RnoINT0107084 @ rn6
Intron Retention
Gene
ENSRNOG00000009448 | Papln
Description
papilin, proteoglycan-like sulfated glycoprotein [Source:RGD Symbol;Acc:1311176]
Coordinates
chr6:107261241-107261675:+
Coord C1 exon
chr6:107261241-107261423
Coord A exon
chr6:107261424-107261533
Coord C2 exon
chr6:107261534-107261675
Length
110 bp
Sequences
Splice sites
5' ss Seq
CTAGTAAGT
5' ss Score
8.78
3' ss Seq
CTCCCACCCTGGGCCTTCAGTGC
3' ss Score
5.95
Exon sequences
Seq C1 exon
TGCTCAGTTACATGTGGAGCTGGCATCAGGAAGCGGAGTGTCACATGCCGAGGGGACGAAGACTCTCTGGTCCACCCCGCAGCATGCTCCTTGAAGGACCAGCCAACCCTCACAGAGCCCTGTGTGCGAGAGGCCTGTCCTGGGTTCCGTGGCCAGGCCTGGCATGTCGGCTCGTGGAGTCTA
Seq A exon
GTAAGTGCCCATCCCTTACCAATGCCTGCTATCCAGGCCTGGTTCCTTCTTCAGGGGTGTCCTTGGCCTCAGGGTCTCTCTCTCTCTCTACTCCCACCCTGGGCCTTCAG
Seq C2 exon
TGCTCTAAAAGCTGTGGTTCCGGCATTCGGAGACGGCAGGTCGTTTGTACCATTGGGCCGCCCGGTCGCTGTGTGGACCTGCAGTCGTCCAAACCTGCAGAGGTAGAAGCCTGCAACAGACAACCCTGCCATCTCCCTCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009448:ENSRNOT00000012757:13
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=0.042
Domain overlap (PFAM):
C1:
PF0009014=TSP_1=PD(83.3=73.8),PF0009014=TSP_1=PU(12.0=9.8)
A:
NA
C2:
PF0009014=TSP_1=PD(84.0=87.5)
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:
GGACGAAGACTCTCTGGTCCA
R:
GGTTGTCTGTTGCAGGCTTCT
Band lengths:
255-365
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]