RnoINT0040551 @ rn6
Intron Retention
Gene
ENSRNOG00000023317 | Colgalt1
Description
collagen beta(1-O)galactosyltransferase 1 [Source:RGD Symbol;Acc:1309002]
Coordinates
chr16:20049185-20050205:+
Coord C1 exon
chr16:20049185-20049317
Coord A exon
chr16:20049318-20050077
Coord C2 exon
chr16:20050078-20050205
Length
760 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGT
5' ss Score
7.07
3' ss Seq
GGAGTGGCACCTTCCCTCAGGTG
3' ss Score
5.93
Exon sequences
Seq C1 exon
AGCCATGAACACCAGCCAGGTGGAGGCTATGGGCATCCAGATGCTGCCTGGCTACCGGGACCCCTACCATGGGCGGCCACTCACCAAGGGAGAGCTGGGCTGCTTTCTCAGCCACTACAACATCTGGAAAGAG
Seq A exon
GTGGGTGTCTGGGATGAGGGAGGCCTGACCCACAGTCCCTGGTCTCCTCAGACTAGGTCAGTTACAGAGTCCCAGGGAGGAACTGTGGTCCCCATGTCACCAGTGGCAGAATCTGTGGCTACATTTTGGTGTCTGTTGCATGAACTGTTGTCACAGTGGCCTGATACACGTGAAGGGGCAGTCACAGTCTTGGCATTGCCAAGATGCAGAAAGTGGACCTGGGGAGTGAGGAGACTGCAGGCAAAGTCTGGGGCTGTGACTCCCAAGAGAGACCTGCTTGCCCCACAACTTGACTCTGGACAACAGCTGATAATGTGCCATGATGTCACACAAGAACCAGATTTGGAACCTGCAAGCAAGGCTGGATGGGTGGAGTGTTGGCTCCAGATGATGAGGGGAAGGAAGTAGGATATCTAAGTGCCCAAGGTGATAGGTGCTCATGTGAGCCACTCTCCTTTCCTAAACTTCCTCAAGGGCATTCTGTTAGCTCTCTTGGTTGATAGTGAAGCCACTTAGACTGGGGCACTGTACCAAGGAGGAAGGGTAAGAGGAGCCTGCCTGTTGCCAAGAGGAAGGCTTCTGAGTATCACAAGCTAAACACAGGCAGAGGTCCCAGACAGGAAAAGCCCTAACAGATAGGCAGGAGAAGAGTGACAGGATGGGCACATAGCTGGATGTGGAAGGTTGGGATGCATACTTCCTTCCTAGCAAGCATCTTTGGGGCTGGGTCTCCTTAACTTGGAGTGGCACCTTCCCTCAG
Seq C2 exon
GTGGTTGACCGGGGACTACAGAAATCACTAGTCTTTGAGGATGATCTACGTTTTGAGATCTTCTTCAAGAGACGTCTGATGAACCTCATGCAGGATGTGGAGCGTGAGGGGCTGGATTGGGACCTCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023317:ENSRNOT00000024866:9
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(23.7=100)
A:
NA
C2:
PF0175512=Glyco_transf_25=FE(22.6=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:
GCCATGAACACCAGCCAGG
R:
ATGAGGTCCCAATCCAGCCC
Band lengths:
260-1020
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]