GgaINT1009910 @ galGal4
Intron Retention
Gene
ENSGALG00000026836 | COL16A1
Description
collagen, type XVI, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2193]
Coordinates
chr23:4922516-4922841:-
Coord C1 exon
chr23:4922797-4922841
Coord A exon
chr23:4922705-4922796
Coord C2 exon
chr23:4922516-4922704
Length
92 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
GCTTGTCTGTGTCCCCTCAGGGT
3' ss Score
11.46
Exon sequences
Seq C1 exon
GGCCCCCCAGGAAAGCCTGGCACTGCAGGACCTGCTGGCCAGAAG
Seq A exon
GTGAGAGTTGTCAGAGCTCCCCCATGGTGCCCCCAGCTCCACACCACACCAGGGGTGCCATGGTGAAACTCTGCTTGTCTGTGTCCCCTCAG
Seq C2 exon
GGTGAAGCCGGGTCCCCTGGAATGCGAGGGTACCCTGGGGAGAAGGGCCGTGCTGGCGCGCCTGGGGGGCCGGGGAAGAGTGGCTCCATGGGCCCCATAGGGCTGCGGGGTCCTGCAGGAGAGAGGGGTCCCCCCGGCTCACCAGGACCTGCGGGCAGCCCTGGGCTGCCAGGACCCCCCGGGATGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000026836:ENSGALT00000045237:65
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:
NO
A:
NA
C2:
PF0139113=Collagen=PU(93.9=98.4)
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:
GGAAAGCCTGGCACTGCAG
R:
GGACCCCTCTCTCCTGCAG
Band lengths:
167-259
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]