RnoINT0107092 @ rn6
Intron Retention
Gene
ENSRNOG00000009448 | Papln
Description
papilin, proteoglycan-like sulfated glycoprotein [Source:RGD Symbol;Acc:1311176]
Coordinates
chr6:107267586-107268096:+
Coord C1 exon
chr6:107267586-107267723
Coord A exon
chr6:107267724-107267971
Coord C2 exon
chr6:107267972-107268096
Length
248 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGT
5' ss Score
6.99
3' ss Seq
TCTCCCCTCCCTCCATTCAGGTA
3' ss Score
12.86
Exon sequences
Seq C1 exon
GATCAACTTGGCAGACTCGGAACCGTCCCTGGTACAGGCAGCTCCAGGGCAGGCGGTCCAACTCTTTTGCCCTGGCAACATCCCCCCGGAATTCCAGGCAGGGTGGCAGAAAGAGGGCCGGCCCATCTCCTCTAACAG
Seq A exon
GTGTGTTTAAATCCATGGTCCCATGTCCTGTGTGAGAGGTTCACCGTAAGGTGCCGGTGAACAATAGCTACCTTTCATCTCCTGTATGTGCAATGTCCTTTCTCGTACAGAAGCCCTTCTGGCATTCCTTGGGAGTGAGAGTGCTCAGAGTGCTGTGGGGCTAATAGTCTTCTCTGGTAGTATGGGAGCTGGAGGACTCTTACTGCCCTCAGGAGCCCGGAAGTCATGTCTCCCCTCCCTCCATTCAG
Seq C2 exon
GTACCAGCTACAGGCAGATGGCTCCCTCATCATCAGCCCCTTGAGGCCAGAAGATGCTGGCATCTATAGCTGTGGCAGCCAGAGGTCAGGCCATGAGCCCCAGAAGATACAGCTTCGAGTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009448:ENSRNOT00000012757:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.860
Domain overlap (PFAM):
C1:
PF0767911=I-set=PU(50.6=89.4)
A:
NA
C2:
PF0767911=I-set=PD(48.2=93.0)
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:
GATCAACTTGGCAGACTCGGA
R:
GTGACTCGAAGCTGTATCTTCTGG
Band lengths:
261-509
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]