCCCCAGAGCCTGTGTCCTGGGAGGAAGCCGGTGTTGCAGAGAGGGAGGGCCGGGGGAACGGGGTCACCAGTGTTCCCACACCTCTCATCTGCCCACTCTTGCTCTTGGGACCTGGCTTGCTGCTCCCAGTGGCGGGCGCAGGGCCCACTCTGGCCATCAGACCCGAAGCCAGGGTCCCAGGAGCTGCCACTGTCTCTCTGTCACTCCAATTCATCTCGCCACCTGCCTTTGGTCCCCTCAGCCCCTTCCTAAATCTCGGTGCGCTTCCTCTGGGGTCAGAGTGGCTGGTGGGGCCTGTGGGGGTGACTCACCCAGTGTTCAGGGGGCTCCTCCTCCTTGGGGCACCCATACACCAGGGGCACCTTGGAGCCAGGGAACCAGGTGGACCTTTGCTGGAAGAGAGCCAGCTGAGGACCCCACCCCGCCTCCCCAAACCCAGTCCCAGCACAAGGAAGGTCAGGCCGGAGACCCTGGCAGCAGCAGAGGCCGCCTGCGAGCGTGGGGCCGGCGGCTGGTCCATCCAGCACAGGGAGGCAGGCAGGAGCGAGGGCCCGAGTGGCCAGCCAGGCTGGGCAGCAGCCCCCAGGAGCAGGCGAGGGCAGGTGTGGCCGCCACCCTCAGCCGTCTAATCACTTATACATATTCATTTTAG
Seq C2 exon
GATAGAAAGAGTGGTAGAGCAGAACCCGACCCTAAAAAGAAAGCCACATTTAGGGCTATCACCTCCACCCTGGCTTCCAGCTTCAAGAGACGTAGGTCCTCCAAAGACACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000047202:ENSBTAT00000065439:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.010 A=NA C2=0.635
Domain overlap (PFAM):
C1:
PF0006021=Lig_chan=PD(3.2=18.4),PF105624=CaM_bdg_C0=WD(100=59.2)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCTTCATGCTGGTGGCTGG
R:
CGTGTCTTTGGAGGACCTACG
Band lengths:
255-1455
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development