DreINT0049594 @ danRer10
Intron Retention
Gene
ENSDARG00000011407 | col2a1b
Description
collagen, type II, alpha 1b [Source:ZFIN;Acc:ZDB-GENE-050302-9]
Coordinates
chr11:41655-41860:-
Coord C1 exon
chr11:41807-41860
Coord A exon
chr11:41709-41806
Coord C2 exon
chr11:41655-41708
Length
98 bp
Sequences
Splice sites
5' ss Seq
GCCGTGAGT
5' ss Score
8.56
3' ss Seq
TGTGTGTGTGATGTTCATAGGGC
3' ss Score
8.64
Exon sequences
Seq C1 exon
GGTCTGCCTGGTAAAGATGGAGAGACCGGTGCTGCTGGGCCTCCAGGACCTGCC
Seq A exon
GTGAGTGTGTTACGCATGTTTGAGTGTGTGATGTTCACATGAGTCTGTGTGTGATGCTCATAAATATATGTGTGTGTGTGTGTGTGTGATGTTCATAG
Seq C2 exon
GGCTCTGCGGGAGAGCGAGGCGAGCAGGGACAGCCGGGACCATCAGGCTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000011407:ENSDART00000159169:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(15.7=72.2)
A:
NA
C2:
PF0139113=Collagen=FE(28.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCTGCCTGGTAAAGATGGA
R:
CTGGAAGCCTGATGGTCCCG
Band lengths:
108-206
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]