DreINT0050127 @ danRer10
Intron Retention
Gene
ENSDARG00000101816 | col5a3b
Description
collagen, type V, alpha 3b [Source:ZFIN;Acc:ZDB-GENE-110728-4]
Coordinates
chr1:58556115-58556373:-
Coord C1 exon
chr1:58556320-58556373
Coord A exon
chr1:58556223-58556319
Coord C2 exon
chr1:58556115-58556222
Length
97 bp
Sequences
Splice sites
5' ss Seq
GCAGTGAGT
5' ss Score
7.39
3' ss Seq
GTGTGTGTGTGTGTTGTCAGGGG
3' ss Score
7.29
Exon sequences
Seq C1 exon
GGGGAAGATGGCGAGTCTGGTGATCCTGGAGCAGTTGGTGTTTCTGGCAGCGCA
Seq A exon
GTGAGTCCATCCTGCTTTCCTGAACTTCCTGTGTGAGGTTCATCTATTGCTGTATCACCACTGCAGCATGTGTGTGTGTGTGTGTGTGTGTTGTCAG
Seq C2 exon
GGGGAGAAGGGTGAGCAGGGGGAGAAAGGAGACACTGGACCCCCCGGAGCTGCTGGCTCAGCAGGAGCCCGAGGAGCCTCTGGAGAAGACGGAGCGAAGGGCAATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000101816:ENSDART00000170580:48
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(25.8=100)
A:
NA
C2:
PF0139113=Collagen=PD(16.7=30.6),PF0139113=Collagen=PU(51.5=97.2),PF0139113=Collagen=PU(2.2=5.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAAGATGGCGAGTCTGGTGA
R:
CCCATTGCCCTTCGCTCC
Band lengths:
160-257
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]