RnoINT0039058 @ rn6
Intron Retention
Gene
ENSRNOG00000031475 | Col16a1
Description
collagen type XVI alpha 1 chain [Source:RGD Symbol;Acc:1310982]
Coordinates
chr5:148270377-148270618:+
Coord C1 exon
chr5:148270377-148270421
Coord A exon
chr5:148270422-148270582
Coord C2 exon
chr5:148270583-148270618
Length
161 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
TTTTTTCACTTTCCCAATAGGGG
3' ss Score
10.38
Exon sequences
Seq C1 exon
GGCAGCTCTGGAATACCAGGAAAGGAAGGCCCAGGAGGGAAGCCG
Seq A exon
GTGAGTGACCACAAACAGGGGAGGGCCTTCTTGCTCACCATGCTCAGATCTGTTCCTCCAAAGCCTCCATGGTGAAGGGCTTGGGTCCTCAGCTCCTTCCCGCCATAGCAATCCCTGTGCCTGGTATTAATGCCCCATGCTTTTTTTCACTTTCCCAATAG
Seq C2 exon
GGGAAGCCAGGAGTACCCGGGACTAAGGGAGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000031475:ENSRNOT00000067663:21
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(25.0=100)
A:
NA
C2:
PF0139113=Collagen=FE(19.6=100)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]