DreINT0048988 @ danRer10
Intron Retention
Gene
ENSDARG00000012422 | col11a2
Description
collagen, type XI, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-000208-23]
Coordinates
chr19:7274383-7274635:-
Coord C1 exon
chr19:7274582-7274635
Coord A exon
chr19:7274491-7274581
Coord C2 exon
chr19:7274383-7274490
Length
91 bp
Sequences
Splice sites
5' ss Seq
AGGGTACGC
5' ss Score
8.18
3' ss Seq
CATTTCAACTGCATTAACAGGGA
3' ss Score
4.88
Exon sequences
Seq C1 exon
GGAGAGGATGGATTCCCAGGAATTAAAGGAGACTTTGGTGTGAAGGGAGAGAGG
Seq A exon
GTACGCACATACAACACCAGTGGATAGAGAATTTTCGATATGCATGTGATTTAGCATTGGCTGCATTGACCCATTTCAACTGCATTAACAG
Seq C2 exon
GGAGAGGTGGGCGTGCCCGGCCCAAGAGGAGAAGATGGTCCTGAGGGGCCAAAGGGTCGCGTCGGACCCCCTGGTGAAATTGGTCCCCTCGGCCTGTTGGGAGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000012422:ENSDART00000104799:29
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(18.5=100)
A:
NA
C2:
PF0139113=Collagen=PD(7.6=19.4)
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:
TGGATTCCCAGGAATTAAAGGAGAC
R:
CTTCTCTCCCAACAGGCCGAG
Band lengths:
154-245
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]