GgaINT0033775 @ galGal3
Intron Retention
Gene
ENSGALG00000005550 | ST6GAL1
Description
NA
Coordinates
chr9:6318438-6320119:+
Coord C1 exon
chr9:6318438-6318566
Coord A exon
chr9:6318567-6319443
Coord C2 exon
chr9:6319444-6320119
Length
877 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
GAGATGCTCCTCTCCCCCAGGCC
3' ss Score
8.53
Exon sequences
Seq C1 exon
GTGTTTCTTGAACTCTTCAGCGCCTCACGCGGCTGTTGTGTTTGGGGATATCCTGCCTTAAATCCTGGACAAAAATCTGCCAACAGCCAAAAATGACCTGAGTGGGAGAGCCACTGCTTTGTCCAACAG
Seq A exon
GTAGGACGTCGGTCGTTGGTGGCTTCTGGTACAGGCATGGTTTGCTGTCAGCAAGCAGTCTGCACAGGGAGCTGCTGCCAGTGCCATGCTAGGGCAGATAGTGATCTCTGAGGTGCACTGGGAGATGGTTGGTGTAAAACTGTTTTATTGGGGAATGCGGCGTTGTAGAAAAGACATGGAGACAAAGCCATCCAAAAGCCATCTGCTGTTGGAGCGCTCCCTTTTATAGCACGGCTGGCGGGAGCTGGAGGTGACTGCTCACATAAGGGGATGGGCAGTGCTGTACAACAGGATCTGGCTTTACTACCTGTAAGGATAACGTACCTTGAATAACATTTATCAAAGAGCATTTGTGAATGCAGCCGTGCTGTGGCTTAATTGGCTCCCAGCAGCTGGTTTCCTTCCCAGGAGCACGCCCAGCCCACTGAGGGTTTGCAGAAGTTTCCTGTGTAGTTGCTAGATGTCAGTTGATGAAACTCCTGCTGCTTGTGAACTCAGCTTTTTCTCTGCACAGTTATGTGCCTCGTTATGTGCTTCGTTAGTGTTCAGGCTTGCAATCAAGTGACAGCTCAGTTCTGGGAATGCTGCTGGTGGGGTTTGCGTGTTGGCTCACTGGGATGGGAGGTGAAGGAAAGCAAAATGGAGACCTACGCTCCTGCTGGTGTGCTTCTCGCTGTGTTAAACTTGTTAAACACTTCAAGTCTATTCGTTTGACATTTGAGGTGGTGGACTTCTGAAATCTTTAAATGGGCTGAGGTGTTAAAATCGCCCCTGCGTTCTCCCTGTCCCCACCCATTGCCTCACACCGCTGCCTGTGATTTTTGTATGTCTGTGTGGATGTGCACACCCCCTTGACTGAGATGCTCCTCTCCCCCAG
Seq C2 exon
GCCCAGCTTCCTGCCCCGTGCTCACTGTCCCGTTTGGATGCGACGTACACTATGGTTCACATCAATGTGCTGAAAAAATTCATGTGTGTTCTTGTGGTGATACTGATAGCTCTGACGGTTTGCCTGTGGAAAGAGACAAGAGGAAGCTACTATGTTCCTTTGAAGAACGATGGCACACAGGTTCACAGGGCTCTGGACAAATGGAACCTACTTAAATCGCAGGGCCTCCTCCATGAAGCTGGTGGTGAAATGGGTCAGATGCCTAAAGCATTGCCCAACAACCAAAACAAGGTAAAAGGCATCACCTCTGGAGCAGTAGAGAAGTCCAGGAAAGCAGCAGAGCACGTGAAGGTATGGGATAAGGACAGCTCGTCCAGAAACCTCATACCCAGGCTGCAGAAGGTCAGGAAGAACTACCTGTCCATGAACAAGTACAATGTGACTTACAATGGGAAGATGAATGCTGCTAAACTCAGCCCAGAGCAGCTGCTGTGCCGGCTGCGGGACAGGGTGAACGTGACCATGATACGGGGATCGGACGGTCCATTTAATTCCTCAGAATGGCAGCACTACCTGCCAGACAAAAGCCTCAATGAGACGGTGGGCCGCCTGGGTCGCTGTGCTGTTGTGTCCTCAGCAGGCTCTCTGAAATCATCTCACTTGGGACCAGAGATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005550:ENSGALT00000008903:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.110
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0077713=Glyco_transf_29=PU(27.3=34.4)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGCTGTTGTGTTTGGGGATA
R:
ACCCATTTCACCACCAGCTTC
Band lengths:
355-1232
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]