DreINT0049652 @ danRer10
Intron Retention
Gene
ENSDARG00000055009 | col4a1
Description
collagen, type IV, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-081105-114]
Coordinates
chr9:8690612-8690860:-
Coord C1 exon
chr9:8690798-8690860
Coord A exon
chr9:8690666-8690797
Coord C2 exon
chr9:8690612-8690665
Length
132 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAA
5' ss Score
6.82
3' ss Seq
TCTTTATTTGTGCTTTGCAGGGG
3' ss Score
9.99
Exon sequences
Seq C1 exon
GGTCTTCCTGGTCTAGAAGGAGCACCTGGACCTCAAGGAATCCCAGGCTGCAATGGAACAAAG
Seq A exon
GTACAAAGAGTGTTTTTGAGACCTATGAACCTGCTAGTCCATCCACGATTAACATGATCCATGTAGGATAATAATTCTATGTCTTCAGTTAATCATAAAACCTCTTTATTTGTCTTTATTTGTGCTTTGCAG
Seq C2 exon
GGGGAGCGAGGATTTGATGGGATCCCAGGTATTACGGGATTGCTGGGACCACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000055009:ENSDART00000077296:4
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(36.4=100)
A:
NA
C2:
PF0139113=Collagen=FE(30.9=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:
GGTCTTCCTGGTCTAGAAGGAGC
R:
TGGTCCCAGCAATCCCGTAAT
Band lengths:
114-246
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]