MmuINT0153248 @ mm9
Intron Retention
Gene
ENSMUSG00000079442 | St6galnac4
Description
ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 4 [Source:MGI Symbol;Acc:MGI:1341894]
Coordinates
chr2:32449510-32451321:+
Coord C1 exon
chr2:32449510-32449922
Coord A exon
chr2:32449923-32451213
Coord C2 exon
chr2:32451214-32451321
Length
1291 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGC
5' ss Score
8.69
3' ss Seq
CGGTGTCTCATCCTCCTCAGGAG
3' ss Score
8.3
Exon sequences
Seq C1 exon
CCTCTTATCCGAGAACTGTGCCACAGCTGTGCGGTGGTGTCCAGCTCTGGCCAGATGCTGGGTTCAGGCCTGGGTGCCCAGATCGATGGCGCAGAGTGCGTGCTACGCATGAACCAGGCACCCACCGTGGGCTTTGAGGAGGACGTGGGCCAGCGCAGCACTCTGCGCGTGATCTCTCACACAAGTGTGCCATTGCTTCTGCGCAACTACTCACACTATTTCCAGCATGCCCGAGACACGCTCTACGTGGTGTGGGGCCAGGGCAGGCACATGGACAGGGTGCTGGGCGGCCGCACCTACCGAACGTTGCTGCAGCTCACCAGAATGTATCCAGGCCTGCAAGTGTACACCTTCACTGAACGCATGATGGCCTACTGTGACCAGATCTTCCAAGATGAGACAGGCAAGAACCG
Seq A exon
GTGAGCTGGAGACCCCTGGCCCCTGGAGTTTGCATTCTCTAAAAGCCTCTTTCTGCTAGGAAGTGCTTTAAGGTCTGAGGTGGTCTCTGAGGTCATTCCAGATAACTGAAGTAAGAGTGACTTCAGGCTGGGGATGTGGTTGTGTTGGCAGAATGGTTGCCTAGTGTGCATGAGGCCCTGGGTTCCATCCCCAGCACTGAATGAACTGGCCTTGCATGCCTCTGTAGTCCCAGCACTCTGGAGGTAGAGGCAGGATGGTTAGGAGTTCAAGGTTAGGGAGTTCAATTCACTTAAGCTTAGGCGGCGTGAGCCTGTCTCAGAAATGAGAAGGAAAACAAAACAAACCAAACAACTGTTTTTGAGTCCTAAGGCTTTGAGCTGAGCACTCTGCATCAGACATCTCTAATCCCTCAGCACTTCCCGAGGCACCTCACTACATACCTGTGCCCTGGCCCTCGTCCTCAGACTTGTCCCCAGCTGCAGTCCCTTGCACATGCTCTGTTCCTTCTGCCTAGAACATTCTTCCAAAAGTTCCCATGATTGGCCCCTTCCAGCCGCTCCGGTCTGGATAAACTCTCCACTTCCTCAGGGAAGCCCCTCCGAGACCATCCCTCTGCAGCAGAAGCAGCCCGCCTTGGCGACCTGCATCTCGCCTTTCCCTTTTCAGCTGCTGACACCATCTGACATTACAGTTTATGTTTCCTCCCTGAAACTGTTAGCTCCAGGTGGGGCAGGTGCTGGCTGTGCACAGCTTGAATAGTTGAGCTGGCCTGTACTCTCAGGAGAGGCAGAGGAGGAGGTGGCCTTCTACTTGGAGGGTACCCAGAGCTGCCACCTCAAGAGAGCTGAGGCCTGGGGCTGTTACAGCACCTTTACGCAGGTGGGCTGGGTGCAGGGTGGAATGGGCAAAGCTGACAGGGTTCCCTCTCCAAAAACACCTTCAAATCTCCATGTTTCACAGCCGGGTCTCTGAGACTGAGACTCTCAAGAGTGAGTTAGGTGCCCTACGGGAGAGGCAAGGCTAAAAGAGAAGACAGAGCCCTCAATTTTACCCTCTGTGCTCTCTTGTACCTGTGGGCTCTCCGGGTCTAGTTCTCAAGAACCCTGATACCGTCCTCTGCTCGGGCAGCCAGACCGAACAAGCCCAGGTTTGTGTCCAGCACCACCTCTAACCCACTGCCGATGGCAAACTGCCTCTCCGCTGCTTCCCCCTTCCTGGGACCTCTTTCAGGTTGTCAGGTGGGAGTAGGGGATGCTGGTGGGGCCACTGACGGTGTCTCATCCTCCTCAG
Seq C2 exon
GAGACAATCAGGCTCCTTTCTCAGCACCGGTTGGTTCACCATGATTCTGGCCCTGGAGCTGTGCGAGGAGATCGTGGTCTACGGGATGGTCAGCGATAGTTACTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079442-St6galnac4:NM_011373:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.005 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0077713=Glyco_transf_29=FE(54.6=100)
A:
NA
C2:
PF0077713=Glyco_transf_29=FE(14.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCTGCGCGTGATCTCTCAC
R:
AACTATCGCTGACCATCCCGT
Band lengths:
354-1645
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: