DreINT0050597 @ danRer10
Intron Retention
Gene
ENSDARG00000073974 | colgalt1
Description
collagen beta(1-O)galactosyltransferase 1 [Source:ZFIN;Acc:ZDB-GENE-070720-6]
Coordinates
chr3:52472770-52473192:+
Coord C1 exon
chr3:52472770-52472897
Coord A exon
chr3:52472898-52472985
Coord C2 exon
chr3:52472986-52473192
Length
88 bp
Sequences
Splice sites
5' ss Seq
CATGTAAGT
5' ss Score
8.31
3' ss Seq
TCATCTCCAACTCTTTGCAGTTA
3' ss Score
7.07
Exon sequences
Seq C1 exon
ATTGTAGATCGAGGATTGAAGACCTCGCTAATTCTTGAAGATGACTTAAGATTTGAGATTTTCTTCAAGCGTCGCCTGCAGAATCTGTTGCTTGAGCTCCAAAGTCAGAGTCTGGACTGGGACCTCAT
Seq A exon
GTAAGTCTAAAGTCTCTGTCACATTTTTGGTTTTTGCATCGATTAAAGATCTGTTCATGCTGGCTATTTCATCTCCAACTCTTTGCAG
Seq C2 exon
TTATATTGGGAGGAAGAGGATGCAAGTGGACCGGCCTGAAAAAGCAGTACCAAATATTCGCAACCTAGTAGAGGCAGACTATTCCTACTGGACCTTAGGTTACATGATGTCCTTACAAGGAGCCAGAAAGCTTCTCAAAGCCCAACCACTTAGTAAAATGTTGCCTGTCGATGAATTCCTTCCTGTTATGTTCAATAAGCATCCTGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000073974:ENSDART00000154410:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0175512=Glyco_transf_25=FE(22.6=100)
A:
NA
C2:
PF0175512=Glyco_transf_25=PD(32.3=85.7)
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:
CAGAGTCTGGACTGGGACCTC
R:
AAGTGGTTGGGCTTTGAGAAG
Band lengths:
174-262
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]