MmuINT0125729 @ mm9
Intron Retention
Gene
ENSMUSG00000041805 | Pramel1
Description
preferentially expressed antigen in melanoma-like 1 [Source:MGI Symbol;Acc:MGI:1890541]
Coordinates
chr4:142986333-142987519:+
Coord C1 exon
chr4:142986333-142986650
Coord A exon
chr4:142986651-142986952
Coord C2 exon
chr4:142986953-142987519
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-Pramel1:NM_031377:2
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=0.000 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
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:
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: