RnoINT0040544 @ rn6
Intron Retention
Gene
ENSRNOG00000023317 | Colgalt1
Description
collagen beta(1-O)galactosyltransferase 1 [Source:RGD Symbol;Acc:1309002]
Coordinates
chr16:20041044-20041901:+
Coord C1 exon
chr16:20041044-20041154
Coord A exon
chr16:20041155-20041783
Coord C2 exon
chr16:20041784-20041901
Length
629 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
CCACAGTTGTTCTTTTGCAGCTC
3' ss Score
7.5
Exon sequences
Seq C1 exon
GGTGGCCACAGATCATAATACTGACAACACTTCAGCCATACTTCGAGAGTGGCTGGTGGCAGTGAAGGGTTTATACCACTCTGTGGAGTGGCGGCCGGCAGAGGAACCCAG
Seq A exon
GTGAGCCTCAAGCCTGGACTGGAGAACCCAAGCTAGTGTGCCCCGCCCGCTCCCACCATCGACTTCACCATCAGGTCCGGATCCTCCCAGCAGACCTCTGTCCCCATTGTTCTTCACTCCATTGTCTAACATTGGACACAGCTGCCACACCTTTGTGGCTGAATTCCTTTGTGTCTGCTGGCCACCTATGCTGTATTCCTGGCCTAGGGTCTTGCCTGCATCCACTCTCCTGCTTAACTTCATGATAAGCCTGCCTCATTGTGTAGTATAGTGTAGTAGAAGGAGCGGTCTTCCCTGCACTACCAGATCAGACTCAGAGCCTGTATCCTGTAACGTGTGTGGGTGCTCATGCTCCTGTGCTCAGAAGCACCGGGGTAGCCCCAGGCTCTCCCCAGCCATGCGGGCTCTCTGTCCCCAGCTATGCAGAATTTGGCCCTTAGCTTGCCAGTAGCTTTTGTGCCCCTGGACCCTTGCACCCTGTGCCCCGAGTCCCCATGTTCTACAAGGAGGCCTTCAGATCCACTTGCCTGCCTCCTCCTCTGTGAAGCCCTCTATGATCCCCCTGCAGCTATGCTGTCTGGGCCCCCACGGTGCCCCATGATGTCCACACCACAGTTGTTCTTTTGCAG
Seq C2 exon
CTCCTACCCAGATGAAGAGGGCCCCAAACACTGGTCTGATTCCCGCTATGAACATGTCATGAAACTGCGCCAAGCAGCCTTGAAGTCAGCTAGGGACATGTGGGCTGACTACATTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023317:ENSRNOT00000024866:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.132 A=NA C2=0.250
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:
GGTGGCCACAGATCATAATACTGA
R:
GTAGTCAGCCCACATGTCCCT
Band lengths:
223-852
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]