DreINT0050605 @ danRer10
Intron Retention
Gene
ENSDARG00000073974 | colgalt1
Description
collagen beta(1-O)galactosyltransferase 1 [Source:ZFIN;Acc:ZDB-GENE-070720-6]
Coordinates
chr3:52470427-52470763:+
Coord C1 exon
chr3:52470427-52470533
Coord A exon
chr3:52470534-52470630
Coord C2 exon
chr3:52470631-52470763
Length
97 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGT
5' ss Score
9.1
3' ss Seq
TTTGTTTTTTTTAAACCTAGAGC
3' ss Score
6.47
Exon sequences
Seq C1 exon
GTGTTTATAATCAACCTGAAGCGACGAGGTGACAGGCGTGAGCGCATGCTGAGGGCATTGACAGAGCAAGAGATTGAATGTAAGATTATCGCTGCTGTTGATGGCAA
Seq A exon
GTGAGTCTGCTTGTGTTATCTTCAAACAAACGAGACCTTCTTTATCAGGTCAAAACACTCACTCACAGCTTGTCTTTTTTGTTTTTTTTAAACCTAG
Seq C2 exon
AGCTATGAACGTCAGTGAGATCCATGCTTTAGGAATACACATGCTGCCTGGCTACAGTGACCCTTATCACGGCAGACCTCTCACTAAAGGAGAGCTGGGCTGCTTCCTGTCCCACTATAACATCTGGAAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000073974:ENSDART00000154410:8
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(18.8=100)
A:
NA
C2:
PF0175512=Glyco_transf_25=FE(23.7=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:
AATCAACCTGAAGCGACGAGG
R:
TCTGCCGTGATAAGGGTCACT
Band lengths:
175-272
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]