MmuINT0067912 @ mm9
Intron Retention
Gene
ENSMUSG00000026829 | Gbgt1
Description
globoside alpha-1,3-N-acetylgalactosaminyltransferase 1 [Source:MGI Symbol;Acc:MGI:2449143]
Coordinates
chr2:28358646-28360935:+
Coord C1 exon
chr2:28358646-28358780
Coord A exon
chr2:28358781-28360230
Coord C2 exon
chr2:28360231-28360935
Length
1450 bp
Sequences
Splice sites
5' ss Seq
GAAGTGAGT
5' ss Score
7.97
3' ss Seq
AACAGAGCTATCATCCCCAGGTA
3' ss Score
4.05
Exon sequences
Seq C1 exon
ACCCACAGAGCTGCTGACACTTACCCCGTGGTTGGCACCCATCGTCTCCGAGGGAACCTTTGACCCGGAGCTTCTGAAGAGCATGTACCAGCCGTTGAACCTGACCATTGGCGTCACCGTGTTTGCCGTGGGGAA
Seq A exon
GTGAGTCATGGCTGAGGCAGGAGTGGGGCTTGGTCTCCCTGAGCCACAGGGGCTTCTGGTCTAGGGGGAAGCCTGCCTGGCCAAGTGCTGTGGAGTATGGGAGAGCTTTCTGATATAAGGGCTCGCCTGCCATGGAAAGGGAGACGTCTAGGTCAGGATCAGCAGGGTATGTATTGTCCTCCCTACCTCTCCTTGTCCCTACCTGGCCTTTCCTTTAAGTCTGTCTGGAACTGTGTTTGGGCCCTAGAACTTAAAATACTGGCCAGATGAAAAACGGACCACATAGGTGAGGTGAGCCCCTGGTTTTAGGGATGGATTCTGCTCTATGTCCCATTGTCTAGCATTCATTTTCCCTTGATTCTGACCCCTGGTCAGAATAGCCTCTCAACTACTTTCGTCCTCCTGGTGTTCAGTTTGAGTGTGTATAAAGTGGTCAAGTTTCTGAGCAGAACATTAATAGAGATCATAGGAATCCCAAACAACACTGTCTGCCATGCTCAATCAAAACATGATGACTCAGGAGGTAAAGGCTCTTGCCTCTAAGCCCAGTGACTTCAGTTCAATCCCCAGGATGGGAGGAGAGAAATAACTCCTGGCAGCTGTCCTCTGCATTCACACATATAAATTAATTAATTAATTAATTAATTAAAAAAATTTAAGGAAGCATATCAGACACAGAGGAAGACAGCCCAGCTGATAAAATGCTTTCATGCAAACATGAAAACCTGTGTTCCATCCCCAGCATCCATGTTGAAAAAAAAAAGACACACACAATAGCACATGCCTGTAATGCTAGCACCAGGGATGCAGACATAGGAACATCACCGAGTCTTGCCACCTAGCCGGCTTTGCCAGATTATTGAGGTCCAGATTCATTAAGGCCCTATCACAAAAAAATAAGATGGTGGTGGTGCATGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGAGGATCTCTGTGAGTTTGAGGCCAACCTGATCTACAGAGCTAGTTCCAGGACAGCCAGGGCTACACAGAGAAAAACCCATCTTGAAAAAACCAAAAACCAAAACCAGAACAAACAGCGAGGAAGATGCCCAAGTGCCTAGTGCCAGCCTCCAGGACACGTGTGCATACAGCCTACAGGTGACTAAAGACAATCTCAAATGGTTGTCACACTCTAAGTATCCCTGGTATCTCTAATTATAAACACTTGAACCAGAAATGTCTCGTGGTATAGAATTTGTGTAGACTTTAACAATTATACATCTTAATCCAAAACTCAGAAGCAGGGCTTTCAGATGAGGGTGACCAACTTTGACAAGGATTGTGGGAGTTTGACAGATAAGGACCCCAAGGTAAGACCTCAATGACTTCCTGAGGTGAAAAACTAGTGTGTAGACTTCAGCGCATACTGGGGACCCGGGCAGTTGTGGACAGCAGTGGCTAACAGAGCTATCATCCCCAG
Seq C2 exon
GTACACCTGCTTCATTCAGCGCTTCCTGGAGTCAGCTGAAGAGTTCTTTATGCGTGGGTACCAAGTACACTATTACCTCTTTACCCATGATCCTACAGCCGTTCCCAGAGTTCCCCTGGGCCCCGGTCGGCTCCTCAGCATCATCCCTATCCAGGGTTATTCCCGGTGGGAGGAGATCTCCATGCGCCGAATGGAGACCATCAACAAACACATTGCCAAGAGAGCCCACAAAGAAGTGGATTACCTCTTCTGTGTCGATGTGGATATGGTCTTCCGTAACCCATGGGGCCCCGAGACCTTGGGGGATCTAGTGGCTGCCATTCACCCAGGCTATTTTGCTGTACCTCGCCGGAAATTCCCTTATGAACGCAGGCAAGTTTCCTCTGCCTTTGTGGCAGACAATGAGGGGGACTTCTATTATGGTGGGGCACTCTTTGGGGGACGAGTGGCCAGAGTGTATGAGTTTACCCGGGCCTGCCACATGGCCATTCTGGCAGACAAAGCTAACAGCATTATGGCAGCCTGGCAGGAGGAGAGCCACCTGAACCGCCACTTCATCTGGCACAAACCATCTAAGGTGCTGTCCCCAGAGTACCTCTGGGATGAAAGGAAGCCTCGGCCCCGAAGCCTGAAGATGATTCGATTCTCCTCAGTGAAAAAGAATGCCAACTGGCTGAGGACCTAACATCCGGGCTAAGACCCGCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026829-Gbgt1:NM_139197:6
Average complexity
IR-S
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:
PF034148=Glyco_transf_6=FE(13.4=100)
A:
NA
C2:
PF034148=Glyco_transf_6=PD(67.4=99.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGACACTTACCCCGTGGTTG
R:
CTTTGTGGGCTCTCTTGGCAA
Band lengths:
355-1805
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: