DreINT0049956 @ danRer10
Intron Retention
Gene
ENSDARG00000012593 | col5a1
Description
procollagen, type V, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-041105-6]
Coordinates
chr21:6782887-6783074:+
Coord C1 exon
chr21:6782887-6782922
Coord A exon
chr21:6782923-6783020
Coord C2 exon
chr21:6783021-6783074
Length
98 bp
Sequences
Splice sites
5' ss Seq
AGTGTAAGT
5' ss Score
8.46
3' ss Seq
ATCTGCTTCTGTCTCTATAGGGT
3' ss Score
10.81
Exon sequences
Seq C1 exon
GGTCCTCCTGGTCCTAAAGGAGCTAAAGGATCCAGT
Seq A exon
GTAAGTTATTCATGTCCTTGTTAATCTAATTATCATTTTAATTAGCTGTGATTTGTTTAACTTGACGATTAAAGCTGCATCTGCTTCTGTCTCTATAG
Seq C2 exon
GGTCAGACTGGCCCGAAGGGAGAATCTGGAATACCGGGACCTCCAGGACCTCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000012593:ENSDART00000139598:59
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(19.4=100)
A:
NA
C2:
PF0139113=Collagen=FE(29.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCCTCCTGGTCCTAAAGGA
R:
GAGGTCCTGGAGGTCCCG
Band lengths:
88-186
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]