RnoINT0107096 @ rn6
Intron Retention
Gene
ENSRNOG00000009448 | Papln
Description
papilin, proteoglycan-like sulfated glycoprotein [Source:RGD Symbol;Acc:1311176]
Coordinates
chr6:107270660-107271010:+
Coord C1 exon
chr6:107270660-107270787
Coord A exon
chr6:107270788-107270901
Coord C2 exon
chr6:107270902-107271010
Length
114 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGG
5' ss Score
5.42
3' ss Seq
CAATGTCTTCCCATGCTTAGGGG
3' ss Score
6.41
Exon sequences
Seq C1 exon
GCACCAGGTGCAGCATGATGGCTCTCTGGTCATCAGCCGAGTGACTGTGGAAGATGGTGGCTTTTACACCTGTGTTGCTTTTAATGGGCATGACCGAGACCAGCGCTGGGTCCAGCTCAGAGTTCAGA
Seq A exon
GTAAGGAGGAAGTCCTGAGTGGGGGGGGGGGGTGTGCAATGGGTGTCAAGTGGTGTGAGGTGGCAGAGGGAGGGGTTGAGGAGTCAGCTACTGACAATGTCTTCCCATGCTTAG
Seq C2 exon
GGGAGCTGACAATCACAGGCCTGCCTCCTGCCATGACGGTGCCAGAGGGTGACACTGCCAGGCTTCTGTGTGTGGTGGCTGGAGACAGTGTGAACATTAGGTGGTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009448:ENSRNOT00000012757:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.182 A=NA C2=0.162
Domain overlap (PFAM):
C1:
PF0767911=I-set=PD(49.4=93.2)
A:
NA
C2:
PF0767911=I-set=PU(39.1=91.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACCAGGTGCAGCATGATGG
R:
GGACCACCTAATGTTCACACTGT
Band lengths:
234-348
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]