BtaINT0037060 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000099 | CERS2
Description
Bos taurus ceramide synthase 2 (CERS2), mRNA. [Source:RefSeq mRNA;Acc:NM_001034667]
Coordinates
chr3:19840678-19841061:+
Coord C1 exon
chr3:19840678-19840796
Coord A exon
chr3:19840797-19841003
Coord C2 exon
chr3:19841004-19841061
Length
207 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGG
5' ss Score
8.76
3' ss Seq
ATGTCTGCTTCCTCTTCCAGCTG
3' ss Score
11.84
Exon sequences
Seq C1 exon
GCAGATGTGGAGCTTCTGTCACGGCAGAGCGGGCTCTCTGGCCGCCAGGTAGAGCGCTGGTTCCGCCGCCGTCGCAACCAGGACCGGCCCAGTCTCCTCAAGAAGTTTCGAGAAGCAAG
Seq A exon
GTAGGGGCAGTTGAGGCAAGAGAAACTGGGTGGCAGAGGAAGGTCTACTGTGTTTTGCTGGGAGGTGGGGCTGCAGCTGTATGTGGAGAAATTACTCCCGGGTGAGGAGGCACATTTGGTTGAGTATTTCCTTGAGAGGGTATCTGGGGGGAGGGCTGCGCCGTTCTTCCATTCCACTCTCCTAGCCATGTCTGCTTCCTCTTCCAG
Seq C2 exon
CTGGAGATTCACATTTTACCTGATTGCTTTCATCGCCGGCACGGCCGTCATTGTAGAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000099:ENSBTAT00000000109:4
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:
PF0004624=Homeobox=PD(50.9=72.5),PF0379811=TRAM_LAG1_CLN8=PU(2.6=12.5)
A:
NA
C2:
PF0379811=TRAM_LAG1_CLN8=FE(9.8=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:
GATGTGGAGCTTCTGTCACGG
R:
GTCTACAATGACGGCCGTGC
Band lengths:
174-381
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]