DreINT0049666 @ danRer10
Intron Retention
Gene
ENSDARG00000055009 | col4a1
Description
collagen, type IV, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-081105-114]
Coordinates
chr9:8687815-8688018:-
Coord C1 exon
chr9:8687956-8688018
Coord A exon
chr9:8687851-8687955
Coord C2 exon
chr9:8687815-8687850
Length
105 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
TCATGCTATTTTGCTTTAAGGGA
3' ss Score
6.96
Exon sequences
Seq C1 exon
GGTCAAAAAGGTAATGCTGGACAACAAGGGCCTGTTGGTCCACCTGGACCTTATGGACCTCCG
Seq A exon
GTGAGTCTTAGGCTCAAATCTCTGAAACAAATAACAGCTTAATGCACAATCAATTAACATAGTGAACTCCGTCTCGGATCTCACATCATGCTATTTTGCTTTAAG
Seq C2 exon
GGAAGACCAGGTGATCCTGGACAAAAAGGAGAGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000055009:ENSDART00000077296:8
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(32.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(17.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCAAAAAGGTAATGCTGGACA
R:
CGGCTCTCCTTTTTGTCCAGG
Band lengths:
99-204
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]