RnoINT0039064 @ rn6
Intron Retention
Gene
ENSRNOG00000031475 | Col16a1
Description
collagen type XVI alpha 1 chain [Source:RGD Symbol;Acc:1310982]
Coordinates
chr5:148275552-148275719:+
Coord C1 exon
chr5:148275552-148275587
Coord A exon
chr5:148275588-148275674
Coord C2 exon
chr5:148275675-148275719
Length
87 bp
Sequences
Splice sites
5' ss Seq
GCGGTAGGT
5' ss Score
9
3' ss Seq
TTATGTGACTTCTCATGCAGGGA
3' ss Score
7.89
Exon sequences
Seq C1 exon
GGTAGTTTTGGCGATGCTGGGCCGGCTGGAGTTGCG
Seq A exon
GTAGGTATAGGGGAACCGAGAGGCTCGGGCTGTGTCTGCACAGGCTAGGTTGGTGCTGAGCAGTGTCTTATGTGACTTCTCATGCAG
Seq C2 exon
GGACCACCAGGACCAGTGGGACCGGCTGGTATCAAAGGGGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000031475:ENSRNOT00000067663:27
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=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(18.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(23.3=100)
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:
GGTAGTTTTGGCGATGCTGGG
R:
TTTGCCCCTTTGATACCAGCC
Band lengths:
80-167
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]