GgaINT1009853 @ galGal4
Intron Retention
Gene
ENSGALG00000026836 | COL16A1
Description
collagen, type XVI, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2193]
Coordinates
chr23:4933229-4933401:-
Coord C1 exon
chr23:4933360-4933401
Coord A exon
chr23:4933274-4933359
Coord C2 exon
chr23:4933229-4933273
Length
86 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
CTGTCCCCTTCTGTCCCCAGTGC
3' ss Score
12.05
Exon sequences
Seq C1 exon
GGTGCTGACTGCGTGCGCACAGACCCCAGTGGCCCTGTGCAG
Seq A exon
GTGAGACCCCCCCACCCCACACACCCCTTTGCCCCATCTCCAACCCCATCTCATCCCCATCCCCTTCTGTCCCCTTCTGTCCCCAG
Seq C2 exon
TGCGCCGAGGGGCCGCGGGGTGAGCAGGGGCAGCGTGGAGAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000026836:ENSGALT00000045237:13
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=35.7),PF0139113=Collagen=PU(5.0=21.4)
A:
NA
C2:
PF0139113=Collagen=FE(23.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCGCACAGACCCCAGTG
R:
CTCTCCACGCTGCCCCTG
Band lengths:
71-157
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]