DreINT0048856 @ danRer10
Intron Retention
Gene
ENSDARG00000026165 | col11a1a
Description
collagen, type XI, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-070209-167]
Coordinates
chr24:28755764-28755941:-
Coord C1 exon
chr24:28755888-28755941
Coord A exon
chr24:28755809-28755887
Coord C2 exon
chr24:28755764-28755808
Length
79 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
TGCGCAATTGATTTCTGCAGGGC
3' ss Score
6.56
Exon sequences
Seq C1 exon
GGGCCGCGAGGTCTTCTCGGCCCAAGAGGCCCTCCTGGACCTCCTGGACAACCT
Seq A exon
GTGAGTGTGTTTTTAATGTGTAATCTGCAAATCTGAAGCTGATTGCTCTCTTCTAATCTTGCGCAATTGATTTCTGCAG
Seq C2 exon
GGCATTGCTGGTGTTGATGGTCCGCAGGGTCCCAAAGGAAACATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000026165:ENSDART00000003503:21
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(20.7=100),PF0139113=Collagen=FE(23.9=100)
A:
NA
C2:
PF0139113=Collagen=FE(17.1=100),PF0139113=Collagen=FE(19.7=100),PF0139113=Collagen=PU(9.6=53.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGGTCTTCTCGGCCCAAGAG
R:
ATGTTTCCTTTGGGACCCTGC
Band lengths:
91-170
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]