DreINT0048890 @ danRer10
Intron Retention
Gene
ENSDARG00000026165 | col11a1a
Description
collagen, type XI, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-070209-167]
Coordinates
chr24:28715321-28715588:-
Coord C1 exon
chr24:28715535-28715588
Coord A exon
chr24:28715375-28715534
Coord C2 exon
chr24:28715321-28715374
Length
160 bp
Sequences
Splice sites
5' ss Seq
GCTGTAAGT
5' ss Score
8.56
3' ss Seq
TTTGTATCTAAAATCCTCAGGGA
3' ss Score
6.12
Exon sequences
Seq C1 exon
GGCCCTGTTGGTTTTCCTGGAGACCCAGGTCCACCTGGTGAGCCAGGTGTTGCT
Seq A exon
GTAAGTGCCGAAATCCATCAATTAAACAACTGTAACTTACTTTTCTATAAATAACTTTTCCATGTACAAACACCTTGTAACTAGATAAAGACATTTGCTTATTTTGTCAATTGTCAAGTTATTTGCCTCTAAAATATCTGTTTGTATCTAAAATCCTCAG
Seq C2 exon
GGAATAGATGGAGGCCCAGGAGAGAAGGGAGAGGATGGAGAGTCTGGTCAGCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000026165:ENSDART00000003503:52
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(25.0=100)
A:
NA
C2:
PF0139113=Collagen=FE(25.0=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:
GCCCTGTTGGTTTTCCTGGAG
R:
AGGCTGACCAGACTCTCCATC
Band lengths:
107-267
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]