BtaINT0069126 @ bosTau6
Intron Retention
Gene
ENSBTAG00000047202 | GRIN1
Description
glutamate receptor, ionotropic, N-methyl D-aspartate 1 [Source:HGNC Symbol;Acc:HGNC:4584]
Coordinates
chr11:105927550-105928441:-
Coord C1 exon
chr11:105928284-105928441
Coord A exon
chr11:105927712-105928283
Coord C2 exon
chr11:105927550-105927711
Length
572 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGG
5' ss Score
5.85
3' ss Seq
GACCCCGCCCTTGCCCGCAGCAA
3' ss Score
8.79
Exon sequences
Seq C1 exon
CTGAGGAATCCCTCGGACAAGTTCATCTACGCGACGGTGAAGCAGAGCTCGGTGGACATCTACTTCCGGCGGCAGGTGGAGCTGAGCACCATGTACCGGCATATGGAGAAGCACAACTACGAGAGCGCGGCGGAGGCCATCCAGGCCGTGCGCGACAA
Seq A exon
GTGAGGGGCGGGGCGGGGCCAGCGAGGGGGCGGGGCCAGCGAGGGCGGCTCGGGGCCACCCAGGTCGCGCCGACAAATGAGGGGCAGGGCCAGTGGAGGCGGGGCGGAGCCATCCACGCCGTGCGCGGCAAGTGAGGGGCGGGGCGGGGCCAGCGAGGGGGCGGGGCCAGCGAGGGCGGCTCGGGGCCACCCAGGTCGCGCCGACAAATGAGGGGCAGGGCCAGTGGAGGCGGGGCGGAGCCATCCACGCCGTGCGCGGCAAGTGAGGGGGCGGGGCGGGAGAGGGGCGGGGCCACCCAGGTCGCGCGCGACCAATGAGGGGCGGGGCCTGTGAGGGGGCGGGGCGGAGCCATCCGGGCCGTGCGCGACGAGTGAGGGAGGGGCAGGCGGAGCGCGAGTGAAGGGCCGGCAGGACAAGCTGGGGGCGTCCACATCTACAGTCAGTGTCCCGGCCGTGTGGGAGCCACGGGGAGGGGGGACAGACGGCGGGTCCCCAGCTGGCAGGAGGAAGGCTCGCGGGGAGCCAGGGCCACCTGGAAGCGTGGCCGCCGTGACCCCGCCCTTGCCCGCAG
Seq C2 exon
CAAGCTGCACGCTTTCATCTGGGACTCGGCGGTGCTGGAGTTCGAGGCCTCGCAGAAATGCGACCTGGTGACCACGGGCGAGCTCTTCTTCCGCTCGGGCTTTGGCATCGGCATGCGCAAGGACAGCCCCTGGAAGCAGAACGTCTCCCTGTCCATCCTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000047202:ENSBTAT00000065439:16
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=0.000
Domain overlap (PFAM):
C1:
PF0049715=SBP_bac_3=FE(15.7=100),PF0006021=Lig_chan=FE(18.5=100)
A:
NA
C2:
PF0049715=SBP_bac_3=FE(16.3=100),PF0006021=Lig_chan=FE(19.2=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:
CCTCGGACAAGTTCATCTACGC
R:
TTGAGGATGGACAGGGAGACG
Band lengths:
310-882
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development