RnoINT0005608 @ rn6
Intron Retention
Gene
ENSRNOG00000048676 | AABR07051445.1
Description
phosphatidylinositol-4-phosphate 5-kinase-like 1 [Source:NCBI gene;Acc:687758]
Coordinates
chr3:11593655-11594966:+
Coord C1 exon
chr3:11593655-11593870
Coord A exon
chr3:11593871-11594912
Coord C2 exon
chr3:11594913-11594966
Length
1042 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAAT
5' ss Score
5.43
3' ss Seq
CCCTCTACCAACCCCTGCAGGGA
3' ss Score
8.49
Exon sequences
Seq C1 exon
GTGTCTTCCCATCAGATCCCGTCCCACTCCCTGGATGTTGGAAACAGGTCCACTTCCTCAGGGAGCCGCCGTGGCCTCTTTTGGCACCTCCGAGCCAAGCATTCTAGAGTTGGCCTGTTTGAGATCGGTCCAGGACACGAACTGCATAGAATGACACGGATGATGCAGGAAGGGCTGTGGGCTGCCACCCAGGTCTCCATGAACAACCCACCCACG
Seq A exon
GTGAATGGCCCATCCTGTCTCATAACCCTCAAACCTAGCTGTTGTTCTCTCTCTCTCTCTAATACTTTGACACTGGGAATCAAAGAGACCTACCAAAAAGGAGGGAGGCAGGGATTTGTGTCAGGAAGCAGAAATTCTGAGTTGAGAAGCTGGAAAGAAAGTCCAGGAGGTATGAGGGACACCCTACTTAAAGTAGTAGATGTATGGCCTCTGTCTCTCTGGGCCTCAAGTACCCCTATCTGTATAATGGGTGGAGGGGTTAATATACCTTGTTTCTGAGGCCCCTGGGACCCCCACCCCCACCAGCCCAATCCAGTCCATCCTCCCTGGAGCCTGTCAGACTGAGGCCACGCTGGCTCAGCAGAAAGCATCACCTAGCTGCCAGCTCAGCAACCCGATAGGCTGGTGAGCCTGCATGTTGTTTGTGTGTGTGCACACATATGCACAGTTCAAAAACAAGATCTGGAGGGGGTTCTCTAGAACACAGCCTGACCCTCATCACCCACAGGACGCCTCCTATGGTTCCCCAGGACTGAGAACAGCCTGAAGATACTGCTGGCTGAAGGGCTGGCTGTTGGAGCCTGCCTCTGGCCGCCAGGGCAGTTCCCCATACCCTGTTTCTCTTCTCCATGTCCCTTCAGATTTCTACTCAGAGGTCACCTCCCCCAGGCAGTCGTCCCCAGTGAGACTCTCCCAGCCTCTCCCCTCCTGGAATCACTTGGCTCCAGGGTGATAGCCCCATAGACGGTGCGGTCTGGCTGTACACAGCCCGAATGAGTTTGAGAGCATGCACCAGGCTTGGACTTGGACCTGACCCTGAAGATCCAGATGTGGGGGATAACACTCAGGGGACCCTGTTTTAGGCCATTCCCATCCTTCCTCCAGCCCCGGGTGAACCAGAAGCTCAACTGCCCAATTTAGGCTAACAAGACTTGTCAGGTCCCTGTTTGCTAAAGGAAAGGGCAAGGCCCCGTGCTGGACTCACAATCTAGGTAGGCCATAGCAGATGCAGACTTCTGAAACCCTCTACCAACCCCTGCAG
Seq C2 exon
GGACCTCCTACCCAGAAGGATTTCCTGGAAGTCATGACCCAGGTTCACAAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000048676:ENSRNOT00000074122:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.444 A=NA C2=0.500
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGTCTTCCCATCAGATCCCG
R:
CTCTTTGTGAACCTGGGTCATGA
Band lengths:
270-1312
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]