MmuINT0127367 @ mm10
Intron Retention
Gene
ENSMUSG00000015476 | Prrt1
Description
proline-rich transmembrane protein 1 [Source:MGI Symbol;Acc:MGI:1932118]
Coordinates
chr17:34629533-34631171:+
Coord C1 exon
chr17:34629533-34629704
Coord A exon
chr17:34629705-34630632
Coord C2 exon
chr17:34630633-34631171
Length
928 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
CTCGGCTTTTCCATGGCCAGGCC
3' ss Score
6.13
Exon sequences
Seq C1 exon
CCCCCCCAACACACACTGTCTTCATCTCTCCATTTCCGCGCTGCTGCTGCTACCGCCGCTGCGCCATCCCGGACTGAGACACTAAGACTCCTGCGCCAGCAGTCAGGGGGCCCTGACTCCAGCTTCAGAGACCCTGTCCCAACGATTGCAAACATGTCGTCAGAAAAGTCAG
Seq A exon
GTAAAAAAAAAACTATATATATATATATCCCTCCCCCAACCCCCTCTGTCATCTCCTACCTAACCTCCACTTGCCCTAATCCCCTTCTTTGACCCCCTCTGGGATGTTGTGTGGCTCAGTTCCATTCCTTCTCTCCATGCATACCCCACCCCCTCCCCTTTCTATATCCCATCCTTCTCTTCCTTCGGGTCAGTCTGCCTCTGTCCCTTGGTCCCTTGTCAACAACATGGGGGGGGGGTGCAGTTTTGAAATGGAAAGGGAGGCAGAGCCAGGTTCTGCAGGGACATCATCCCTGGGAGTGACAGATGGACAGTCACCGGTTCAGTGGCATGGAGACACCCAGTGGAAAAATAACGGAGACTTAATCAGACTGGGTTGTTGGGAAAGTAATATCTAGAAGACAATTTTTTTTCTTCTTTGAGATGAGATTCCCCTCTGTAGCCCAGGCTGGTCTTGAACTTCCCAGTTCTTCACCCTTCCCCGGCTGCTTCACAAGTACAAGGATTACAGGCATGAACCACTATGCCTAGTCCCAGAAGCTTTGTCATGGACCTTAACGGAGGCCCATGAGATTCCCAGGTAACTCCACCTGAAGCAAAGTGGAAATGTTAAACTGAGCGTGCATGACCCCTGTGACACGACCACATGTGCAGGAAGAGGGGACAGCTGGCTCAGAGACAACCCTGAATGAGGGTTGTGGTTGACAGCAGCGGAGCCTGGGAGGAGCTGTGACAGTTGTGACGGCAAAACTAGATTGGGGCCAGGTGGCCTACATACAACCCCTTCCCTGACCCCAAAATGGGAGATGTCGTCTCGGCTGTATCTCCCTCGCTCTTTCTCCATCTCTTGCTGTCTCATGTCTCTTACCCTTCTGATCTCTGCTGTCTTCTCTCTCCCCTTATCCTCTCCTCGGCTTTTCCATGGCCAG
Seq C2 exon
GCCTTCCAGACTCGGTTCCCCACACTTCACCGCCGCCCTACAATGCCCCCCAGCCACCGGCCGAGCCCCCCATCCCGCCCCCACAAACGGCCCCATCCTCACATCACCACCACCACCACCATTACCACCAGTCTGGCACCGCCACCCTCCCGCGCTTAGGAGCAGGTGGCCTGGCCTCTGCTGCGGCCAGTGCTCAACGCGGTCCTTCGTCTTCCGCCACGCTACCGCGGCCCCCCCACCATGCCCCGCCCGGCCCCGCCGCTGGGGCTCCCCCACCCGGCTGTGCTACCTTACCCCGCATGCCACCCGACCCTTATCTGCAGGAGACTCGCTTCGAGGGTCCACTTCCCCCACCACCGCCTGCGGCCGCCGCCCCGCCCCCACCAGCGCCTGCCCCGACGGCCCAAGCCCCGGGCTTCGTGGTTCCCACGCACGCGGGGGCGGTGGGCACGTTGCCGCTGGGGGGCTACGTGGCGCCGGGCTACCCGCTGCAGCTGCAGCCGTGCACTGCTTATGTCCCTGTGTATCCGGTGGGCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015476:ENSMUST00000015620:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.800
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
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAGACCCTGTCCCAACGATT
R:
CATGCGGGGTAAGGTAGCAC
Band lengths:
348-1276
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