DreINT0049948 @ danRer10
Intron Retention
Gene
ENSDARG00000012593 | col5a1
Description
procollagen, type V, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-041105-6]
Coordinates
chr21:6769498-6769692:+
Coord C1 exon
chr21:6769498-6769551
Coord A exon
chr21:6769552-6769638
Coord C2 exon
chr21:6769639-6769692
Length
87 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
TATTTGTTTTATTCTTTTAGGGA
3' ss Score
9.73
Exon sequences
Seq C1 exon
GGTTTGGATGGTTCTCCTGGTGATAAGGGTGATGATGGAGAGCCTGGTCAGCCA
Seq A exon
GTGAGTGTGCTTCTAACTCAACCATTTGACATGTCTGAAGTGTGCATTTATAAGCAATGCTATTTTTTATTTGTTTTATTCTTTTAG
Seq C2 exon
GGATCCCCTGGACCCACTGGTGAAACTGGTCCTCCTGGCCCTCCAGGAAAGAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000012593:ENSDART00000139598:51
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(23.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(9.5=38.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTTTGGATGGTTCTCCTGGT
R:
TCTCTTTCCTGGAGGGCCA
Band lengths:
108-195
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]