DreINT0049831 @ danRer10
Intron Retention
Gene
ENSDARG00000052063 | col4a5
Description
collagen, type IV, alpha 5 (Alport syndrome) [Source:ZFIN;Acc:ZDB-GENE-030131-2281]
Coordinates
chr7:50893443-50893816:+
Coord C1 exon
chr7:50893443-50893593
Coord A exon
chr7:50893594-50893702
Coord C2 exon
chr7:50893703-50893816
Length
109 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGAG
5' ss Score
6.38
3' ss Seq
ATTTTTATTTGTGAACTTAGGTG
3' ss Score
6.29
Exon sequences
Seq C1 exon
GGAGATCCTGGTTATGGTCTGCCTGGTCCTCCAGGTCCCACAGGATCACCAGGCATTAAAGGTGGACCCGGTCCGAAAGGTGATTCTGGTTTCCCTGGAAGCCCTGGTCAACCAGGCCGCCCAGGTCTCGATGGGGCTCCTGGACCTAAAG
Seq A exon
GTAGAGAATTATTTCATGTTCAAACAGAAATTAAATAGTAATGCTGTTCTCAACTCCACTGAAGATGCTGGAATCATCTAAGACTTGACATTTTTATTTGTGAACTTAG
Seq C2 exon
GTGATGCTGGTTTTCCTGGTGGTCCTGGTCCTCGTGGCCCCCCTGGGGCTCCTGCTTTTGGTCTTCAGGGCCCTCCTGGTCCTCCTGGAGCTCCAGGCTCTATTGGATCTCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052063:ENSDART00000073827:29
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(10.2=9.8),PF0139113=Collagen=PU(70.8=90.2),PF0139113=Collagen=PU(8.5=11.8)
A:
NA
C2:
PF0139113=Collagen=PD(27.7=46.2),PF0139113=Collagen=FE(53.5=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:
TTATGGTCTGCCTGGTCCTCC
R:
GAGATCCAATAGAGCCTGGAGC
Band lengths:
251-360
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]