BtaINT0084739 @ bosTau6
Intron Retention
Gene
ENSBTAG00000017395 | LASS5
Description
Bos taurus ceramide synthase 5 (CERS5), mRNA. [Source:RefSeq mRNA;Acc:NM_001102132]
Coordinates
chr5:29925285-29926158:+
Coord C1 exon
chr5:29925285-29925415
Coord A exon
chr5:29925416-29926100
Coord C2 exon
chr5:29926101-29926158
Length
685 bp
Sequences
Splice sites
5' ss Seq
CATGTAGGT
5' ss Score
4.94
3' ss Seq
TCTACTCTTCACCCATCTAGGTG
3' ss Score
9
Exon sequences
Seq C1 exon
TATCCTGATGAGAAAAGGCTGGAGGGCCTGTCAAAGCAACTAGACTGGGATGTCCGAAAAATCCAATGCTGGTTTCGCCATCGGAGGAATCAGGACAAGCCCCCAACGCTCACTAAATTTTGTGAAAGCAT
Seq A exon
GTAGGTGTATGGAAGGAGGTGGGGAGTGAGGAGAAGGGTGGGGTATGACTGGACTAAGGTTTTCTTTTTGGAAATCACTTCTCCTCTTAGGATAATAGTCAATGGATGCAGAAGGCTAACTCTGTTATAGGCTGGAAAGAAGAGAACTGAAAGCTTGGTCACCCTTAGTTTCTTGGACATGCTTGTCTCTAAGCTAGCTGTAGTTGCATTTCGTTCACGTTTCCCAAAGAAATTGGGAATGAATTTCTCTGCTTTCACTTACGTAGGTAGATATGCACACCCTTGTATACCTTGGTAGAGATAGTTCCAGCTTGCTATAGGTTGACATTTTAATAGGAAGCATCCCTTTTCTGGACATGCTATAGTTCATTTCACTGGGTTTTTTACTGATTATCCTCTGGACACCAAGCACTATATCTCATTGTCACGCAAAAAAAAAAAAAATAGGCACTATCATCGGGGAGTCTGATATAAAAGAAAAGTTCACTGAAACCAGTATATATTTGTAGAAATCTATTTTTAAACAGAGGCTGGAAAATTTGTATCTCTTTGGCTTTTTAGGTAACTGTATATCATCAGTTTCTTACCAGTAAACTGTGTTATCCCCAAATGTGCAACCTTGAATTCTTTAGCTCACTTTCTTTTGAGTAATTGTTTGTCTAATTTCTACTCTTCACCCATCTAG
Seq C2 exon
GTGGAGATTCACTTTTTATTTATGTATATTCTGCTACGGAATTAGATTTCTCTGGTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017395:ENSBTAT00000029121:3
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=PD(62.3=75.0),PF0379811=TRAM_LAG1_CLN8=PU(2.6=11.4)
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:
GATGAGAAAAGGCTGGAGGGC
R:
CGACCAGAGAAATCTAATTCCGT
Band lengths:
183-868
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]