DreINT0050091 @ danRer10
Intron Retention
Gene
ENSDARG00000101816 | col5a3b
Description
collagen, type V, alpha 3b [Source:ZFIN;Acc:ZDB-GENE-110728-4]
Coordinates
chr1:58568235-58568490:-
Coord C1 exon
chr1:58568437-58568490
Coord A exon
chr1:58568289-58568436
Coord C2 exon
chr1:58568235-58568288
Length
148 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGT
5' ss Score
8.68
3' ss Seq
TGTGTGTGTGTGTTTATCAGGGG
3' ss Score
9.85
Exon sequences
Seq C1 exon
GGTCGTGGTGGGATGGATGGAGGCAGAGGTGAGCCTGGAGAGACTGGAGTGAAG
Seq A exon
GTCAGTGATAGTGTTGTGTGTAGTATTGTGTAGTGTTGTGTGTTGTGTTGTATGAACGATACTCCATTTCACTTTATTTAATCATATCTCAATGTTTAACTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTATCAG
Seq C2 exon
GGGGACAGAGGCTTTGATGGTTTACCAGGTCTGCCCGGAAACAAGGGTCACCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000101816:ENSDART00000170580:15
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(5.2=16.7)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCGTGGTGGGATGGATGGAG
R:
CCGGTGACCCTTGTTTCCG
Band lengths:
106-254
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]