RnoINT0040553 @ rn6
Intron Retention
Gene
ENSRNOG00000028207 | Colgalt2
Description
collagen beta(1-O)galactosyltransferase 2 [Source:RGD Symbol;Acc:1304702]
Coordinates
chr13:69894741-69896019:+
Coord C1 exon
chr13:69894741-69894873
Coord A exon
chr13:69894874-69895891
Coord C2 exon
chr13:69895892-69896019
Length
1018 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAT
5' ss Score
8.39
3' ss Seq
CCCGCTGATGGCCTTTACAGGTT
3' ss Score
8.45
Exon sequences
Seq C1 exon
GGCACTCAACACAAGCCAGCTGAAGGCCTGGAACATTGAAATGCTCCCAGGTTACCGGGACCCCTACTCCTCCAGGCCCTTAACCAGGGGTGAAATCGGTTGCTTCCTTAGTCACTTCTCTGTCTGGAAAGAG
Seq A exon
GTAAATATTCTTTAGGGGAACACTCTGGTCATGAGGGGAAGGGAGACTGGAACTTCCCAGGTGAATTAGGATCAGATGCAGGAGAGCCCATGACTGTCCCGGAAGTAAGCTTGAAAATTGCTCTTGCTTTGTGCATTCCATCAGCCCAAGGCCAGCAGCAAAGGCACTAGGATGGTGGCCTTAGTGCCACATGGGACAGTGGTGGGTGAAAGTTTTCACATTGTAGGAACTTTGTTTTCCTGAGTTCCCTTTCCCTGTAAAGAGGAATGTTTTGTGTATGTCTGTCTTGTTATTACCTATCAAACGAATTCATGCAGGAATCACACAGAAGGCACGTGAGACAGGGTTAGGCAGGATGGATTCTTCTCACAGCAGGCAGAAGGTTTTAACTGTTTTCAGGTAAGAAGAGGCAAAGCTGTCACTGGACCCTGTGTCTTATACATCAAGATACTGTTGGAGCTGGCACTGAATCTCATGAATAAGGGTCACTTCCCACAAGAAGGAGATGAACACAAAGGAAACAATAAACCTCTTGGTGCCTTCTCTCCTTTAATGATCCAGTTTCGACTTGTCTCTTCTTTTTCTATGCTTTAAGTAAAATGTTATAGAAAAATATAGAAGTGCATAGATCAGAAGATAGTCAATGAAATGGCACACATAGAACAAGACACCCATGTTGATCAATTCTGAGATTAAGAAAAAGGTGGCAGGCACCTGAGGTGCCCCTTCTGTACAGCCTTGGAGTCACCATCTCCCCAGGGTAAACTTCATCCTGGCATGTGACAGCATGGCATGACCTGTCTTTGAACAACACAATGCATATGACCTCTCGGTGTTGTGTCTGAGAGATATTAACCTGCAAGGTTGCTACCATATAGTCTCGTTGCTATAAACATGGTGCAATCATCTATACGACCTGCTGTCAATGGATATTTTCTTGGATCTAAGTTATGGGTTTCTAAAATAAAAATGGGTATCGACGTTCTCACACAGTGTTCCCCGCTGATGGCCTTTACAG
Seq C2 exon
GTTATTGACCGAGAGCTGGAGAAGACTCTCGTCATTGAGGACGATGTGCGTTTTGAGCATCAGTTTAAGAGGAAGCTAATGAAGCTGATGGATGACATTGACAAGGCTCGGCTGGACTGGGAACTGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000028207:ENSRNOT00000030109:10
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:
CACTCAACACAAGCCAGCTGA
R:
ATCAGTTCCCAGTCCAGCCG
Band lengths:
259-1277
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]