RnoINT0107100 @ rn6
Intron Retention
Gene
ENSRNOG00000009448 | Papln
Description
papilin, proteoglycan-like sulfated glycoprotein [Source:RGD Symbol;Acc:1311176]
Coordinates
chr6:107254082-107254471:+
Coord C1 exon
chr6:107254082-107254142
Coord A exon
chr6:107254143-107254368
Coord C2 exon
chr6:107254369-107254471
Length
226 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAG
5' ss Score
8.27
3' ss Seq
ACACCCATGTTCTCCTGCAGAGC
3' ss Score
9.61
Exon sequences
Seq C1 exon
GAGAGACGGAGGCGCCAGCTGCGTGGGCCCTGCACGCAGCCACCGCACCTGCCACACGGAG
Seq A exon
GTAAAGTCTGCCTGCCCCTCCCCCAGCCTCTCCCCCAGTCCCTTCTCTCTCCCCAATTCCTCACGGCCCGCCTTCGGCCTGCCACTGAGGGAGAGCAAGAGGCCTCTCCTGGGACAGGTGTGGTTGGGACGGAATCGCAGGACCCCAGGGCTCCAGGACACCGAGGATGGATAAGGGAGAACCTTAACCTCCCCAGTGCACACCTGACACCCATGTTCTCCTGCAG
Seq C2 exon
AGCTGCCCAGACAGCGTGCGGGACTTCCGGGCAGAGCAGTGTGCAGAATTCGATGGCACCGACTTCCAGGGTCGGCGCTACCGGTGGCTGCCCTACTACGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009448:ENSRNOT00000012757:4
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:
PF0009014=TSP_1=FE(40.0=100)
A:
NA
C2:
PF0009014=TSP_1=PD(2.0=2.9)
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:
GAGAGACGGAGGCGCCAG
R:
TAGTAGGGCAGCCACCGGTA
Band lengths:
159-385
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]