RnoINT0000090 @ rn6
Intron Retention
Gene
ENSRNOG00000005935 | A3galt2
Description
alpha 1,3-galactosyltransferase 2 [Source:RGD Symbol;Acc:727913]
Coordinates
chr5:146940511-146941025:+
Coord C1 exon
chr5:146940511-146940600
Coord A exon
chr5:146940601-146940887
Coord C2 exon
chr5:146940888-146941025
Length
287 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGC
5' ss Score
8.69
3' ss Seq
TTTCTTCCTGCTCATGGCAGGGC
3' ss Score
8.37
Exon sequences
Seq C1 exon
GCTCTTTGAAGTGTTCATCCCCATGGGCATCTGCCCTATGGCCATCATGCCTCTGCTAAAGGACAATTTCACCGGAGTGCTGCGTCACTG
Seq A exon
GTAAGCAGCCACTATTCTCCCGCTCAGGATGCCCACAAACTATATAGGTCTGCCCCAGACCCCTGCTCTCTGCTCTCCCACACAAAGGCATTCTGGTTTGAGGGAATCCAATGGGGGCCCATCGGGTCACACGCCAACCAGGTTATCAGGTTGGGTCTAAGATAGGGATGCTTGGGGACAGGTCTAATATGCCTGAGGGTCCCTAGGGTCTAGTGATGGGGAGATCGCAATAATCAGGTGCCAGGCAGCTAAGTGAATACAACTGTGTTTCTTCCTGCTCATGGCAG
Seq C2 exon
GGCCCGGCCTGAAGTCCTGACCTGTACCTCTTGGGGAGCCCCAATTATCTGGGATGAGACCTTCGACCCACACGTAGCTGAGCGAGAGGCGAGACGGCAGAACCTTACCATTGGACTGACTGTCTTTGCGGTAGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005935:ENSRNOT00000007851:3
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:
PF034148=Glyco_transf_6=PU(4.8=45.2)
A:
NA
C2:
PF034148=Glyco_transf_6=FE(15.9=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:
TGAAGTGTTCATCCCCATGGG
R:
GCCTACCGCAAAGACAGTCAG
Band lengths:
220-507
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]