BtaINT0037069 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003434 | CERS4
Description
Bos taurus ceramide synthase 4 (CERS4), mRNA. [Source:RefSeq mRNA;Acc:NM_001015520]
Coordinates
chr7:18158011-18159056:+
Coord C1 exon
chr7:18158011-18158128
Coord A exon
chr7:18158129-18158937
Coord C2 exon
chr7:18158938-18159056
Length
809 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
CCCCATCACCCGCTCTCCAGTCC
3' ss Score
6.21
Exon sequences
Seq C1 exon
ATTCGTCGCCCTGCCCCTGAGCCGGTGGCTGGGCGTGCGGAACCAGATCAGGAGGCCAGCGGACCCCAATGCCACGCTGGAGAAGCATTACCTAATGAAAGGGCGGGAGCCCACGGAG
Seq A exon
GTGAGATCCCCGACCCTCTCCTCCGTCCCCGTTGGCCTGCTTGGGTGCCCTGGGGGTAGCTCTGGAAGGGGTGCAAGAAAACCCCCACCGCCAACCCCTTGAATCCCAAGGCCCATCAGCCTGTGAGCAGGACTGGGTTTTGGTTTTTATCCTTATTTTCGGCTGTGCTGGTTCTCTTGTTGCTCTGCATAGGCTTTCTCTGCTTGTGGTGAGTGGAGGGAGGGCTGCTCTCTAGATCGGCATGCAGGCCTCTCATTTTGACTTCTCTTGTTGCACGGAGCATGGGCTTCAGGGCGCTCGGGCTTTTGGCACACGGGTCTGGTGGCCCTGAGGCATGTGCAGTCTTCCTGGACCAGGGATTGAACCTGTGTTCCCTGTGTTGGCAGACAGATTTTTAACTGTTAGACCATCAGGAAAGTCCCAGGGATGGGTTTTTATAAGGCCTGCTTTGGGGGCTCCACCCTATGGACTTCCCCATGGCTCAGCAGTAACAAATCCACCTGCCAATTCGGGAGACTTGGGTTCAATCCCTGGGTTTGGGAAGATTCCCCTGGAGGAGGAAATGGCAGCCCACTCCAGTATTCCTGCCTAGAGAATCCCAAAAGAGTTAGACATGACTGAAGCGACTGAGTACACACACATCACCCTGTGAAACCCCCTATTCCCCTATCAACATAGGTAGACCACCCCACAGGTGAGGTTTAGGACCACGGCGCGGGGAGGGGGTATGCAGAGCTGGGTCTTGGCTGTCCTGGGACAGTGGCGGGAGGCCACCTCTGTGACCCTGGCCCCCATCACCCGCTCTCCAG
Seq C2 exon
TCCCAGATGAACCTCCTGGCCACGCAGTGCGGCCTCACGCTGCGGCAGACTCAGTGCTGGTTCCGGAGACGCCGGAACCAGGACCGGCCCTGCCTGACCAAGAAGTTCTGTGAGTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003434:ENSBTAT00000004459:3
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=PU(38.0=47.5)
A:
NA
C2:
PF0004624=Homeobox=PD(58.0=72.5),PF0379811=TRAM_LAG1_CLN8=PU(2.6=12.5)
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:
GGCGTGCGGAACCAGATC
R:
CTGGACTCACAGAACTTCTTGGT
Band lengths:
206-1015
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]