RnoINT0144222 @ rn6
Intron Retention
Gene
ENSRNOG00000048870 | St6galnac4
Description
ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 4 [Source:RGD Symbol;Acc:1303005]
Coordinates
chr3:11616202-11619593:+
Coord C1 exon
chr3:11616202-11616309
Coord A exon
chr3:11616310-11617592
Coord C2 exon
chr3:11617593-11619593
Length
1283 bp
Sequences
Splice sites
5' ss Seq
CAGGTTAGA
5' ss Score
5.94
3' ss Seq
TCCCTGTTCCCTCCCAACAGTGA
3' ss Score
11.17
Exon sequences
Seq C1 exon
GAGACAATCAGGCTCCTTCCTTAGCACCGGTTGGTTCACCATGATTCTGGCCCTGGAGCTGTGCGAGGAGATCGTGGTCTACGGGATGGTCAGTGATAGCTACTGCAG
Seq A exon
GTTAGACTGGCGCCCAGGCTGCGGGTAGGGGCAGGGAAGGAGGGGGAGGCGAGGCGTGAGACCTTGAGTCAGAGGGTCTGTGAGCTGTGAGGGCTCCATGATGGGTGACCCAGGCACAGACACCCCCAAGTGCAGGCCTTTGGGAAAAAGTGTAACCTTGAGCCGGGCATAGAAATCCCACTTAGGAAGCGAAAACAAAAGAATCAGGATCAGAGCTAACCTTGGCTCCACATCCATTCAAGGCTACCCCCTCACCCCCCCAAACACACACACTTTTTGAGAGTCTCTCTAAAAAACTAAAACCAAAGCAAAGACTTGTACATCTCTCAGGTCAGATGTAGCCAGTGTATCTGACCTTGAGACATTGCTACCTGACCTTGTCCAATACAGAGTTCACACATAAGAACCAGGAGGTGTGCACAGCTTTAATACAGCACTCAGGAGGCAGAGGCAGGCAAATCTCTGAGTTCAAGTCCAGCCTGGTCTGCAGAGGGAGTTCCAGGACAGCCAGGGCTACACAGAAAAACCCTGTTACAAAAAAACAAAACGAAACAAACAAAAAAATCCCAAAGGCACCCACATGGTGGACTCTCAAAATGTCTTTTGACCTCCACGTGTACTTTGTGGCAGCCTCTCACCCCAACACCCTCCCACATGCAAATAAAAATAAGTAATGAATAGATGCAAAAAAAAAATTTAAGTTGCCAAAAAGATGTGGCAAAGTGGGCCTTGGGTTAGACCCACCTGGTGGAGTGCTCACCCCGTGGAGCCTATATCTGTTTGAATAAAACACTTCGGGTAGATTTAGTTGTGGTATTACTTAAATACTGTGAGTTCAGGTATGGGATTCTATATGTTACATTCTTACATTTCAATGTTACTATAACTCAGGAGTCTGGGGAAGGCCCCAGGTTTTCACACTTTCCCTTTAGAACCTGTGTCTCGAGTGTATGAGAGAAATGGTAGGGTTAGCCGGTGTCACAGCCGGTGTCGCAGCGGCCTGCAGTGGGCGTGCAGGGCTGACTGCTCTGGATCTGGGAGCTTAGGCGCTGCCACCTGTGGAGTTTATCCTTTGACTCCAATTCCATAGGGGCTGTTGTAGGGCAACAGTCCAGATGGACTCCAGCTTGCAAGGAGCAGTTTCTGAGTCCAGGCCAGTGGGCTCCTCACTTGCTGGCCTCCGCGCCACCTGTCCAGATGTGGGTCTCCCTTGCCTGAACAGCTAAGGTATAGCCCTGGAGATGGGGCCTTGTTCCACCTCTGTCCCTGTTCCCTCCCAACAG
Seq C2 exon
