RnoINT0039082 @ rn6
Intron Retention
Gene
ENSRNOG00000031475 | Col16a1
Description
collagen type XVI alpha 1 chain [Source:RGD Symbol;Acc:1310982]
Coordinates
chr5:148288203-148288468:+
Coord C1 exon
chr5:148288203-148288256
Coord A exon
chr5:148288257-148288435
Coord C2 exon
chr5:148288436-148288468
Length
179 bp
Sequences
Splice sites
5' ss Seq
CTGGTGGGT
5' ss Score
6.29
3' ss Seq
CCTGCTTCTGTCTCTTGCAGGGA
3' ss Score
13.4
Exon sequences
Seq C1 exon
GGAGTGCCTGGACACAACGGTTTGCCAGGACAGCCTGGGCTCACTGCCGAGCTG
Seq A exon
GTGGGTATCAGCCAGGACGCACTGGCCATCGTCCTTCTTGTCCTTCCCGGGGATGAGCTGGCCAGGCGCTGGGGGTGGGGGGTGTCCTCCTTCACTCCCGGATCTTGAGGCTGGCTGCTCCTCTACGCCGTATGAGCTTCCCCTCCTGACCAGCTAGAACCTGCTTCTGTCTCTTGCAG
Seq C2 exon
GGATCCTTACCCATCGAGCAGCATCTCCTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000031475:ENSRNOT00000067663:43
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=0.600
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(26.2=100)
A:
NA
C2:
PF0139113=Collagen=PD(1.5=9.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGTGCCTGGACACAACG
R:
GGAGATGCTGCTCGATGGGTA
Band lengths:
82-261
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]