MmuINT0125716 @ mm10
Intron Retention
Gene
ENSMUSG00000028591 | Pramef12
Description
PRAME family member 12 [Source:MGI Symbol;Acc:MGI:1924882]
Coordinates
chr4:144394575-144396002:-
Coord C1 exon
chr4:144395680-144396002
Coord A exon
chr4:144395160-144395679
Coord C2 exon
chr4:144394575-144395159
Length
520 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
ACTTCTACTTTCTCCCACAGGAA
3' ss Score
12.41
Exon sequences
Seq C1 exon
GATCATCAGTCTCCCTACAGATCTGTGAAGATGAGCTTGCGTGCCACACCCACACTCCTACAGCTCGCAATGCAAAGCCTGCTGAGGGATGAGGCCTTGGCCATCTCTGCTCTGCAGGACCTGCCCATGGAGCTCCTCCCACCACTCTTCAAAGATGCCATCACTCACAAACGACTTAACATCCTGAGGAAGATGGTGCAGGTCTGGCCTTTTCCCTGTCTCCCGCTGGGTGGTCTGATGAAGATGAAGACACCATACCTGGATATCTTGCAAACCGTACTGGATGGGGTTGATGCACTGCTTGACCAGAATACTCACCCCAG
Seq A exon
GTGAGGGAGCCCCAGGGACTCTGAAGGGAGGCCTGGTAGTCTAGGGTAGAGAAAGAATAGAGAATGGAAGGAAGGTTAGAAGCTTATATTGGTCTCAGTGATGAAGATTTCACAGGCCATTGGACCATTGCTGAGTATCTAGGGGAAGGATTTGAGTGTTTAAGGCCATTTAGGACAGACATAGCTATGACTGAAGGTGCCTGGCCCCTGTCTTTTCCCATAGGCACTAGTAATGGGACCAAACTGGATTCAAGAGGCAGGGATGAAGAACATCAGCATAAATAGAAGGAGCATAGGAGGAGGAAAGTGATGTTGGGAATAAGGAGTCCTTGCAGATCTGGATTGGTAGTGCTAGCCTGTTATTTCAGGCCTCTAACTTTGAAGTAGTGGGACTGCATTTTGATGCCAGTCTTGCCTTTGTAGTAAGAATGAAACCATATTTTTTAAAAAATGGGAACAAAGTGTAATGGGGAAGGATGAATTCCTGCCTTAAGTCTAAGACTTCTACTTTCTCCCACAG
Seq C2 exon
GAATTACAAACTGCAAGTTCTGGATTTGCGGGCTTTGCACAAGGACTTCTGGACCGTATGGGCTGGAGATACGACAACATCTTGCGCTCCAGGGGTCAAGTGTAGGAGAAAAATACAAAAGAGAGGTCCAAAGATAGAAGCCAAGCAAAACTCATTGAAAGTGTTTATAGACCTGTACCTCAAACCAAGAGCCTTGGATACATGCCTGTCCTATGTCTTCCTGTGGGCGAGAGAGAGAAAAGCTTTGTTGCAGCTTGGCTGTAAGAAGCTGAAGATCAACACAGTAGCTATCCAGAATATTGTGAAGATTCTGGAAATGCTAGACCTGGACTATGTGGAGGAAGTAGAAGTATGTTGTACCTGGAAGCTGTCTACTCTGGCCATCTTTGCTCCTTACCTGGGCCAAATGAAAAATCTTCTCTCGATCATTCTCTCTCACATTCATGTGCCTGCCTCTATTACCCCAGAGGAGGAGAAGCAGCTGGTCAGCCAGTTCACCTCTCAGTTTTCCAACCTGCAGTACCTCCAGGACCTCTCCCTGGACTCCATCGACTTCCTCAAAGGTCAAATGGACCAGTTGTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028591:ENSMUST00000030326:2
Average complexity
IR
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
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:
CTCCTACAGCTCGCAATGCAA
R:
TCGTATCTCCAGCCCATACGG
Band lengths:
343-863
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