BtaINT0084738 @ bosTau6
Intron Retention
Gene
ENSBTAG00000017395 | LASS5
Description
Bos taurus ceramide synthase 5 (CERS5), mRNA. [Source:RefSeq mRNA;Acc:NM_001102132]
Coordinates
chr5:29924423-29925415:+
Coord C1 exon
chr5:29924423-29924528
Coord A exon
chr5:29924529-29925284
Coord C2 exon
chr5:29925285-29925415
Length
756 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
CTCTGGTCATACGTCTACAGTAT
3' ss Score
4.39
Exon sequences
Seq C1 exon
GTTTATTGCCAAACCCTGTGCACTCCATGTTGGCATCCAGGACAGTGGTCCTTATCAGGCACAACCTAATGCTATCCTTGAAAAGGTGTTCATGTCTATTACTAAG
Seq A exon
GTAAGTGGGCAAAAAAAAAAAAAAAAAAACAGGAAGATTTTTGTTAGGGTTCATCCCCCATAGGGCATGGGAGGATAGAGAGCAAGTATTTCCAAGGCTAAGGATAGGACGGGATGATCTTTCACATTTGGATAGTCCATAGAGCTATTAGGAGAACTTTATCCACTCAAGGAAATACCTTTGGGCTAGGATACCTTAAATAATTCAAAATTACATACATTGGAGATTTAGGCCTAGCAGTCACCACCACCCCTACTCCCCAAGACACACATCATATTTTGATTTTGTTTTTCCCTGCTTCAGCTCTTGTCATTACCTAGTTGCATAATCAAGATAGAGATGGTACTGATAGCCTTTACAGGTTGGATTTTTGTGTTTTTTTTTTAATTGAAGGATAAATACTTTACAGAATTGTGTTGGTTTCTGCCAAATATCAACATGAATCAGCCATAGGTATACATACGTCCCTTCCCTCTTAAACCTCCCTTCCAGGTTGGGTTTTTAATATTTTTTTTTTTACTCACTTGGGCTAGAGGGAGAAAACCAAATAGCTATGTGTATAGGGGAATGGTAAAGGTTCTTGATGTGTAAAATAGTACTTCTTACATAAAAATGACTTTGGGGATGAAACCTGGAAAGAAAAACATTACTTAAGTCACTGTAGTTATTACCCCTCTGCCACTCAGCTTGTCAAAGGGCTTTAATGAGTAGATTTGAAGAAAAAGCAATGTTCTGACTCTGGTCATACGTCTACAG
Seq C2 exon
TATCCTGATGAGAAAAGGCTGGAGGGCCTGTCAAAGCAACTAGACTGGGATGTCCGAAAAATCCAATGCTGGTTTCGCCATCGGAGGAATCAGGACAAGCCCCCAACGCTCACTAAATTTTGTGAAAGCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017395:ENSBTAT00000029121:2
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(34.0=50.0)
A:
NA
C2:
PF0004624=Homeobox=PD(62.3=75.0),PF0379811=TRAM_LAG1_CLN8=PU(2.6=11.4)
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:
GTTTATTGCCAAACCCTGTGCA
R:
CACAAAATTTAGTGAGCGTTGGGG
Band lengths:
230-986
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]