DreINT0048864 @ danRer10
Intron Retention
Gene
ENSDARG00000026165 | col11a1a
Description
collagen, type XI, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-070209-167]
Coordinates
chr24:28747266-28747517:-
Coord C1 exon
chr24:28747464-28747517
Coord A exon
chr24:28747374-28747463
Coord C2 exon
chr24:28747266-28747373
Length
90 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAAT
5' ss Score
5.83
3' ss Seq
TTTTATATCTTTACAATCAGGGA
3' ss Score
8
Exon sequences
Seq C1 exon
GGTGAGGATGGATTCCCAGGTTTCAAGGGAGACATGGGTCTCAAAGGCGACAGG
Seq A exon
GTAAATAAATTGCATACAGCCTGGCTCAAGTTCATTTCACTTCACAAACAACACACACTGAATGACTGTATTTTATATCTTTACAATCAG
Seq C2 exon
GGAGAGCTGGGACTGGCTGGACCCAGAGGAGAAGATGGTCCAGAGGGCCCGAAGGGTCGTGCAGGGCCTAACGGTGAATCTGGACCCCAGGGATCTGCCGGAGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000026165:ENSDART00000003503:29
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(11.6=44.4),PF0139113=Collagen=FE(27.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(9.0=16.7),PF0139113=Collagen=FE(57.4=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:
TGGATTCCCAGGTTTCAAGGG
R:
CTTTTCTCCGGCAGATCCCTG
Band lengths:
154-244
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]