GgaINT1009885 @ galGal4
Intron Retention
Gene
ENSGALG00000026836 | COL16A1
Description
collagen, type XVI, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2193]
Coordinates
chr23:4927888-4928089:-
Coord C1 exon
chr23:4928036-4928089
Coord A exon
chr23:4927933-4928035
Coord C2 exon
chr23:4927888-4927932
Length
103 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGT
5' ss Score
8.37
3' ss Seq
CCCTCCCTCATATCTTGCAGGGA
3' ss Score
11.06
Exon sequences
Seq C1 exon
GGGGTCCCAGGACACAACGGATTGCCAGGGCTGCCCGGACCGGCAGGAGACCTG
Seq A exon
GTAGGTGGTGGCTGTGCTGGGCACAGTGCCCCACGGGCATCCGTCGTGCATCCCTTCCACATCCCTTCCACATCCCTATGCATCCCTCCCTCATATCTTGCAG
Seq C2 exon
GGACCATTGGCTGTCATGGCTGAGAGGAACATCGAGGTGCTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000026836:ENSGALT00000045237:42
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=0.467
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(28.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(5.0=20.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGTCCCAGGACACAACGG
R:
CTTCAGCACCTCGATGTTCCT
Band lengths:
98-201
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]