DreINT0050599 @ danRer10
Intron Retention
Gene
ENSDARG00000073974 | colgalt1
Description
collagen beta(1-O)galactosyltransferase 1 [Source:ZFIN;Acc:ZDB-GENE-070720-6]
Coordinates
chr3:52454838-52455152:+
Coord C1 exon
chr3:52454838-52454948
Coord A exon
chr3:52454949-52455034
Coord C2 exon
chr3:52455035-52455152
Length
86 bp
Sequences
Splice sites
5' ss Seq
AAGGTTTGC
5' ss Score
5.42
3' ss Seq
CTTTTATTTTCCCTACTCAGTCA
3' ss Score
7.72
Exon sequences
Seq C1 exon
GGTAGCGACTGACCACAATGTAGACAACACCACATACCTGCTGCGAGACTGGCTCATCAACGTACAGAAACTCTACCATTATGTGGAGTGGAGGCCGAAGGAGCAACCAAG
Seq A exon
GTTTGCCTTGTTCCGTCACTTGTGGTTTCATAGAGCCGGTAAGTTGCATTTTCTTGAATCTTTTTACTTTTATTTTCCCTACTCAG
Seq C2 exon
TCAGTATAATGATGAGGAAGGACCAAAGGATTGGACAAATGAGCGTTATGCTTACGTCATGAAACTTCGACAGGCAGCGCTGGAGTCTGCACGAGAAATGTGGGCCGACTATCTTATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000073974:ENSDART00000154410:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.053 A=NA C2=0.200
Domain overlap (PFAM):
C1:
PF137041=Glyco_tranf_2_4=FE(30.6=100)
A:
NA
C2:
PF137041=Glyco_tranf_2_4=FE(32.2=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:
CACATACCTGCTGCGAGACTG
R:
ATTTCTCGTGCAGACTCCAGC
Band lengths:
180-266
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]