GgaINT1009886 @ galGal4
Intron Retention
Gene
ENSGALG00000026836 | COL16A1
Description
collagen, type XVI, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2193]
Coordinates
chr23:4927690-4927932:-
Coord C1 exon
chr23:4927888-4927932
Coord A exon
chr23:4927807-4927887
Coord C2 exon
chr23:4927690-4927806
Length
81 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
ACCCCCCCACCTTCTCCCAGAAC
3' ss Score
8.76
Exon sequences
Seq C1 exon
GGACCATTGGCTGTCATGGCTGAGAGGAACATCGAGGTGCTGAAG
Seq A exon
GTGAGAGCTTGGGGTGGGATCTGGGGTCACACCACCCCCTGAGCCCCTCGGGGAGCCGCTGACCCCCCCACCTTCTCCCAG
Seq C2 exon
AACATCTGCGGGGACTGCGCCCACCTGCAGGCGGCCTTTGAAGCACCCAGAAGCTTCAAGGGGGAAAAGGGAGACCAAGGCATGCCAGGAGCCCCCGGCAACGAGGGTTGTGCACGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000026836:ENSGALT00000045237:43
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.467 A=NA C2=0.692
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(5.0=20.0)
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:
CCATTGGCTGTCATGGCTGAG
R:
ACGTGCACAACCCTCGTT
Band lengths:
159-240
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]