MmuINT0123390 @ mm10
Intron Retention
Gene
ENSMUSG00000038902 | Pogz
Description
pogo transposable element with ZNF domain [Source:MGI Symbol;Acc:MGI:2442117]
Coordinates
chr3:94862422-94864378:+
Coord C1 exon
chr3:94862422-94862530
Coord A exon
chr3:94862531-94864087
Coord C2 exon
chr3:94864088-94864378
Length
1557 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
TTTTGTCTCTCTTTTAAAAGCCC
3' ss Score
8.06
Exon sequences
Seq C1 exon
GGATTTCCTGTAAGGAATGTTCGGCCTGTACAAAATGCAATGAATCAGGTTGGGATTGTGCTGAACGTACAGCAAGGCCAAACAGTTAGACCAATTACATTGGTCCCAG
Seq A exon
GTAAGGAGATACTTATAACCTGGCATCCAGATACTTTTATAGTTTCAGGATATTCTAGGTCATTTGGAAGCATGTATTTAAACAGAATTTTAAAGCACCATGTTAACAATTTAAGCCCAATTTTAAAAAGTCTTCCTAAGCTTTGACCAGGTGGTGATTTTATGTTGGTAACTTCACTACCCTTCATGAGGTAAAATACATCTTATTTAGTCATTACCAGTGTCTGCTGATGAGGTCAGCTATTGTCCTCAAAGAATATTATTAATGCAAACTCACAAATCTAATACTCCATATACATATACTCACTTATGTGGTAGGATTATAAATTGAATTTTACTTTAGTTTTAAAGCATTGGTTTTGGATATGCCACCAGGTATGGTGGCACACTTCCTGGAATCCAACATTCAGGAGGTTGAAGCAGGATTACTGTGAATTCAAGGCCAAGTCCTGTCTCAAGAAACAAACTAAGGCAGAGGTTGGGGGAGGACTTTAGATATAAATGAAGTAAATGGTATGTGCTTTGAGGATAATACTACCAATGACCATATAATGGAATATTGGGGTTGGAGGGTGTAGCCAGGGGTAGAGTGCATGCTTAGCATTGTTGAGGCCTTGGGGTCAACTTCCAGTACCAAAAGAAGATTCTTATAATTCCCCCCAAGTCACATTTCTTAAACATTAGATTTTCTACAATTTGGCTCAAAAAGAGAATAACTTTATTTAATTGTGTAAATGGTCCTCAGGACCATTAGGTGTCTTGGAACTAAAGGGACTTGCCTCCAAGCCTGACAACCTGTGTTCACTCCCTAGAAGCCACATGGCGGAAAGAAAGAACCAGCTCCCACATGGTGCACTGACCTCCACTTGCACACTGTGGTGTGCATGCCGCCCACACATAGATACTCACAGACTCAAAGAAATACAAGTACAGTCGGGAGCCGCTGTAGTTGGCTTTCTAAAGCTTTTTTGTTTTTGTTCGTTTGTTTCTTTTGTTGTTGTTTCAGAGCCTTCAGGGCTTTTTAGGGCATAAATCTGATCCAATTTCTCTGTAACATTCTGGTGTTCCCTAAATATTTCTCACTGGAATTGTCTACAGTTCTAGAAAATTGTTAACCTTTGGGACATCCTAGTAGAGTAGATTGCTTGCCCTATTTGAATGTATAGAAGAAAATGGAAAATTCTTTCAGAATTCTGAAAAAAGACTTTACGGATCAAGTCTGCCCTTTGGCCTGTATATAACCATTCTTTTCCCACTTCTAATATGGAGGCCAAGCTACTGTAAAAAAGATAATGTGGAAGGTATCTGAAAGGAGTTGGTGAGGATTTCTTCTAATTACTGCTTTATGAAACTTTGGATAATTCCTTTTGTTCAGTGGACAGCTACAGCTTTCTTAGATGTTAAGATGGACACTACTCTTAGTAACCTCTGGTGGTCACTCAGTCAGCTCAGGGAATAACTTTTTCCTGTTCTTGTATTTCTAGGAAAGGCAAGAAAATATTTTATAGGTGAGCTCACTGATGAAGGTTTGGGACTCTTTTTGTCTCTCTTTTAAAAG
Seq C2 exon
CCCCAGGTACACAGTTTGTTAAGCCGACAGTTGGCGTCCCACAAGTGTTCTCTCAGATGACCCCCGTGAGGCCAGGCTCCACAATGCCTGTGAGGCCCACCACCAACACCTTTACCACCGTCATCCCAGCTACTCTCACCATCCGAAGCACTGTCCCACAGTCCCAGTCCCAGCAGACCAAGTCCACCCCCAGTACCTCCACTACTCCCACTGCCACACAACCAACCTCACTGGGGCAGCTAGCTGGTCAGCCTCCAGGCCAGTCCAACCAGACCTCGAATCCCAAACTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038902:ENSMUST00000107270:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.358 A=NA C2=0.941
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:
AGGTTGGGATTGTGCTGAACG
R:
GGGATTCGAGGTCTGGTTGGA
Band lengths:
347-1904
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