DreINT0007399 @ danRer10
Intron Retention
Gene
ENSDARG00000058270 | COLGALT1 (1 of 2)
Description
collagen beta(1-O)galactosyltransferase 1 [Source:HGNC Symbol;Acc:HGNC:26182]
Coordinates
chr1:57282934-57283214:-
Coord C1 exon
chr1:57283095-57283214
Coord A exon
chr1:57283011-57283094
Coord C2 exon
chr1:57282934-57283010
Length
84 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
TTCTGTGTGTGTGTTTCCAGTGC
3' ss Score
9.49
Exon sequences
Seq C1 exon
AGGTTCAGATGTACATCTGCAACAGAGAGACGTATGGGTATTTCCCGGTGCCGCTGCGCTCCCAGAACAGCCTGCAGGATGAGGCGGAGAGCTTTCTGCACTCTCAGCTGGAGGTTATGG
Seq A exon
GTGAGTTTAAGAAGTTTGGAGCTGCTCTGATCAAATCTGAGAGAAAAACTAAACATCCTGATCCTTCTGTGTGTGTGTTTCCAG
Seq C2 exon
TGCGCAATCCTCCAATAGAGCCGTCCGTGTATCTGTCACTAATGCCAAAACAGACGGATAAAATGGGCTTCGATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000058270:ENSDART00000081122:6
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:
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:
TGCAACAGAGAGACGTATGGG
R:
TCGAAGCCCATTTTATCCGTCTG
Band lengths:
176-260
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]