DreINT0048979 @ danRer10
Intron Retention
Gene
ENSDARG00000012422 | col11a2
Description
collagen, type XI, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-000208-23]
Coordinates
chr19:7277436-7277720:-
Coord C1 exon
chr19:7277676-7277720
Coord A exon
chr19:7277490-7277675
Coord C2 exon
chr19:7277436-7277489
Length
186 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
CCTTTTTCTCATTTTTGTAGGGA
3' ss Score
10.37
Exon sequences
Seq C1 exon
GGAGATGATGGAGATGTTGGACCCAGAGGTCTTCCTGGCGAACCT
Seq A exon
GTGAGTGTTTTTGTTGAGTGTGTATTTCACAATCTGGTCAGAATTAAGCAAGGCTCTAGAACCTGACTGTGATATTATAGACATATGCAACCTTGATTTGCCCTTTTGTTATAAATCTGTAAAGCTCTATGTTTTGCTTGAATTTTATTGTATGTATTTTGATGAGCCTTTTTCTCATTTTTGTAG
Seq C2 exon
GGACCCCGTGGTTTGTTGGGGCCTAAAGGGCCTTCTGGACTTCCTGGACCTCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000012422:ENSDART00000104799:20
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(11.0=60.0),PF0139113=Collagen=FE(15.6=100)
A:
NA
C2:
PF0139113=Collagen=FE(18.9=100)
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:
GGAGATGATGGAGATGTTGGACC
R:
GGAGGTCCAGGAAGTCCAGAA
Band lengths:
98-284
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]