BtaINT0069122 @ bosTau6
Intron Retention
Gene
ENSBTAG00000047202 | GRIN1
Description
glutamate receptor, ionotropic, N-methyl D-aspartate 1 [Source:HGNC Symbol;Acc:HGNC:4584]
Coordinates
chr11:105929156-105929632:-
Coord C1 exon
chr11:105929505-105929632
Coord A exon
chr11:105929321-105929504
Coord C2 exon
chr11:105929156-105929320
Length
184 bp
Sequences
Splice sites
5' ss Seq
CGGGTAGGA
5' ss Score
7.22
3' ss Seq
CCGGCGGTGTCGCCCCACAGGTG
3' ss Score
9.75
Exon sequences
Seq C1 exon
CGCGCCACACGGTGCCTCAGTGCTGCTACGGCTTCTGCGTCGATCTGCTCATCAAGCTGGCGCGGACCATGAACTTCACGTACGAAGTTCACCTGGTGGCCGATGGCAAGTTCGGCACTCAGGAGCGG
Seq A exon
GTAGGAGTGGTTCCTAGGAGCCGGCGCAGGACCGGGTCCTGCTCCCCCGAGGGTCTTCTGTAGGCGGGGCCTGAGCCTGGGAGGAGTCTGGAGTGGGTGACCCCTGAGATGGGTCGGGGCGGGAGCCTGTATGGGGAGTGGGGCCCGCGGTGTCCGCGTCCCCACCGGCGGTGTCGCCCCACAG
Seq C2 exon
GTGAACAACAGCAATAAGAAGGAGTGGAACGGGATGATGGGCGAGCTGCTCAGCGGGCAGGCGGACATGATCGTGGCCCCGCTGACCATCAACAACGAGCGCGCGCAGTACATCGAGTTCTCGAAGCCCTTCAAGTACCAGGGCCTGACCATTCTGGTCAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000047202:ENSBTAT00000065439:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.047 A=NA C2=0.109
Domain overlap (PFAM):
C1:
PF0049715=SBP_bac_3=PU(10.9=83.7)
A:
NA
C2:
PF0049715=SBP_bac_3=FE(16.3=100),PF0006021=Lig_chan=PU(4.3=21.8)
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:
TGCGTCGATCTGCTCATCAAG
R:
AATGGTCAGGCCCTGGTACTT
Band lengths:
246-430
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development