MmuINT1027351 @ mm10
Intron Retention
Gene
ENSMUSG00000025839 | Pramel7
Description
preferentially expressed antigen in melanoma like 7 [Source:MGI Symbol;Acc:MGI:2156391]
Coordinates
chr2:87490824-87492418:-
Coord C1 exon
chr2:87492135-87492418
Coord A exon
chr2:87491406-87492134
Coord C2 exon
chr2:87490824-87491405
Length
729 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
GTCTCTTGTTTTATCCACAGGAT
3' ss Score
11.27
Exon sequences
Seq C1 exon
ATGGTCAGTGCCCCACCCACACTCCAGGATCAGGCTTTCAGGAGCCTGGTGAGGAATGAAGTATTGACCGTCTCTGATGCGGAGTGCCTAATAAGGGAATTCTTCCCACCTCTGTTCAAGGAGGCCAGCACTCAAAAAAAACCAAAGACAATTATGATCCTGGTGGAGCACTGGCCCTACCCTTGCCTTCATGTTGGGTTGTTGATTGATAAACCCAACTTTCAGATCTTCCAGGCTATACTGGATGGAGTAGACACATGGCTGAAACGGAAGTATCGCCCCAG
Seq A exon
GTAAGCTGAATACCAGGTAAATGGCTGGTGGTGGCACACGCCTTTAGTTCTAGCACTTGACAGGCTAGGCAGGTGAATTTCTGAGTTTGAGGCTAGCCTGGTCTACAGAGTGAGTTCCAGGGCTGCCAGGGCTATACAGAGAAACCCTGACTCAAAAAACAAACAAACAAACAAACAAAAAATCTGTGATAAGAATATGGTAAAAGATGGATCAGAGGTTTTGGCTGGTGTCTTAGAGAGCTATTGGTGCCTGGAAAGCTTGTGAGTCTTTGTATAGTAAATTATGAGATACAGGTTGGTGCAGCTTTAGCCACAGAAGAATGACCCTGTCCCTGCGTCTCCACCAGTTAACAGAAATAGGATCTGATATGCAGGTTAGTCACCCTTAATCCCAACACATGGGAGGCAGAGGCAGGTGAATCTCTGAATTGGAAGCCAGCTAGAGAGCCAGGGATACACAGAGAAATCATGATCTGAAAAATACAAACAAAAAGAAATAGGAGCTGACAGAACTCCCAAGACAACTGAATGGAGGGAAATAGGACAGGTCTTCAGATGCAGCTCAGGCAAGGTGCCCCTTGGCAACTAGAGGCTGTGTTGGAGACCCAGTACTGGAAACCATGAGTATACAGAAGACAGCAGAACAAGGAACAAATAACACCAGAGATTATGAAAAAAAAGTGTTGGGTCTCAATTTCCCTTCTAACACGTCTCTTGTTTTATCCACAG
Seq C2 exon
GATGGGAAGGCTTAAAAAGGTTGACTTCAGGGATGCACAGCATCATGCTTCCTTAGATATGCAGGATGAGAGAGAGGGTAGAGACTACTTAGTAGGAACTTTGCCTAAGAAGCAAATAGTGGAGGACCACTCAAGAACAAGGAAAGAGCGTTTGAAGCTGTTCCATGACCTTTCCTTTATGTCTTCTCTGCATGAGGATAAACACCAAACACTGTTATTGGAGTGGGCAAAGGAAAGGACGAGTTTCCTGCATCTGTGCTGTGAGAAGTTGGAGATAGGAGCAGTAGAAGTGTCTAAGGTCAGGAATGTATTAAAATTTCTACAGCCAGAGCTCATCAAGGAGTTGAAACTGAATACAGTGGGGAATCTGTCCAAACTGGCAAAATTCGTACCTTTCATTAGAAAGATGAGAAACCTTCAGAAACTCATGCTAGTACGCACCTTTGGAACAAGGACTTTCACTCAAGAGGAGAAGCAGAACATCAGCAAGATCATTTCTCTGTTCTGCAAACTCAGCTGTCTCCGGCATCTCACTATTGATGATGTCTATTTTCTCACAGATCAGATGAAAGAGTTGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025839:ENSMUST00000026957:1
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=0.005
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
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:
CCCTTGCCTTCATGTTGGGTT
R:
GTCCTTTCCTTTGCCCACTCC
Band lengths:
345-1074
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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