DreINT0050053 @ danRer10
Intron Retention
Gene
ENSDARG00000098294 | col5a3a
Description
collagen, type V, alpha 3a [Source:ZFIN;Acc:ZDB-GENE-030131-968]
Coordinates
chr3:53640515-53640840:+
Coord C1 exon
chr3:53640515-53640604
Coord A exon
chr3:53640605-53640786
Coord C2 exon
chr3:53640787-53640840
Length
182 bp
Sequences
Splice sites
5' ss Seq
CTGGTAACA
5' ss Score
4.6
3' ss Seq
TTATTTTTATGCTTTAATAGGGC
3' ss Score
8.53
Exon sequences
Seq C1 exon
GGAGATCCAGGCCCCGCAGGGCAGCCCGGGAAGAGTGGTCCTGCTGGGCGGCGTGGATTCAGAGGAGAAAGAGGCTTACCTGGCATTCTG
Seq A exon
GTAACACACCTCAAAGCATCTGAGAGAATAGCTTCTTATAATCTCCGCTGTGATGGATGCTGCCTTTACATAACCTTCAACCAATATGAAAAGCTGACTTTGTGCAAAAAAGGCAGATTGTGGTTGTATGATTTTTTAGCATGGATCCTCATATTTTTTTTCTTATTTTTATGCTTTAATAG
Seq C2 exon
GGCTCTTCTGGTTTGAAGGGTGGAGAGGGCCCACTTGGTGTTGCAGGGCCAATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000098294:ENSDART00000170461:40
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:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGATCCAGGCCCCGCAG
R:
AATTGGCCCTGCAACACCAAG
Band lengths:
143-325
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]