RnoINT0040549 @ rn6
Intron Retention
Gene
ENSRNOG00000023317 | Colgalt1
Description
collagen beta(1-O)galactosyltransferase 1 [Source:RGD Symbol;Acc:1309002]
Coordinates
chr16:20047845-20048099:+
Coord C1 exon
chr16:20047845-20047921
Coord A exon
chr16:20047922-20047992
Coord C2 exon
chr16:20047993-20048099
Length
71 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGC
5' ss Score
6.32
3' ss Seq
CACTGAGGCTCTGGCTGCAGGTC
3' ss Score
4.59
Exon sequences
Seq C1 exon
TGAAGCATCCACCAGTGCAGCTCTCCCGATTCATCTCAGCACCCAAGAAAACTGCAGACAAGATGGGCTTTGACGAG
Seq A exon
GTGGGCTGGGGCCTCCTGGGTGGGTGGAAGCAGTGGTCTGACCTCCCCCCTCACTGAGGCTCTGGCTGCAG
Seq C2 exon
GTCTTCATGATCAACCTGAAGCGGAGGCTGGACCGGCGAGAGCGCATGCTGCGGGCACTGCATGAGCAGGAGATTGACTTCCAGCTGGTAGAGGCTGTGGACGGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023317:ENSRNOT00000024866:7
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=PU(1.1=7.7)
A:
NA
C2:
PF0175512=Glyco_transf_25=FE(18.8=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:
CATCCACCAGTGCAGCTCTC
R:
AGCCTCTACCAGCTGGAAGTC
Band lengths:
168-239
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]