BtaINT0069124 @ bosTau6
Intron Retention
Gene
ENSBTAG00000047202 | GRIN1
Description
glutamate receptor, ionotropic, N-methyl D-aspartate 1 [Source:HGNC Symbol;Acc:HGNC:4584]
Coordinates
chr11:105928557-105928910:-
Coord C1 exon
chr11:105928778-105928910
Coord A exon
chr11:105928706-105928777
Coord C2 exon
chr11:105928557-105928705
Length
72 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
TGACGGTCCTCTGCCCGCAGGCG
3' ss Score
11.33
Exon sequences
Seq C1 exon
CGCCCTTTGCGCCCCCGCAGCCCCTTCGGCCGGTTCAAAGTGAACAGCGAGGAGGAGGAGGAGGATGCGCTGACTCTGTCTTCGGCTATGTGGTTCTCCTGGGGCGTCCTGCTCAATTCAGGCATCGGGGAAG
Seq A exon
GTGAGGCGACGCCAGGCCAGGGCCCCATCCTGCCCCGCCGCCCGCCCCGAGCTGACGGTCCTCTGCCCGCAG
Seq C2 exon
GCGCCCCCAGAAGCTTCTCGGCGCGCATCCTGGGCATGGTGTGGGCGGGGTTCGCCATGATCATTGTGGCCTCTTACACCGCCAACCTGGCAGCCTTCCTGGTGCTGGACCGGCCCGAAGAGCGCATTACCGGCATCAACGACCCGCGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000047202:ENSBTAT00000065439:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.044 A=NA C2=0.060
Domain overlap (PFAM):
C1:
PF0049715=SBP_bac_3=FE(13.3=100),PF0006021=Lig_chan=FE(15.7=100)
A:
NA
C2:
PF0049715=SBP_bac_3=FE(14.8=100),PF0006021=Lig_chan=FE(17.4=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:
CTTCGGCCGGTTCAAAGTGAA
R:
ACAATGATCATGGCGAACCCC
Band lengths:
177-249
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development