DreINT0048997 @ danRer10
Intron Retention
Gene
ENSDARG00000012422 | col11a2
Description
collagen, type XI, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-000208-23]
Coordinates
chr19:7272335-7272520:-
Coord C1 exon
chr19:7272467-7272520
Coord A exon
chr19:7272389-7272466
Coord C2 exon
chr19:7272335-7272388
Length
78 bp
Sequences
Splice sites
5' ss Seq
GTCGTATGT
5' ss Score
5.35
3' ss Seq
TAACCTTTTTGCATTCAAAGGGT
3' ss Score
6.52
Exon sequences
Seq C1 exon
GGACCTCCAGGGAAAGATGGACTTCCTGGACACCCTGGACAGAGAGGCGAAGTC
Seq A exon
GTATGTACCCTCTAAACTACAGTATTATCTGTGAACATGATTAAATGCGCAGCAACATTAACCTTTTTGCATTCAAAG
Seq C2 exon
GGTTTCCAAGGCAAAGTTGGACCACCTGGCCCACCTGGAGTTGTTGGCCCACAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000012422:ENSDART00000104799:37
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=FE(20.5=100),PF0139113=Collagen=PU(11.2=61.1)
A:
NA
C2:
PF0139113=Collagen=PD(19.1=72.2),PF0139113=Collagen=FE(23.0=100),PF0139113=Collagen=PU(20.2=94.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGACCTCCAGGGAAAGATGGA
R:
GTGTGGGCCAACAACTCCAG
Band lengths:
108-186
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]