MmuINT0123389 @ mm10
Intron Retention
Gene
ENSMUSG00000038902 | Pogz
Description
pogo transposable element with ZNF domain [Source:MGI Symbol;Acc:MGI:2442117]
Coordinates
chr3:94860796-94862530:+
Coord C1 exon
chr3:94860796-94860971
Coord A exon
chr3:94860972-94862421
Coord C2 exon
chr3:94862422-94862530
Length
1450 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
CATTTTTCTTTTTAATTCAGGGA
3' ss Score
8.52
Exon sequences
Seq C1 exon
CTGGTAATACTTTGGTCCAGCAAGGTGGACAGCCACTCATCCTCACCCAAAACCCAGCACCAGGTCTGGGAACAATGGTTACTCAACCAGTATTGAGACCTGTCCAGGTCATGCAGAATGCCAATCATGTGACTAGCTCCCCTGTGGCCTCACAACCTATCTTCATCACTACCCAG
Seq A exon
GTGAGTGGGACTTTGAATTCTAGGCCTGGTAGGGGAGATAGACTGTGAGCCTCTAGAGGCTTAGCCTTGGACAGGGTCTTCATCACTGTTAGAGTTCTGTCTGTTGAACTGAGTTTCTCTGGACTGTTTCACGGGATCCTGCCTATGAAGTGCCCAGCATAGCATCATGGCTACATGATATTTTCATACACCTGAGAGGTCTGTTGAGTTGATTCAAGTCTGAACAGAAATCATCATTGGGAAACTTAAAATTAGAAAGGCTTCACTCAGGACTAGAGAGCTGGCTTACCCAAGAAGAGCATTTGTTGTTCTAGCACAGGACCCAGGTTCAATTCCCAGCACCTATATGTCAGCTCACAACTGTGTCTGTAACTTCACTTTCAGAAGACCTGATACCTTCTGACCTCCATAGACACCAGGCATCCCTGTGGTGCGCATACATATGTTCAGGGAAAACACTCATACGCACAAAAGAAATCTTAAGAAAAAAAGCGAAGCCTTCGAATTTGCCTTGCAAGGGATACCTTTTATCTGGGCTGCTTCTGCCCCCTGGGGTGAATTCATTGACTTTTGAATACAAGTATAAAATAAGTGGTCTTTGAAGAAGAGGACGAGGAAGAGGAAGAAAAGAGGAAGAAGAAGAAGACGACGACAACTTCGTTGGAAGTTGAAAGCCCAAATCTGAGTAGAATTTAAAGGCACATGCTTCAGAGGTTTGTTGCCTTTGAAATGGGCTTTGATAGCAACATTAAAAAAAAAAAAAGGATGATTTATATGTTGAATACTAGGTTAAATACATTAGGGATTTCTTTTCCCTCTTCAAAGCACCAGTGTGTGGATGCATAGGTTTGTTGGTTTTGGTTATTTAATAGTTTGCTAAACACTGTGGGTGTGGAGCAAACTTGTAACCCCAGCTTTTAGGAGAATGAAGCAGAAAACTGTCATAAATTCAAGGCTTGCCTAAGCTCCATAGCAAGTTTAAGGCCAACCTGGGGTATATAAACCTCGTCTCAAAAGACAAAATCTGGGCAGTGGTGGTGCACGCCTTTAATCCCAGCACTTGGAAGGCAGAGGCAGGCGGATTTCTGAGTTCAAGGCCAGCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGGCTAAACAGAGAAACCCTGTCTAGAAAAACCAAACCAAACAAAAACCCCCAAAGATGTTTGCCATAATTAAGAGTTTGGAGGCAGCCTAGGCTACATAACAACCTGTCTCAAAGCAAAAACAAACAAACAAAAAACCAAAAAAACACCCCGCAAAAACCTAGCATGCCAGATTTTCCTAAAATTCTCCATTTTGGTCATTTGAAAGCTGAAACTGTAGAGAGAGCCGCTAGGTGAGACTGGAGCCTTCAGTCATATTGTATTTAGAGTCCGGCTAGTTGATCTCTATATTAAAGGTCATTTTTCTTTTTAATTCAG
Seq C2 exon
GGATTTCCTGTAAGGAATGTTCGGCCTGTACAAAATGCAATGAATCAGGTTGGGATTGTGCTGAACGTACAGCAAGGCCAAACAGTTAGACCAATTACATTGGTCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038902:ENSMUST00000107270:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.607 A=NA C2=0.358
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CTGGTAATACTTTGGTCCAGCA
R:
CAATGTAATTGGTCTAACTGTTTGGC
Band lengths:
278-1728
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types