MmuINT0125726 @ mm9
Intron Retention
Gene
ENSMUSG00000046862 | Pramef8
Description
PRAME family member 8 [Source:MGI Symbol;Acc:MGI:2140473]
Coordinates
chr4:143006543-143007863:+
Coord C1 exon
chr4:143006543-143006855
Coord A exon
chr4:143006856-143007275
Coord C2 exon
chr4:143007276-143007863
Length
420 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
CTACCTTTTTTCACTCACAGAAG
3' ss Score
9.4
Exon sequences
Seq C1 exon
GATCCTTGACACTGAAGATCTGAAGGATGAGTGTCCAGGACCCACCCACACTCCTGCAGCTGTCAGTACAGAGACTACTGAGGGACGAGGCCCTGGCCATTTCTTCTCTGCAGTACCTTCCCAGGGCGCTTTTCCCACTGCTCTTCAAGGAAGCCTTCAATCACAGACAAACTAATGTCCTGAGGGCCATGGTGGCAGTGTGGCCCTTTCCCTTCCTCCCTCTGGGGACCCTGATGAAGACTCCCCACCTGGAGATCTTGCAGGCTGTGCTGGATGGAGTAGACATGCTTTGGACACAGAAGGTTCTTCCCAG
Seq A exon
GTAAGCAAGACCCAGGTAGGGGGATACTAGGGTACAGGGGAGGGACATCTAGAGTAGGGGAGAGTGGGTCAAAGGTAGATCAGAAGCTTCTGGGGGTGTCATTTTGAAGACTGCAGAAGCCCTAGCCAGTATAGCTTAAAGCAGCTGACGCCACAGTGGGATCAGTCTTTCCTTGGCTCTTGGAGAGGTACTAGAAGTGGAAGAGGCAGAAGTCAAGAGTAACTGAATGGAGGAAGCAGGGCAGGTCTCCAGATGAAGTTAATACTTAAGAGTCCTCTTCTGGAGGCATGAGGTGCTATCTGGATACCACAAACATACATAAGACAGCAGGGAACAGGCAGCGTCAGAGATACAGAAGAAAAGCTGGCCATTGTTTGGTCTTTTGTATTTCCTGACACTTCTACCTTTTTTCACTCACAG
Seq C2 exon
AAGGAGGAAGCTCCAAGTGCTGGACCTGAGGAATGTGTACCATGACTTCTGGGATGTTTGGGTTGGACCAGAGGATGGAGACCACTCAGCAGAGACTGTGTGTGAAAAGCAGATAGCAAAGCGCCTTCATCAATATGCACTGAGGCGACGTTTGAAGGTGGTCACTGACCTGTGCCTCAGGTTCCATTTGAATGAACACCAAGCATACTTGTTACAGTGGGCCCAGCAGAGAAGAAGTTCCATACGGCTATGCTGTGTGAAGATGCAGATTTGGGCTTTGCCTGTGTACACTGTCAGGAAGGTCTTGATGGTGTTCCAGCCAGACAGCATCCAAGAATTGGAACTAAATACAGGTTGGAGCCTGTCCACTCTGGTGCATTTTGCATCTTACCTGGACCAGATGAGAAACCTTCAAAAACTCCTTTTAACACGGATTCACAAGAACACCTTCAAGGTTCTAAATACCTCCTCGGACATCCAGAAGTGTATCACCAAGTTTGTCTCTCAGTTCTCCAAACTCAACTCTCTCCAGCATCTCTCCATGAATGGCATCTACTTTTCCAGTGAGCACATGAAACAGTTGTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000046862-Pramef8:NM_172877:3
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=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTCCTGCAGCTGTCAGTACA
R:
GCTGAGTGGTCTCCATCCTCT
Band lengths:
354-774
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: