GgaINT1009904 @ galGal4
Intron Retention
Gene
ENSGALG00000026836 | COL16A1
Description
collagen, type XVI, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2193]
Coordinates
chr23:4934956-4935342:-
Coord C1 exon
chr23:4935262-4935342
Coord A exon
chr23:4935088-4935261
Coord C2 exon
chr23:4934956-4935087
Length
174 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
GCCCTCTTCTCTCCCATCAGTGC
3' ss Score
9.81
Exon sequences
Seq C1 exon
TTCGACCTGCAGCAGGCGCACATCTACTGCGACGCAGAGCTGGCCCGGCACGAGGGATGCTGTGAGATCTCAGCCAGCGGG
Seq A exon
GTGAGTGCTGCAGGCAGGGCCGTGCTGGGAGGGGGAACCGGGGCACGCTGCAGGTGGTTGGGGTGCATCGTGAGCGGGGCGGCACGTCTCCCCACCAGCACCATGGTGCAGGGCGCATCCCTGTCTCCGATTGCGTCCGCTCACAGCCCCCTGCGCCCTCTTCTCTCCCATCAG
Seq C2 exon
TGCCAACCTGAAGCGCCCAAAACGCGGCGTCAGGCAGAGCTGATGCAGAGCAGCAACCTCATCGAGATCTCACCGCAGCCGCAGGGCCGGGTGTACACGCGCTGCTTCTGCCTGGAGGAGCCGCTGGGCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000026836:ENSGALT00000045237:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.455
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
GCAGCAGGCGCACATCTAC
R:
GCTCCTCCAGGCAGAAGCAG
Band lengths:
194-368
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]