BtaINT0084742 @ bosTau6
Intron Retention
Gene
ENSBTAG00000017395 | LASS5
Description
Bos taurus ceramide synthase 5 (CERS5), mRNA. [Source:RefSeq mRNA;Acc:NM_001102132]
Coordinates
chr5:29929149-29930990:+
Coord C1 exon
chr5:29929149-29929241
Coord A exon
chr5:29929242-29930861
Coord C2 exon
chr5:29930862-29930990
Length
1620 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
CTATTTGCATTCCTTCCTAGGAC
3' ss Score
10.06
Exon sequences
Seq C1 exon
CCTCTCACAAGTGGACTTTATTACTATTATATCATGGAATTGGCTTTCTATTGGTCTCTTATGTTTTCTCAGTTTACAGACATTAAAAGAAAG
Seq A exon
GTAAGGACGTTGGCTCCCTTAACACCCTGATTTATGGCACCCTCCTTTCCGGCAGCTACCATTATTGTCATTGTGATGGATTCTCTGTCCTGATTAGGACCACAAAAGAGGGTGAAAGTAGGTTCAGTGTGACTTTTAGCTCTTTGTAATGTTCTCAGAAGTGAGCCCTGACTAGTGAAGTATATTTGAGTCATTCAGGGCAGCCCAGGATGAAAACAGTTAACCAGCTAAGAAGCATACCCTTTTCTTTGTTTTTCTCCAAGGTTCTTACACATATAAAGCTCAAGAAACTAGTCTAAACTTAGGGATAGCAAGGCCTGATCCAGGAAAAGCTTCGATTCCAGAAAAACTTTTGCCATTAGTGACCCTTGTTCCCTCTCTGTTCTCTGTTCTTGGTGACCCCACTTACTTAAAAGAATGTGGTTGGAAGGGGTTTTAGATGTTTTAGTTTACCCTTTTCTTGCTGTTGTTTAGGAAACAGATTCAGAGAAGTGAGTTGACTTGCCTACAGAATGGCAAAGTTGCAAATGACTTAAGTTTTTTGTAAGTATACAGAAAGGGCAGAATCTTCACCTTTTATTGGCATCCACCTGACATAATGCAATTCCAGCAGCTCTAACCCTAATCTGTCACTAACTCATGGTTATCTTTGGTAAGGAAAATCAGGGTTAGCACTTGTGGGAATGGATTGACATTAATCTGGCATATTAGTTGTTGTGTAACCTAGAAGCATGATATATAATTTAAATGCCTCTCACCCTCTTTTAGTTACTCAGGACAGTTACACACCCTCCTATGAAGACATAGGTCTCCTTATTAAAATTTCATTTTAATGTATGACATATATAAAAAGGTTTATAGTATGTATGTAGGTTTTAAAACTTTCTAGAATGTGTACTTGTGAACTCATCCCCAACTCAAGAGCTAGAACGTGTGATTGTATCCATCCATATGGAGAGCATAGACTTTATATCCTTGCTTCTCTGATGCAATTTACCTGCCTCCTCCCACCCTCTATCCTTCACTGGGCTGAGAAGTATTTATTAGATATATGTAATAACTCAGGTATTTAGAGATTTCTCAGGGTCTAACCTTGTTATTTGAACCCAAGAGGAAATTAGAGCTTTAAATCTGAGAGCAGGAAGTGCTTGTAGTAAGATGGACTATTTAGCATTTCTCTGAAATGTTTTGGAATAGCTTCTCCTCTCCACAAACCTCCCCTTTCTCTTAGGTCCCTTTGGTTGAAATTCCCTTCATCAATGCAGAAGAGTCTTAGATACTCAAGGAATCTAGAGGTATAAGGCTTATATGCCTGACTACCACCTGGGAAATTATCTCCAGGTATCAGCTAAGCATCTGAAGTCTACATGTTCTGCAGCTACCAAAGAAAATTGCTCTTTTCTGTGTTTTGAGCTATAGATTGAGTGTAGATTATGGGTCAGTCACTGATGTAGATAGTTTTGGGTGAAATGTTAGGCAGCTCCCTAGGGGAGAATTGAAACAAAATGAAACTCAGAAGGGGTGGGATGAGGCCCTCTGAGAACAGTACAGGGCACTGAGTTGCATAGCAGTTCTGCGGCCTTGCCTTTACCTGCGTCTGCTATTTGCATTCCTTCCTAG
Seq C2 exon
GACTTCCTGATCATGTTTTTGCATCACCTGGCCACCATTGGGCTTATTACCTTCTCCTACATCAACAACATGGTTCGAGTGGGAACGCTGGTCTTGTGTCTACATGATGTCTCAGACTTCTTGCTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017395:ENSBTAT00000029121:6
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:
PF0379811=TRAM_LAG1_CLN8=FE(15.5=100)
A:
NA
C2:
PF0379811=TRAM_LAG1_CLN8=FE(21.6=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:
CCTCTCACAAGTGGACTTTATTACT
R:
CTCCAGCAAGAAGTCTGAGACA
Band lengths:
222-1842
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]