DreINT0050130 @ danRer10
Intron Retention
Gene
ENSDARG00000101816 | col5a3b
Description
collagen, type V, alpha 3b [Source:ZFIN;Acc:ZDB-GENE-110728-4]
Coordinates
chr1:58553924-58554105:-
Coord C1 exon
chr1:58554052-58554105
Coord A exon
chr1:58553978-58554051
Coord C2 exon
chr1:58553924-58553977
Length
74 bp
Sequences
Splice sites
5' ss Seq
AACGTGAGT
5' ss Score
9.54
3' ss Seq
TAGGTCATCTGTTCCCTCAGGGC
3' ss Score
7.25
Exon sequences
Seq C1 exon
GGCCCCATTGGTCTTCCTGGAGACATGGGCGCTCCTGGAGAGCCGGGTGTAAAC
Seq A exon
GTGAGTATCTTCACACTCATCTCAGATCTGCACAGTGAACAGCGCATGGTGAAATAGGTCATCTGTTCCCTCAG
Seq C2 exon
GGCATCGACGGGACTGCTGGATCTAAAGGAGATGCTGGAGATCCGGGGAAACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000101816:ENSDART00000170580:50
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(25.0=100),PF0139113=Collagen=FE(18.7=100)
A:
NA
C2:
PF0139113=Collagen=PD(19.1=72.2),PF0139113=Collagen=FE(18.7=100)
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:
CCCCATTGGTCTTCCTGGAGA
R:
TTTCCCCGGATCTCCAGCATC
Band lengths:
103-177
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]