MmuINT0123387 @ mm9
Intron Retention
Gene
ENSMUSG00000038902 | Pogz
Description
pogo transposable element with ZNF domain [Source:MGI Symbol;Acc:MGI:2442117]
Coordinates
chr3:94657872-94660123:+
Coord C1 exon
chr3:94657872-94657996
Coord A exon
chr3:94657997-94659964
Coord C2 exon
chr3:94659965-94660123
Length
1968 bp
Sequences
Splice sites
5' ss Seq
CCGGTAACT
5' ss Score
6.39
3' ss Seq
ATGCCTTCCCTTCCCCACAGTTT
3' ss Score
11.38
Exon sequences
Seq C1 exon
CATGGCGGACACCGACCTGTTTATGGAATGTGAGGAGGAGGAACTGGAGCCATGGCAGAAAATCAGTGATGTCATTGAGGACTCTGTAGTTGAAGATTACAATTCTGTGGATAAAACTACTTCCG
Seq A exon
GTAACTAAAGCTCCTTTGTTCTTAGGTTGTTTACATTAATTACATTGAATTATGAAGAATATGTGATACAAAGAATTTAAGAATCCAGAGAGAGGGATGGGGGTGTTGTTCAGTTATGTAGTATTTGCCTAGGCTCTGTCTCCATTGCTACATAAGCTAGGGATGGTGGGACATACCTGGAATCTAAGCAATGGAGGTGGAGACAGGAGAATCACAAACACAAAGTCATTTTCAGTTATACAATAGGGTTTGAAACTAGCCTTGTGATGCATGAGACCTTGTTTCAAAAAAAGAAACCAGAGAGAGCCGTTGTGGCTCACACCTATAATTCTGACTCTTAGGAGGCTTTGAGACACAGTGCCTTAAGCTGGAGGTAAATAATGAGTTCCAGGCCAACCAGGAACTACAGAGTGAGACCCTGCGCTCGGGTGTGCATGCTCAAACGCATGTGCTTTCTTGCTCTTTATCTTGCTCTCGCTCTCGAGCTCTCTGTGTCAGAGACAGAGACAGAGAGACAGAGAATGACTATCTAAGGCTGCCTTTTTATGGCATTGGTATTCCTCTTTTCTGTGCTGTAGCATGTGAGTATCTGCTGCTTCATAAAGTTTGTAAAATACTGTTTAATTGACTTAAAACATTGAGAGATTGGATTAACTGATGTTTCTCAAATACAAAAACAGGATTGTAAAGCAATGTGTATCAGAGCTGGTCTGTGTCCCTAGTCAGTGCACTTTTTGTTTTTCTTGAATTTGGCTTCCTTTATAAGCTAAGGAAACATTCTTTTGTGTCTGTCTTAGTGGCCAGTTTATAATTAAGATTTGTTGCCTTTTATTTTATCAGTGATATAGGGTAAAATTCTGTTGCACTGAATTAACAAAGTAGAGGTTTTCTCATAAGTTATACCAGTTTTTTGTTTTGTTTCTTTCCTTGAGACCTGAAGATAGCTTTGATTTAGGTTGAAACACAGTATAGGTTTTACAGGTGGTTTATTATGAAGGATTATAAATTCTAGAAGTGGTGATGTTAAATCTGAGAGTCCTAAAGAGACACTAGTGCTGTAGAAAGCAAAACATTCAAGTCCTGCTTCAGAGGTTGGTGACCTAACTTTGTTGAGATTTAAAAAAAAACAAGCAAACAAACACATGGGTGTTTTGCCTGCATGTATGTCTGTACCACGTGCATACATGGTGTACACAGTAACCAAAAGATGGCACTGGATCCCCTGGAATGAGGTTTCAGACAGCTGTAGCTGTCATGTGTGTGCTGGGAATTAAACCTGAGTCCTCTGGAAGCCAGTACTCTCTGTTGATCCATCAACAAAGATGGATCCAGCCACTAATCCATCTCTTAGTCCCGCAGTTACTTAATTAACCAGGAAATGTAAGACAAAGATTGTATGATGGTTGGTTTTACTTGTCGAATTGACACAATCTAGAGTCACAAGAGACTAGATTAGGTTGGCCTTGAACATGTCTGTGGAGGATTCCTAGTTATATTTCATTGATGTCAAAGTCTTACCTATTGTGGGTAGCACCATTCCCTAGGAAGAAGATTCTAAACTGTTGAGGAGTGGAGTAAGCTGGGTACTGGCGTGCATGCATTCACTTATGTTCTTTGTTCTTGACTCAGTATAATGTGATGAGCAGCTTCAAGCTCCTGTAGTCTTGAGTTCCCCCACAATGATGGACTGTAATCTGAAATTGTGATCCATATAAGCCCATTCTCCCTTAAGCTGAGTTTGTCAGGGTAGTTATCAGAGCAACAGAAGAAGATAGAAAGACCAAAGAAATTGTGTCTAAGTGGTAGTCTAAGAGACAATTAGGAGGACAAATCATGTCAACAGTTAGAATTTTGAATGAAGTTAGAAACTTTTTTTGGCTGTCAAAACACAAAGGAATGAGAGGAAGCAGAATCCTTTAGTGTCACCTGTCCCTGTCTCCAAGTGACTATGCCTTCCCTTCCCCACAG
Seq C2 exon
TTTCTGTGAGCCAGCAGCCAGTCTCAGCTCCAGTGCCCATTGCTGCCCATGCTTCTGTTGCTGGGCACCTCTCTACATCCACTACTGTTAGTAACAGTGGGGCACAGAACAGCGACAGTACAAAGAAGACTCTTGTCACACTAATTGCCAACAACAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038902-Pogz:NM_172683:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.571 A=NA C2=0.802
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGACACCGACCTGTTTATGGA
R:
CATTGTTGTTGGCAATTAGTGTGACA
Band lengths:
278-2246
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: