BtaINT0015854 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004442 | AGPAT1
Description
Bos taurus 1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha) (AGPAT1), mRNA. [Source:RefSeq mRNA;Acc:NM_177518]
Coordinates
chr23:27022202-27022622:+
Coord C1 exon
chr23:27022202-27022377
Coord A exon
chr23:27022378-27022526
Coord C2 exon
chr23:27022527-27022622
Length
149 bp
Sequences
Splice sites
5' ss Seq
GACGTGAGT
5' ss Score
9.22
3' ss Seq
TGACCCCCTCTCTCCCCCAGGTA
3' ss Score
12.34
Exon sequences
Seq C1 exon
GGATGATGGAGGTGCTGCCAGGCCGCTGTGTGCCCATTGCCAAGCGGGAGCTGCTGTGGGCCGGCTCTGCTGGGCTGGCCTGCTGGCTGGCGGGAGTCATCTTCATTGACCGGAAGCGCACTGGGGATGCCATCAGTGTCATGTCTGAGGTCGCCCAGACCCTGCTTACACAGGAC
Seq A exon
GTGAGTCACCCTGGGGAAATGGGGCTTAGAGGATAGAACAGCTGTAAACTGATGTGCAGGGCCCACAGGCCTCAGAAGTCCCATGACAGCATCATAACCATTTTCTGACTGCTCCATGTGTGTCTTCCTTGACCCCCTCTCTCCCCCAG
Seq C2 exon
GTACGGGTCTGGGTTTTTCCTGAGGGCACGAGAAACCACAACGGCTCCATGCTGCCCTTCAAACGTGGCGCCTTCCACCTCGCAGTGCAGGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004442:ENSBTAT00000005821:4
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:
PF0155316=Acyltransferase=FE(45.0=100)
A:
NA
C2:
PF0155316=Acyltransferase=FE(24.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATGATGGAGGTGCTGCCAG
R:
CCACGTTTGAAGGGCAGCAT
Band lengths:
243-392
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]