GgaINT1009859 @ galGal4
Intron Retention
Gene
ENSGALG00000026836 | COL16A1
Description
collagen, type XVI, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2193]
Coordinates
chr23:4931875-4932330:-
Coord C1 exon
chr23:4932292-4932330
Coord A exon
chr23:4931920-4932291
Coord C2 exon
chr23:4931875-4931919
Length
372 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
ACTGCCACCTCTGGCTCCAGGGC
3' ss Score
7.63
Exon sequences
Seq C1 exon
GGTGATCCTGGTGGCCCCCCAGGTCCAAAGGGAGAAAAG
Seq A exon
GTGAGTGGGGGGGATAGGGGGTGTCCACCACCTCCTCCTGCCTGAAGGGTCAGTGCGGAGCTCATGGGACCCTCTCCGGTTGCGTCATGGTGCTGTGGAGTCATTGGGGGCTCATGCTGGGGAGTGGGAACCCCTCACCTGGGGAGGGGCTGCTCAGGACGTGCCGAGGGCCCTCCATGGGGGCTTGGCAGCTGCTGAGGTCCCCTGTAATAGCTGGTGCTGGGGGACACGGGAGCAGGGCTGGTTCCAATCCTTGATTTATGGAGCTGGAGGGGAGTGCTGGGGCGGGGGTGGGATGCTGGGTTGGGGGCGTGGGGCTGAGGGGCTGCAGCTCCCACTGTGCCAGGCTCACACTGCCACCTCTGGCTCCAG
Seq C2 exon
GGCAGCTCAGGAGCTCCTGGACCCGGCGGATCTCCTGGGACACCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000026836:ENSGALT00000045237:19
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=PD(7.7=38.5),PF0139113=Collagen=FE(19.7=100)
A:
NA
C2:
PF0139113=Collagen=FE(23.0=100)
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:
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]