GgaINT1009915 @ galGal4
Intron Retention
Gene
ENSGALG00000026836 | COL16A1
Description
collagen, type XVI, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2193]
Coordinates
chr23:4934547-4935087:-
Coord C1 exon
chr23:4934956-4935087
Coord A exon
chr23:4934595-4934955
Coord C2 exon
chr23:4934547-4934594
Length
361 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGG
5' ss Score
9.35
3' ss Seq
GTGCTCTGCTCTCCCCCCAGGAG
3' ss Score
11.82
Exon sequences
Seq C1 exon
TGCCAACCTGAAGCGCCCAAAACGCGGCGTCAGGCAGAGCTGATGCAGAGCAGCAACCTCATCGAGATCTCACCGCAGCCGCAGGGCCGGGTGTACACGCGCTGCTTCTGCCTGGAGGAGCCGCTGGGCCCG
Seq A exon
GTGAGGCGGCGTGCTGGCGGCGGTGTGCAGCCACGTGGATTCGGCCCCTGGAAAAGCCCTGCCTCACTTTTTCCGCTGTCTGCAGAGCTGGGAGGGAGGGAGCAAACAGGAGCCGGCAGTGCTGAGTGCTGGGGAGGGTGGGAGGATCGGGGGGCTGCTGGCTGCCGGTCCTGTGGGGCGGGGGGGGGGGGGTACACATGTGGGTTGATAGCCAAGGGGGTATGGGGTGGCACTGCCCTGGGGTGCAGCTGTGGGGTAACCCAGGGGGTGCACGGAGCAGCGTCACCCCAGGGTACAATCTCAGGGTACCCCAGGGATGCACATAGAGGTGTCACTGCGGGGTGCTCTGCTCTCCCCCCAG
Seq C2 exon
GAGCCAGCAAGAGAGAAGAGCAGCCTGAAGGCACATCGTGGGGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000026836:ENSGALT00000045237:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.455 A=NA C2=0.938
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0139113=Collagen=PU(10.8=43.8)
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]