DreINT0050615 @ danRer10
Intron Retention
Gene
ENSDARG00000014670 | colgalt2
Description
collagen beta(1-O)galactosyltransferase 2 [Source:ZFIN;Acc:ZDB-GENE-070222-1]
Coordinates
chr8:19338549-19338861:-
Coord C1 exon
chr8:19338788-19338861
Coord A exon
chr8:19338656-19338787
Coord C2 exon
chr8:19338549-19338655
Length
132 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
GTTCTTTTATTTCACCTCAGATC
3' ss Score
8.55
Exon sequences
Seq C1 exon
TCGATCATAACATAAAACCCTCCGAGTTCCTCTTCACTCCAAGCAAACCTCAGGACAAGATGAGCTTTGATGAG
Seq A exon
GTGAGAGAGCAGAATCTCTGGAATGTCTTGCATGACTGGAGACTCATGATAGCAGAAACTCAAAGCTACTTCAAAGTGACATTTCGTCTCGATTTGTTCCTCCAATGCTCTTGTTCTTTTATTTCACCTCAG
Seq C2 exon
ATCTTCTTGATTAATCTGAAGCGGAGGTTCGACCGAAGGGAACGGATGTTGAACACTATGGCAGTTCTGGGTCTTGAGGCGACGCTGGTTGATGCCGTCGATGGGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000014670:ENSDART00000014183:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0175512=Glyco_transf_25=PU(1.1=8.0)
A:
NA
C2:
PF0175512=Glyco_transf_25=FE(18.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGATCATAACATAAAACCCTCCGAGT
R:
TTCCCATCGACGGCATCAAC
Band lengths:
180-312
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]