MmuINT0127137 @ mm10
Intron Retention
Gene
ENSMUSG00000023007 | Prpf40b
Description
pre-mRNA processing factor 40B [Source:MGI Symbol;Acc:MGI:1925583]
Coordinates
chr15:99303283-99304184:+
Coord C1 exon
chr15:99303283-99303363
Coord A exon
chr15:99303364-99304040
Coord C2 exon
chr15:99304041-99304184
Length
677 bp
Sequences
Splice sites
5' ss Seq
TTCGTAAGT
5' ss Score
9.77
3' ss Seq
TTTTCTTTCCTCATTTCCAGATG
3' ss Score
12.87
Exon sequences
Seq C1 exon
TCGGTTCCCGATTCTGGTCCCCGGCCCCCAGCAGCGCCTGCCCCCTTCCCACCGGGGCCCCCCATGATGCCACCACCCTTC
Seq A exon
GTAAGTTTTATGTGTTTCCCTGGGCTTGGCTTTTCCAGCCTGTACCCTCAGCCCCCACCCTACCACTGCTGTGTTGCCAGGAACGACCTGTTACACAGCCTTTGCTGCCATTGGAAGATGGGTGGTGTTGAGCACTGGGTGGGAGAGCTGCTCTCAAGCTCTAGTCTATAAAGTGACAATTGTCCCTTTTTGTTTTGTCTTTGGGATGCCAGGGGCTGGAGGCAGGAGACATGAAAGGGAAAGACTTCAGCAGAGCAAGGCCTGGGAGGCTTCTCTGTTTTTCACTATTCCTTACTGTGCTCCTTATAAAAGCCTCTGCCTTTGGGCTGGAACAGCATTGGTGGTCATGAGTTAGAGAGGGATGGGAGGCAAGAGACTAGGACCCTTGCCTTGTTCCTTCCTCCCTCCACAGGCTCCAGGGCGTGCAGCCTCCCTAGTCTGTCACTGTTTCCTTGCCCTTTGCCTCTCCCTCCCTCATCAGGAAGCTGTGTGCTTGCCATTATGCCCGAGAACTCCTGCCTGTCTTTCTCAGTAGTGGGGAGGGAGACCGTCTTATGCCTTGTACTTCTCAATGGAAAGTCTTGGAATCACCTCTAGGCTGGGATGAGGGCTGGGTAGTTCTGAGATAGTGGTCTCTGCCATAATAAGACAGTTTCTTTTTCTTTCCTCATTTCCAG
Seq C2 exon
ATGCCCCCTCCAGGGCTCCCACCTCCTTTTCCTCCGATGGGGCTCCCCCCTATGAGTCAGAGACCACCAGCCATTCCCCCCATGCCACCTGGCATACTGCCCCCAATGCTTCCACCAATGGGGGCACCGCCACCACTTACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023007:ENSMUST00000145482:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.932 A=NA C2=0.977
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTTCCCGATTCTGGTCCCC
R:
CTGTGTAAGTGGTGGCGGTG
Band lengths:
223-900
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