DreINT0050603 @ danRer10
Intron Retention
Gene
ENSDARG00000073974 | colgalt1
Description
collagen beta(1-O)galactosyltransferase 1 [Source:ZFIN;Acc:ZDB-GENE-070720-6]
Coordinates
chr3:52464028-52464431:+
Coord C1 exon
chr3:52464028-52464147
Coord A exon
chr3:52464148-52464354
Coord C2 exon
chr3:52464355-52464431
Length
207 bp
Sequences
Splice sites
5' ss Seq
ACGGTATGT
5' ss Score
9.94
3' ss Seq
GCTCTTCTTTTATTTCACAGTAC
3' ss Score
8.3
Exon sequences
Seq C1 exon
AAGTCCAAATGTTTATTTGCAACAGAGAAATATATGGGCACCTCCCAGTTCCTCTTCGTGCCCACAGCACTCTACAGGATGAGGCAGACAGCTTCATTCACACTATGCTGGAGGTCAACG
Seq A exon
GTATGTTTCAGCTTTACAAAGAAGGAAATGTAATAGTAGTCTGTGATGCATTCAAACCTTAATCTCGACTGTTACTAAATAAAGTCTGCTTTAATACTGTTGGTGCTAATAACAAGGCTCTCTGAGTTGTACATGCATTGCTTTTAACATTACATGCATTCTGTACCATCTGCTTCATTAAATGTAAGCTCTTCTTTTATTTCACAG
Seq C2 exon
TACGAAATCCTCCAGTTGAGCCTTCAAGATACTTACCCAAACCTGTCAGAAAACCTGATAAAATGGGCTTTGATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000073974:ENSDART00000154410:6
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=0.154
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0175512=Glyco_transf_25=PU(1.1=7.7)
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:
TGCAACAGAGAAATATATGGGCAC
R:
CTCATCAAAGCCCATTTTATCAGGT
Band lengths:
180-387
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]