RnoINT0034884 @ rn6
Intron Retention
Gene
ENSRNOG00000001072 | Cers4
Description
ceramide synthase 4 [Source:RGD Symbol;Acc:1309303]
Coordinates
chr12:4447101-4448802:-
Coord C1 exon
chr12:4448685-4448802
Coord A exon
chr12:4447220-4448684
Coord C2 exon
chr12:4447101-4447219
Length
1465 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
CCTCATTATTCCCTTCTCAGACC
3' ss Score
8.42
Exon sequences
Seq C1 exon
ATTCGTGGCCTTGCCCCTGAGCCGGTGGATGGGTGTGCAGGATCCAATCAGGAGAAAGATAAAGCCCAACCCAGTGCTGGAGAAATACTTCCTCAGGATGAAGCAGAGACCAGTGGAG
Seq A exon
GTGAGCCCCATGTCAGGATGGCCACTGCATGGTGATTGCCCTGGGACCCAGGCGTAGAAGTGCTGTGTGTCCCTTATTAGAGATGGGACAGGGGCCTCTGACATACCCTACACTCAGCTTGAGTCCACAGATTCCCTGATAGGTGAGGCTCTGCTCCTCTGTCTGCAGGTTTGTGAGACCCCACTCCTTCCCACTGTGCAGAGACTAGTGTACCAGTAACATCCTTCTCAGGTTCTGTAGGGCTTGAAACCACTTCTCTCCCAGCATGAGGTCATCCTTCCTAGTCTCAGGTTCCCTAGGTTTTGAAGCCCCATCCCTCATCTCTCTCCTGAAAGCAAAGCCATTCCCCTCATCTCCTGAGTCAAGAGTGTCTGCCCCTTTCAGGCTTCCTGGGTGTGAGGCCCTGCCCTATCTGGTCTCCTTGGGACCTGGGGGAACTTTACTTTCAAGGTCTTGAGTTATGAAATTGTCTCTTCTTAGCCTTCCTGGGACATGAGGCCATGCCTCTCCTGGTTTCCCTGAGATTTGATCCTTCTTAGGGTCCCCAGAGTTTGAAAGTGACGTTCCAGCCTTCCTGGGTAACGAGTCCCTGTACCTCTAGGCTTTTTGGGGATTGTGGTCCTGTTCCTTCCTCCAAGGCTTCTTGGGACATGAGGTCCTACCCCTGTGAGGCTTCCTCAAATTTGAAGCTCTTGTCTCTTAGTCTGGAACATCAACCTTATGATCACTCAACAAACAGATTCTGGGGTCACATTAAGAAGAGTAGGTTGGGGGCTGGAGAGATGGCTCAGTGTTTAAGAGCACTGACTGCTCTTCCAAAGGTCCTGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCTGTAATGAGATCTGATGCCCTCTTCTGGTGTGTCTGAACAGCTACAGTGTACTTATATATAATAAATAAATAAATCTTAAAAAAAAAAAAGAAGAAGAAGAGTAGGTTTCTTTCCAGTTCTGGGAAGGGACAAGATACTTTTGTTCCAGTGTAGTGGCTGGAGTGTCAGAAGCAGCCCTATGGTTCTGCCTCTATTCTTGTCCTTGGTGTGGCAGCCCTGTTGGCCTGGTATGGGTCAGGCTCTACTGGGTAAGGTGGAAGTGATGGCAGTGTGCCCTGGCTGGGTACTGAATAACTTCTATACAGCAGAGAGCTGAAGGGCTGCCTAGGGTAGTGTCCTACTCTGCTTCTTGTTTCAGTGCAAACACCAAATGCAAGCTGGAGAAGAAAGAGTTAATTTCAACTTAAACTTCAGGTAACAGTCCACTGCTGAGGGAAGTGAAGGCAGGAAGTGAAGTAGATGCCACCTTACCTCTCCTCTCTTTCCTCTGTAGGAAAGATCTTAAGCTTCAGTGGGGAATCAAATGGGATCAGAGACAAAGAGTAGGAAACCAGCATTGGGCCTGTGTAATCCTTCTCCTCATTATTCCCTTCTCAG
Seq C2 exon
ACCCAGATGGTCCTCCTGGCTTCCCAGTGTGGCCTCACGTTGCGGCAGATTCAACGCTGGTTCAGGAGACGTCGGAACCAGGATCGGCCTTGCCTGTCCAAGAAATTCTGTGAAGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001072:ENSRNOT00000001418:4
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:
PF0210110=Ocular_alb=PD(32.2=47.5)
A:
NA
C2:
PF0004624=Homeobox=PD(60.4=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:
CCCTGAGCCGGTGGATGG
R:
TGGCTTCACAGAATTTCTTGGACA
Band lengths:
222-1687
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]