BtaINT0037058 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000099 | CERS2
Description
Bos taurus ceramide synthase 2 (CERS2), mRNA. [Source:RefSeq mRNA;Acc:NM_001034667]
Coordinates
chr3:19839783-19840497:+
Coord C1 exon
chr3:19839783-19839956
Coord A exon
chr3:19839957-19840379
Coord C2 exon
chr3:19840380-19840497
Length
423 bp
Sequences
Splice sites
5' ss Seq
GCTGTGAGC
5' ss Score
3.2
3' ss Seq
CACTCCTATCCCTTCCCCAGTTA
3' ss Score
7.55
Exon sequences
Seq C1 exon
GATGCTCCAGACCTTACATGACTACTTCTGGTGGGAACGGCTGTGGCTCCCTGTGAACTTAACCTGGGCTGATCTAGAAGACCGAGATGGACGTGTCTACGCCAAAGCCTCTGACCTCTATATCACACTACCCCTGGCCTTGCTCTTCCTCATCATTCGATACTTCTTTGAGCT
Seq A exon
GTGAGCATACCAACCTACCCCCATGCCTTCCTTGGCTCCCAGCTGCAGTTTCTTGTACTTCAAGTTTGTCTCTTGCTGTTTAATTGGTCCTGCACACTGGTGTTCTCACCACCCAGGTCCCTGCCTACTGTGTGCCCCCCACTAAAGGCAGCATTGTCTTTCTGAGGGCTCAGCACCCCCAGGCCCATTCCTTCAATGGTTATTTGTTCTTGCCCTCCACCCGCCTGGTGGCTAGTGAACACAGGCAGCTTTGTCAGCTATGGGCAGCCCAAGGCAGCCAGAGAGGGGGTTGCTGGGAAACTGAGGCCCAGGATAAAGTTGCCTGAGCTTGCAATATCCCCCTCCAGGCCCTCTAGTTTAGGGGCTAACAGGCTTGCCTGCTTCAAGAGAGTCAGACACCCCTCACTCCTATCCCTTCCCCAG
Seq C2 exon
TTACGTGGCTACACCACTGGCTGCCCTCCTGAATGTCAAAGAGAAAACCCGGCTGCGGGCACCTCCAAACCCCACTTTGGAGCATTTCTACATGACCAGTGGCAAGCAGCCCAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000099:ENSBTAT00000000109:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=PU(45.6=65.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCTCCAGACCTTACATGACT
R:
TGCTTGCCACTGGTCATGTAG
Band lengths:
280-703
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]