DreINT0048955 @ danRer10
Intron Retention
Gene
ENSDARG00000009014 | col11a1b
Description
collagen, type XI, alpha 1b [Source:ZFIN;Acc:ZDB-GENE-070912-607]
Coordinates
chr2:15731176-15731492:-
Coord C1 exon
chr2:15731385-15731492
Coord A exon
chr2:15731230-15731384
Coord C2 exon
chr2:15731176-15731229
Length
155 bp
Sequences
Splice sites
5' ss Seq
GCTGTGAGT
5' ss Score
7.39
3' ss Seq
GTGTTGTTTATTGACTGCAGGGT
3' ss Score
6.82
Exon sequences
Seq C1 exon
GGTCATCCAGGTTTGATTGGTCTGATCGGTCCTCCTGGTGAGTCTGGAGAAAAAGGTGATCGAGGACTGCAAGGACCACAGGGTATTGGCGGAGGCAAGGGTGATGCT
Seq A exon
GTGAGTGAAATGATCATTTTACATACACCTGAGGTCCTTCAGGACATGATGTAGTTATATCTAAATAAATGTTAGATCTTCAGAATGATTGATATTAATTGAAATTATGTTTTGATGTTGCCTCTGAAGAACACTGTGTTGTTTATTGACTGCAG
Seq C2 exon
GGTCCCGCTGGTTCATCTGGTCCAGTCGGTCCCCCAGGTCCTCCTGGTATTCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000009014:ENSDART00000049589:59
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(7.3=16.7),PF0139113=Collagen=FE(49.3=100),PF0139113=Collagen=PU(8.1=13.9)
A:
NA
C2:
PF0139113=Collagen=PD(19.0=83.3),PF0139113=Collagen=FE(27.4=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:
GGTCATCCAGGTTTGATTGGTCT
R:
GACCGACTGGACCAGATGAAC
Band lengths:
139-294
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]