DreINT0049906 @ danRer10
Intron Retention
Gene
ENSDARG00000012593 | col5a1
Description
procollagen, type V, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-041105-6]
Coordinates
chr21:6713010-6713311:+
Coord C1 exon
chr21:6713010-6713102
Coord A exon
chr21:6713103-6713254
Coord C2 exon
chr21:6713255-6713311
Length
152 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAAA
5' ss Score
4.51
3' ss Seq
TCTGTTTTATTTTTGCATAGCTG
3' ss Score
7.3
Exon sequences
Seq C1 exon
TTCCGCATGAGCACAGGAGGAGACGGAGGACAGAAAGGTCCTGCTGTTTCTGCTCAAGAGGCTCAGATGCAAGCTATCATGCAGCAGGCCAGG
Seq A exon
GTAAAACACACTCACACTCACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACAAACATACTTATAAGCATCTGAATGCAAACTAATAGCTCTGTTTTATTTTTGCATAG
Seq C2 exon
CTGGCCATGAGGGGACCAACTGGACCGATGGGTTTGACAGGCCGTCCTGGTCCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000012593:ENSDART00000139598:12
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:
PF0139113=Collagen=PU(26.6=85.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCATGAGCACAGGAGGAGAC
R:
CAGAGGACCAGGACGGCC
Band lengths:
146-298
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]