RnoINT0040543 @ rn6
Intron Retention
Gene
ENSRNOG00000023317 | Colgalt1
Description
collagen beta(1-O)galactosyltransferase 1 [Source:RGD Symbol;Acc:1309002]
Coordinates
chr16:20050463-20052276:+
Coord C1 exon
chr16:20050463-20050669
Coord A exon
chr16:20050670-20050852
Coord C2 exon
chr16:20050853-20052276
Length
183 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGG
5' ss Score
6.17
3' ss Seq
GTCTCTCCTGTCTCCCATAGGTC
3' ss Score
12.96
Exon sequences
Seq C1 exon
CTACGTGGGCCGGAAGCGCATGCAGGTGGAGCACCCTGAAAAAGCTGTGCCCCGTGTAAGGAACCTGGTGGAGGCTGATTACTCCTACTGGACACTAGCCTATGTAATCTCCCTGCAAGGTGCTCAGAAGTTGCTTGCTGCCAAGCCACTGGCCAAAATGCTACCTGTCGATGAGTTTCTGCCTGTCATGTTTGACAAGCACCCAAT
Seq A exon
GTAAGGAAGATATTTGAGGGGCATTGGGTGGCAGTCTGGGGTCTTTGAGTCCTGGAAGATCAGGGCAGGGAACTGTTGGGTTCTGAAGCTAGGCATGGTAGGATTAATCCTAATGGACTCAAAGGAGTCTTCTTTCTGGATCATTGGTCTCCATCTCCCCTGTGTCTCTCCTGTCTCCCATAG
Seq C2 exon
GTCAGAATACAAGAGTCACTTCTCTCCCCGCAACCTGCGTGCCTTCTCCGTGGAGCCCCTCCTTATCTACCCTACACACTACACGGGGGATGATGGTTATGTGAGTGACACAGAGACCTCAGTTGTGTGGAATAATGAACAGGTTAAGACCGACTGGGACAGAGCCAAGTCCCAGAAGATGCGGGAACAGCAAGCACTGAGCCGTGAGGCCAAGAACTCAGATGTGCTCCAATCTCCACTGGACAGCACTGCCCGTGATGAGCTTTGAGGCAACTGGCAAAAAGCCAAAGACACTGCCACCCACCTAAACTTCATGTGCTTGCCTGGAACTGACTATAGGGCCACCTAGGCAGACAACAGAGGGCTCTACAAGCACAGAGGTCTCCATGTCTTCCTGTTTAGCAGCCACTTGCACACAGGCAGCATTTATGGAGTACTTACTGTATGCTGGAAACAGGGCTGGCCACCAAGAGATTGGGCAGGAGCAAGCACAGTGCGTTGGGTCCACCGTGAAGGAAGTTTCCTTGTTAGAGCAGGGAAAGAGGCATGACTCCCCCTTATCAGTGATTGATTTCATCATCAGGTTTTTTTGTTCAGCCTGAGTCAGGTGTTAGGGATACATACTCATTTTTAAAATCTGAGTGTTTATTGAGGGCTTACTGTGTGTTAGGCACCATTCTTAGCTCTGGGAATACTAAAACAAGAAAAAAGTCAATACACCAAGAAACTGCTATAAGCCAGGTCCTAGGAAACACTGATGAGCTGAGTGCCTACTGTGTGTCACTCAGTACATGCTGGGGATGGAGGTCCCAATGGTGCTTATCTTTGTAGTAGGCACGATGTGCTTACAGTGGAAACAGTATTATTGACCCCATGTGCTAGGCGACAGGCTGAGCACAGTGACAGAGTCTGAACAGAATGTAACAAGCATTTATTGAGCACCTAGTGTGTCAGGCCTCAGAATCCCAGTTGGGTTGAGAAATAGCCACCCTTCAACCTGTCTGCAGAGGACACTGTGCTTCCTGTGTCCAGATGGGAGGTTCTTATTCCCTTGGTTGACTGCTGGGTTTCAGGGTATTCATGACTTTGTAAGCTCCTCCCCCCCCACGGGGGGGGGGGCGTGTGTGTGCAGGTAGGGGCTATGGCTCCCTTGCCCACCCCTGGTTTCCAGAGCTTCTCCCTGCCTTTGTGTCTCAGGTGTCTCTTGGCTGCTCATGTGTTTGGGGCCTCGAGAGGCCCAGCTGCATTGGGGTGCTCCTCTTGGCCTGGGTTGTTTTTCCCAGCAGGCCAGGTGGCCGCTGTGCCTTCAAAGCCAAAGCAAATGTCAGCTGGTCAGCAGGTGCCACCTTCTGGGGATGACTGCTTGCCCACTCAGGTCTTGGTAACTTGCTTGTGTTTGTATTAAATCATCCTCATTGGTTTTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023317:ENSRNOT00000024866:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.404
Domain overlap (PFAM):
C1:
PF0175512=Glyco_transf_25=PD(32.3=85.7)
A:
NA
C2:
NO
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:
GGCCAAAATGCTACCTGTCGA
R:
CTTGCTGTTCCCGCATCTTCT
Band lengths:
251-434
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]