RnoINT0040555 @ rn6
Intron Retention
Gene
ENSRNOG00000028207 | Colgalt2
Description
collagen beta(1-O)galactosyltransferase 2 [Source:RGD Symbol;Acc:1304702]
Coordinates
chr13:69899162-69901170:+
Coord C1 exon
chr13:69899162-69899368
Coord A exon
chr13:69899369-69900893
Coord C2 exon
chr13:69900894-69901170
Length
1525 bp
Sequences
Splice sites
5' ss Seq
CGTGTAAGT
5' ss Score
8.58
3' ss Seq
ATTGCACCTCTCGTTTACAGGGC
3' ss Score
8.77
Exon sequences
Seq C1 exon
TTACATCGGTCGAAAAAGAATGCAAGTCAAAGAGCCAGAGAAGGCGGTGCCCAATGTTGTAAATCTCGTTGAAGCTGATTATTCCTACTGGACGCTGGGCTACGTCATCTCCCTGGAAGGAGCACAGAAGCTCGTTGGAGCTGATCCCTTTGGGAAGATGTTGCCAGTGGATGAGTTCCTGCCAATCATGTACAACAAGCATCCCGT
Seq A exon
GTAAGTCTCCTGCCACAGTCACCTGTCCCTTAGACACATACTGTTCCTAGATGAAGCCCCTGGGTAGAATTTGGTGCCTTTATAGTTGTGTGGCTTTCCTAAAGAACCCTTTTACAATCATAACCTGGAGAAGTCAAGTAGACCTTTGAACAGACAGAATGGATGAGAGAGGAGGTGACTGCCTTGTGTAATCCTCTTCACTACTCAGTGCATGGGACAAGGGTCTGCTCAGAATCTGTTTGTCTATGTTCTTCTGTCTTTGTAACCTCACACACCTGAAGCTAAAGGTCATTTCTCTTAAGCCACCCTAGATTTATCCTAGGGTCACTCTGCTCACCCCGTGTGCGTGTGGACCACTGGGGAGTAGTGTGCATATCCTCTCAGTACTCACACTCCGGGAGATAACATGGACCCATGAACGAATCACCATGATGTTTCATGACTCTAGTCACAGAGGTGGCAAGAAATTCAGGGGATGTGGAGATGGCGTCTGAGCCAGATAGCAAAGGAAGCAGGAATCCAGTGCTCAAATCCCAAAGGCCCAGTCGGCTGACCTGACACTTATCAAAGGGTCTAGTAAATGATGGTTGGTTACCTCTTATTCCCCACAGTAGGCTATGAGCCCTTGGAGGCAGGAAGAGCCACACATCTCCGGGTCTTTAGAGTATGTGTAATAGCTGCCAGCTATGTAATAGTAAACCAGTGTTTCCTAAACTCATGATTGGAACAGGAGGCCAGGTTCTAACCTTGCTTGACTCCTTCTCTCAGTTGCTAAGTGACCTCCAACTCTGACCTTTATTTTAGCTGTTGAGGCTCCCACGATACAGCCTGCTCGTTTTGTCACCGGTAAAGATGGGGCCCTGTGCCATCTTTTATGCCACATACTTTTCCTCTGTTTCCTGACAGAAACATAGTCAAGCCACTCTCTCCTGAAACAGAAAGGAACGTAGTACTTAGTTAGTACTTATCTCTCCCATGGATGAAGATACTGTATTGGTATCCTCCACAGAACTTTCAAGAAGCCCTTGGAGGAAAGTGAAGCTGTCCCTCTAGCTTTACAACTGCATAGAGCCAGGGCAGGAGGAAGAACTGGGTGTGATGGCGCCCAGTTAGCATGCCTCCAAACCTTCTCCATAGCTTTTACTCCGTTGCTGCTATCCAGGTCTCAGATGCCTTCGTTGCTTTATCAGTGCAAACAGGAACGGAATGCTGATTGGGAATTGATCAGGTTTATTTATCCCTGTGAGTCCAACGGAGTTGAATTTTCACCTTTCACTCACTAAACTGTTCTAGCCAACTACAGCAGGTCAGGCCTGGCCCTTTGGCTAGTTTGTACAGATCTTCAGAACACTTTAAAGAAACACTTTTCCTGTTTGTAGTCTAAGGTTCTCCACAACTGACTCAACTTTATAAAGCAAGGAATTAGCTTTTACAAAGGCAGCTTCAGAGATGACAAGTAGAGTTCTCTGCCCTCCCCGTTCCCTGAGACTTCTGCCCTCATGTGGATTGCACCTCTCGTTTACAG
Seq C2 exon
GGCAGAGTACAAGGAGTATTACGAATCCAGGGACTTGAAAGCCTTCTCTGCAGAACCTCTGCTCATCTACCCCACACACTACACGGGCCAGCCAGGCTATCTGAGCGACACAGAAACGTCAACCATCTGGGACAATGAGACAGTGGCCACTGACTGGGACAGGACACACTCCTGGAAGTCCCGGAAGCAAGGACCCATCCACAGCAACGCCAAGAACACGGAAGCACTACCACCGCCGACCTCTCTGGACACTGTGCCTTCAAGGGACGAACTCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000028207:ENSRNOT00000030109:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.435
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:
GGCTACGTCATCTCCCTGGAA
R:
GGTGGTAGTGCTTCCGTGTTC
Band lengths:
344-1869
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]