TGAGAAGAGTCCTCGCTCCGTGCCCTACCACTACTTTGAGAAGGGCAGGCTGGATGAGTGTCAGATGTACCGTTTGCACGAGCAGGCTCCGAGGAGCGCCCATCGCTTTATCACCGAGAAGGCTGTGTTCTCCCGCTGGGCCAAGAAGCGGCCCATCGTGTTCGCCCACCCGTCCTGGAAGGCCAAGTAGTTCCTGTTGCCAGTGACCACCAGGCCTGTGACCCATTCCAGGCCAGCTCGCTCCAGTATAAACATTTATGACTTTCACCTTCTACCTGACACCAGGTCTCTGTTACCCAATGCTGGGTGCACTTGGAGGAATCTCAGGCCTTGTGACTTGAAGGGGAGTGGAGAGGGTGCCATTCGTACCACCCCTGCTTCCAGAAGAATCCACTTCATCTTGGGGTTTGTCCCACCTCCAGGTTGTTTAAGTGGCCTTTGTCCTGGGGCCGATGACCCCACCTCACCAGCATTATGGCTTCGTAACAGTCTTCATCTTTCTTCTACCTATCTCCAGCCACATGGTGCCATGTTCTCAGGCTGGTGGCCCTGGTTGGTGCACTCTGGAATTTGGGATTTGATGGGCATGAGGGTGTTTGCGCGTCAGCCTCCCAGGACTGTCTCGGGAGTGTGCCAGTGAATGCATATTTTCTGGACACTATCTATGTGGTAACAGGCGTGGGATGGCGATTAGGACACAGGCCTGTAACTTGTTCGCTGGAGGGCAGACTGAACCCTCCAGCTCTTCCCTAGGCCCACGGCTGCCTGCTCTTCCTGCATTGTCTAGACATCAGCCCCAGCATCCCACAAACTTGGCCTTCTTACGGTCTGACCACAGGACTGTGCAAGCCTAGGAAAGCCACCTTGCCCCCACTTGGCAGGCATAGAGCAGTGCCTGGGCGAACTCAGGGTGAGAAAGAAATTCCACCCAACGCCACTGACCTGCCCCATGAGTCAGATTCCAAAGTCTTTGCCAGTCAAGCTGTCTCTTACTGGGGGACTTGGTTCCTTTGTAAAACAGAAGGCGGAACGCAGCTTAGGGTGGGTGCTACATGGGAAGGAGTGACCTCAGGGCCAGCCCGTTCTCTGAATTTTGCTTTTCAGTGCTAAAACACAGCCACCATCCTGCTCTTAAGGAAGGTGTGATGCTATCCTGAGGAGGGAGCTGGTGCTTATTTCATACAGATGGTGTATCCCGGGCTAGCTTTCTCGAGGTGGCTGAGCTAGGATGCTGTCAGGCTCCAGAGAGCACTACCTGTGCTCTTTGGAAGACTGAAGAATGGAGCCCTGGGCTCTCAGCTTCAGAGTTCAGGACCTTCTGGGTGTAACCTGTGCAGTCCCCCAGAGCCCCGTACTTAGCCTAATCTTTCCTGCTACAAACTTGAAATTCCTTATTTTAAGCTTTGGTTTTGTTTTGTTTTGTTTTTAATGAGGAACCTCTCAGGTTCCTTTTGTACCAGATCCCACAAATGACAGAACCGATCATGCTAAGGACTCTGCCCACTCTCCCTCCTACCCATTTCCCCAGGAGTGACTAGAGACCTGGCATCTGGCCCACAACACTGCCCTTGCTCCCATCCAGTGTCAGGTGGCCCTGAAGCCTCATGAGTGGGAAGGAAAGCAGAGAGGGAAAGCTCTGAGCCAGGGATGCAGGCTGGAAGCCAAGCCATTTCCTCAGATCTGGTGGTGTCGAGGGGCTGTGAGTAGGAACAGGGCATCAGTGCGTATCGGGTAAGACGGGGGTTCCTGGCAACAGGCCTGACCCCACTTTCCCTGGCAATAAAGACGGTAGACTAGCTCCTACCTCACAAGATTGCGTGAGTTCAAAGATGCTGGGGTACCCCTGGGGCTTCGAACACACTTGGCTCTCAGTGTCCAGAAGCCGCCATTTAAATGGGGTGGCCTCTGCCTGGGTGGTCCTGCCCCACCCTGGTATAGGTGGTATCAATGCAAAATAATGACAACAACAAAATAATAATAAAAAGTTCTCATCCCAGCGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000048870:ENSRNOT00000072685:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0077713=Glyco_transf_29=FE(14.8=100)
A:
NA
C2:
PF0077713=Glyco_transf_29=PD(23.0=87.5)
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:
GGTCTACGGGATGGTCAGTGA
R:
GATTCCTCCAAGTGCACCCAG
Band lengths:
356-1639
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]