RnoINT0040548 @ rn6
Intron Retention
Gene
ENSRNOG00000023317 | Colgalt1
Description
collagen beta(1-O)galactosyltransferase 1 [Source:RGD Symbol;Acc:1309002]
Coordinates
chr16:20046965-20047921:+
Coord C1 exon
chr16:20046965-20047084
Coord A exon
chr16:20047085-20047844
Coord C2 exon
chr16:20047845-20047921
Length
760 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
CCCTGCTTTCTTACCCTCAGTGA
3' ss Score
9.73
Exon sequences
Seq C1 exon
AGGTGCAAATGTACGTGTGCAATAAGGAGGTGTACGGCTTCTTGCCCGTGCCGCTACGCTCGCACAGCAGCCTGCAGGACGAGGCAGAGAGCTTCATGCACGTGCAGCTGGAGGTCATGG
Seq A exon
GTGAGTCTCCTTGGGCACTGGCCTCACCATTTTGCATGTATCTCAAGAACTAAGTGGGTACTGTTGGGTGGCAGTCCCTGTGTATGGCGTATGACCGAGAGACACCATAGTCCCTGCCACTGGGAATATGCAGAAGTCACAGGGTTAGATGTCATCCCGGCAGATGCTGACATGCTCTTGTACCCTCTGGTATCCTCACACCGCTGAGAAAACTGAACCATGGGCTGTCATCTGCGACGTATGCTATGAACTTGGCAGTCCAGGGGCTGAGGCCAAGGGATGGCAAGTTGCAGTCATCTTGGGCTACAGCTTGAGAACCCAGCCAAAGAGACTGATCCTGTTTTGCAGCAAAGTTATTCTCTTCCTGGGTTGCTACACCTATGTAGCTTTTAGGAGGTCACATTTGGAGGGACAGCAGCCAGTGTGAGCCTCACTGCATTTATGTAAACTTCTGAGAATGCAGCTGAAGAAAGCAGGTCTGTATCACTCCCTCTGTAACTATGGAGTGACTGCTGTTTACCAGGCTCTGTGTTGGGCTCTGGGCATGCAATGTGAGTAGACAAACCCCCATCCTCTGGACACTTGGGCCAGAAGAGAGGCCTGGAGGCTCCCATTGCCTGGGCTGTCACAACTGAGATCCGAGATTCTCTGGGCAGGAATGTGGCAGGAGTGAAGGACCTGGGGCATAGCCTAGTCATACTGGGAGCTGAGAGAAGGTGGGGTCCTGGGACCCCAGTGACCCCTGCTTTCTTACCCTCAG
Seq C2 exon
TGAAGCATCCACCAGTGCAGCTCTCCCGATTCATCTCAGCACCCAAGAAAACTGCAGACAAGATGGGCTTTGACGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023317:ENSRNOT00000024866:6
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:
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:
AGGTGCAAATGTACGTGTGCA
R:
AAGCCCATCTTGTCTGCAGTT
Band lengths:
190-950
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]