DreINT0049834 @ danRer10
Intron Retention
Gene
ENSDARG00000052063 | col4a5
Description
collagen, type IV, alpha 5 (Alport syndrome) [Source:ZFIN;Acc:ZDB-GENE-030131-2281]
Coordinates
chr7:50894094-50894457:+
Coord C1 exon
chr7:50894094-50894261
Coord A exon
chr7:50894262-50894367
Coord C2 exon
chr7:50894368-50894457
Length
106 bp
Sequences
Splice sites
5' ss Seq
CTGGTAATG
5' ss Score
5.67
3' ss Seq
ACCCATTATCATTACTAAAGGAT
3' ss Score
3.85
Exon sequences
Seq C1 exon
GAGTACCGGGGGCGAATGGAGAAAAAGGAGACAGAGGCCCTCCAGGTCTGAGTACTCCAGGCTTCCAGGGTGATAGAGGAATTTCTGGACTTCCTGGACCTCCTGGTCCAGTTGGTCCACCTGGAGTTCCAGGCCGACCTGGACAAGATGGCCTACCAGGACTCCCTG
Seq A exon
GTAATGCACTGATAGCAATATCCACTAATTAGCAATGTGATTTTTTTTTGTTCTATATGTATGTCTTTTTTGGACTTTCTCTACTAACCCATTATCATTACTAAAG
Seq C2 exon
GATCTAAGGGAGAAATGGGCTCAATGGGGCCTCCCGGATCAAAAGGGAACCCCGGCAACCCTGGAGCTCCCGGCTTTCCAGGACCAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052063:ENSDART00000073827:31
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(40.8=50.9),PF0139113=Collagen=PU(60.9=68.4)
A:
NA
C2:
PF0139113=Collagen=PD(37.5=77.4),PF0139113=Collagen=PU(42.9=87.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGGCGAATGGAGAAAAAGGA
R:
CTTTTGGTCCTGGAAAGCCGG
Band lengths:
250-356
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]