DreINT0049952 @ danRer10
Intron Retention
Gene
ENSDARG00000012593 | col5a1
Description
procollagen, type V, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-041105-6]
Coordinates
chr21:6771173-6771367:+
Coord C1 exon
chr21:6771173-6771226
Coord A exon
chr21:6771227-6771313
Coord C2 exon
chr21:6771314-6771367
Length
87 bp
Sequences
Splice sites
5' ss Seq
ATGGTACAG
5' ss Score
3.5
3' ss Seq
CTCATCTCTCTCTGTTTCAGGGT
3' ss Score
13.23
Exon sequences
Seq C1 exon
GGAGAACAAGGACTGCCCGGTGCTCCTGGACCCGATGGACCTCCTGGACCGATG
Seq A exon
GTACAGACATAATATTCCTCTGAGAATGAGTTCATTACAGTCACAAATGACAATCCACACAATCACTCTCATCTCTCTCTGTTTCAG
Seq C2 exon
GGTCCTCCTGGACTGCCTGGACTGAAAGGAGATCTTGGTATCAAAGGTGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000012593:ENSDART00000139598:55
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(22.0=100)
A:
NA
C2:
PF0139113=Collagen=FE(22.0=100),PF0139113=Collagen=PU(25.4=89.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGAACAAGGACTGCCCGGT
R:
TCACCTTTGATACCAAGATCTCCT
Band lengths:
103-190
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]