DreINT0156608 @ danRer10
Intron Retention
Gene
ENSDARG00000100804 | st6galnac4
Description
ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 4 [Source:ZFIN;Acc:ZDB-GENE-060322-6]
Coordinates
chr21:3691240-3692901:-
Coord C1 exon
chr21:3692492-3692901
Coord A exon
chr21:3691348-3692491
Coord C2 exon
chr21:3691240-3691347
Length
1144 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATT
5' ss Score
8.55
3' ss Seq
ATATATGTTCTGTCTGTCAGGAT
3' ss Score
8.74
Exon sequences
Seq C1 exon
CTGCTGGACTTCCACTGTGGTCGCTGTGCCGTGGTGTCGAGTTCGGGGCAGATGTTGGGCGGTGGACGAGGGCCAGAGATCGACCAGCAGGACTGCGTGATCCGGATGAACGTGGCTCCGACCGCCGGGTACGAGGCTGACGTGGGGAACAGGACGAGTCTGCGGGTCGTCTCGCACACCAGCGTCCCGCTCCTGGTGCGCCAGCAGGGCTATTTCTTCAGACGAGAGGCGGACACTAAATATGTGATCTGGGGCCCTGAGAAAAACATGCGGCAGGATGGAAAGGGCAAAACCTTTAATGCACTGGTGACGCTGGCCAAGAAATATCCACATTCACACGTACACACCATCACCAGAGAGAAAGTGCAGTACTGCGACGGCGTGTTTCAAAACGAGACTGGCAAAAACAG
Seq A exon
GTAATTCCTCCTCGGTTTAATCCAGCAAGCATGTAATTGTTAACCTCTTAAGACCCGAGGTGTTTTTTTATATACATGTTTTATTTCTCTTTGCTATTTGGGCTTATTGGAACCTAATCAGAATAAAAATCTAAGTATCACCTTTTGATATGATGTGCATTTAGAGAAAAATTATGTGAAGTTTATTCATGAACTAATTTCGAGAGGATCACGTGCTTATGATTGACACGGCTGGCCCCGAGTCAAGCTATTGTACGGACCACCAATCAGACTTTTCCTAACCAAGTATAAATAACCAAACACCTTACCTTAAGTCATCTTCGTCTTGAAGAATCCCCCCTTCCACCCCTTCGCCTCCTCTTTTGTCTACAGGGCAGCACGGCGCTCCAGTGGCTAGCACTGCGGCCTCACAGCAAAATGCCTCCGGTACGGGCATCTACCCAAACGGTCAGCATTTTCATGTGGAGTTCATGTTCTCTCCGTGCTTGCGTGGGTTTTCCCCAGGTCCTCCGGTTTCCTCCCACACTCCCAAAAACATGACACTTAAGTAAATTGACTAAACCAAATTAGCACCAAATTCGATTCAATTCTGTCAGCAACGCATCACCTTAGCAACCCTCTCGCAGCAGGAGGGGAGGGGGTTCTCGAGATCTACCCGAGCTCAAACTCCCCTCTCACCCTGCAACGGGAGGGAGCCTCGGGCTCGAGGCTCTCATGAGCTCGGGACTCTCTCCCGGGACAGCATGTCAAACTAGCTTATTACCAATCATCAGCTAAGTGTGAACTCTTGAAGTCCATATATGTAGACTCGTGGTCCCAATTTACATAAAACTATTTTTTTTTTGATCAAGGGATTTTTACCCTTAGTGTTTGTTCTGCACAGTTCATATTACTGTAAAACACATTCTATTGGACTGTCCTGCTTTTAATGACTGCAGAGGGCTTTTTTTAGGAAATGAACTCACTCAAAGAGACTTTGAGTGTGTCACCAGCACAAATTGTGGAAGTTTTATCATATATGAACGTTAAAAATCTGATCTAATTTATGGATTCTTTTGTTTGTGTTTTTAAATTGTATATAGCTGTTGTTGCTGCTGACATGGAATTAAATAAATACTATATAAATATATGTTCTGTCTGTCAG
Seq C2 exon
GATGAAATCAGGAGCGTTTCTGAGTACAGGATTTTTTACCATGATTTTGGCTCTGGAGGTGTGTGACAGTATTCTGGTTTATGGAATGATTGATGGCTCCTATTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000100804:ENSDART00000166652:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.007 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0077713=Glyco_transf_29=PU(58.7=98.5)
A:
NA
C2:
PF0077713=Glyco_transf_29=FE(15.7=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:
GACTGCGTGATCCGGATGAAC
R:
TCCTGTACTCAGAAACGCTCCT
Band lengths:
351-1495
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]