DreINT0049854 @ danRer10
Intron Retention
Gene
ENSDARG00000052063 | col4a5
Description
collagen, type IV, alpha 5 (Alport syndrome) [Source:ZFIN;Acc:ZDB-GENE-030131-2281]
Coordinates
chr7:50872217-50872423:+
Coord C1 exon
chr7:50872217-50872279
Coord A exon
chr7:50872280-50872369
Coord C2 exon
chr7:50872370-50872423
Length
90 bp
Sequences
Splice sites
5' ss Seq
AAAGTATGA
5' ss Score
3.87
3' ss Seq
AAACCTCTCTTCTTTGTCAGGGT
3' ss Score
7.65
Exon sequences
Seq C1 exon
GGTCTTCCAGGACAGGATGGTGCTCCAGGACCCAGAGGAATTCCAGGCTGTAATGGAACTAAA
Seq A exon
GTATGAAACACTACAAACAATCATTGAACAGACAATATAAGCTGAAAACCTAAAAAGTGCTAACAAACATAAACCTCTCTTCTTTGTCAG
Seq C2 exon
GGTGAAAGAGGATTCCCTGGAAATCCAGGTCGCTCAGGTTTAGATGGTCAACCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052063:ENSDART00000073827:6
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=PD(0.1=0.0),PF0139113=Collagen=FE(31.2=100)
A:
NA
C2:
PF0139113=Collagen=FE(26.6=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:
GGTCTTCCAGGACAGGATGGT
R:
ACCATCTAAACCTGAGCGACCT
Band lengths:
111-201
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]