BtaINT0069135 @ bosTau6
Intron Retention
Gene
ENSBTAG00000047202 | GRIN1
Description
glutamate receptor, ionotropic, N-methyl D-aspartate 1 [Source:HGNC Symbol;Acc:HGNC:4584]
Coordinates
chr11:105933923-105934289:-
Coord C1 exon
chr11:105934168-105934289
Coord A exon
chr11:105934098-105934167
Coord C2 exon
chr11:105933923-105934097
Length
70 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGT
5' ss Score
11.45
3' ss Seq
TAAGCCAGCTCTCGCCCCAGGCA
3' ss Score
2.82
Exon sequences
Seq C1 exon
CGAGGACGACGCTGCCACCGTGTACCGCGCAGCCGCGATGCTGAACATGACGGGCTCGGGGTACGTGTGGCTGGTGGGGGAGCGCGAGATCTCGGGGAACGCCCTGCGCTACGCCCCGGACG
Seq A exon
GTGAGTGCTGGGCTCCCGGGTCCCGGCGGGCAGGGGTCCCCCGCGGGCTCTAAGCCAGCTCTCGCCCCAG
Seq C2 exon
GCATCATCGGGCTGCAGCTCATCAACGGCAAGAACGAGTCGGCGCACATCAGCGACGCCGTGGGCGTGGTGGCCCAGGCCGTGCACGAGCTGCTCGAGAAGGAGAACATCACCGACCCGCCGCGGGGCTGTGTGGGCAACACCAACATCTGGAAGACCGGGCCGCTCTTCAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000047202:ENSBTAT00000065439:6
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
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:
CTCGGGGTACGTGTGGCT
R:
TGTTCTCCTTCTCGAGCAGCT
Band lengths:
176-246
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development