MmuINT0125729 @ mm10
Intron Retention
Gene
ENSMUSG00000041805 | Pramel1
Description
preferentially expressed antigen in melanoma-like 1 [Source:MGI Symbol;Acc:MGI:1890541]
Coordinates
chr4:143396430-143397616:+
Coord C1 exon
chr4:143396430-143396747
Coord A exon
chr4:143396748-143397049
Coord C2 exon
chr4:143397050-143397616
Length
302 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
CTCTTCTGTTTCACCCACAGCAG
3' ss Score
10.09
Exon sequences
Seq C1 exon
GAATCCTTCCTGAAGATCCATCAGGATGAGCTGCAAGACTCCACCCACACTCCAGGAACTGGCAGAGAACAGCCTCCTGAAGAACCAGGACTTGGCTATCTCTGCTCTGGATGACATACCCTCACTTTTCTTCCCATCACTGTTCAAAAAGGCCTGCAGAAATAGATATGTTGGGATCATAAAGGCGATGGTGCAGGCGTGGCCCTTCCCCTGTCTTCCTCTGGGGGCCATGATCAGTAGGAAGACTGCCTACAGGAGAATCTTAGAGATTATCCTGTATGGGCTTGATGCCTTGCTTTCCCAGAAAGTTCCCCACAG
Seq A exon
GTGAGTGAAACCCAGAAGGGAATACAAGCAGAGACAGTTGGGGTCAGGTTGAATGGGGGAGACAAGGTAGACAAGGATGGAAGGGAGGCTTTTGATGGCCCCAGCTTGGAGAGCTACAGGGGCTTTTTGGCCATTGCTGAGCCATCTGGGAAAGGACTGTGGAGTGTGCAGGGTTTATCAGCAGTGGCTGAAGTACTCTGCCCCTGTTTCCCATGGGGACTGGACTGGATTCATGGACAAGGGCATGAGAGTCAGAATGTGGTAAATGCCTAGGTGCTGAGACTCTTCTGTTTCACCCACAG
Seq C2 exon
CAGGTGCAAGCTGCAAGTGCTGGATTTACGGGTTATGCCTTTGAAGCTGTGGAACAGGTTGCCTGTGTTTGGGACTGCTGGCTGCAGTGAGAATCCAGCAGTGGTGGGCCATTCGGGAACAGAGGTGAAACAGCCAGTGAAGGTGCTGGTAGACTTGGTCCTCAAGGAAAGCCCACTAGATTCCACAGAGTCCTTCCTCGTTCAGTGGGTGGATAACAGGAATGGTTTGGTGAGTTTGTGCTGTTGCAAGCTGCAGATCTGGGCTATGTCCATGTATTACCACAGAAAACTTTTGGAGATTTTGGATCTGGACTCTGTCCAGGAGCTGCGTATGTACTGCATCAGTAATCCTGTCTGCCTGCTTAACTTCGCCCCTTACTTGGGTCGCATGAGGAACCTGCGCTGCCTCATCCTCTCTCACCTCTGGCAGACCTTCTCGATGACCCCGGTGGAGAAGCAGCAGGTTATTACCCAGTTCACGTCTCAGTTCCTCAAACTGAAATGCCTCCAGATCCTGCATCTGGATACTGTCTTCTTCCTAGAGGGTCATCTGGATGAGCTATTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041805:ENSMUST00000037419:2
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
Other Skipping 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:
TCTGGGGGCCATGATCAGTAG
R:
TGCAACAGCACAAACTCACCA
Band lengths:
347-649
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