MmuINT0045447 @ mm10
Intron Retention
Gene
ENSMUSG00000090700 | Cyp4f40
Description
cytochrome P450, family 4, subfamily f, polypeptide 40 [Source:MGI Symbol;Acc:MGI:3645508]
Coordinates
chr17:32667954-32669895:+
Coord C1 exon
chr17:32667954-32668081
Coord A exon
chr17:32668082-32669773
Coord C2 exon
chr17:32669774-32669895
Length
1692 bp
Sequences
Splice sites
5' ss Seq
CATGTGAGT
5' ss Score
7.83
3' ss Seq
CCCCTCTCCCTCTCTCAAAGGCC
3' ss Score
8.99
Exon sequences
Seq C1 exon
GGGATGGGCTCTTGGTGAGTGCTGGTGACAAGTGGAACCGCCACCGACGCATGCTGACACCTGCCTTCCATTTCAACATCCTGAAACCCTATGTGAAGATTTTCAATGACAGCACCAACATCATGCAT
Seq A exon
GTGAGTCCCCAGAACCCATGTGCCCAGCTAGAGTCTGGGGAGGGGTGGGTAAGGGACTTCAGACAGATCTAGTCCACAGTACTGGCTCTGAAGGATCATGGTGGCCCATTGCAGTTTTCCCCCAGACTTGATTCCCCATGTGTGATTTAGTATTAAAACGTTACTCTGTGTTCATGATGATACCATGGAGTCGTGGCCCCTTACTTGGAGGGTGCTCAGGTGTTCCTTTTTGATGGCCTAAAAACTGAACACAGACATGACTTGGCAGTTCCAAACACTGGTTGTTTCTTCTGGACAAAGTCTAGGTCATTGATATTTTATGATCAGTGTGGATCAGGTGTGGGCAGCTCGGCTGATTCTGGCTCAGTTCTCTCATGTTTGAAGCTTGCAAACATCAAGATAATTTAGACTGGATTTGGCAGAGACACTCAGTAAGCGTTCCCATGGTTCTTTTCCCTTATGAGGCACCCAAGGCTTGTGGCACAGAGTTCCACTGGAATGAGAGAAGCAGGATACGACGTAAAACTTAGATTTAATTGAGATGGTAGCTTCATCATCTCATTAGTTTTTGTAAGTTAAATCATATGCCAAACACAAAATTAAAAGTGGGTCAAAATCTAACTGACATTGCTGGAAATTCACACTGTACTAGATGTAGCTGAATAAGAACTGGGATGAGGGTCCCAGAGTGACTCCTTATTGTAAACTGATATGTTAGCTTGTTTATTGGTTATGGATTCTTCTAGAACATACCAGATCCTTGAGTCAGATGGAAAAGCCAGACATTTACTCAATGTGCAGCAAGCAGCATGTCCATCACTCCAGCTGTTATCCTTTCTTCAAGGTACTCACAGTCTGTGAGAGCAGTATGAGTGGGCTGGAGTAGGGGCACCTCATGACCTAATCATAATGTAATAATATGACTGAGTCTTAGGGAATCTGCTTCTATAACAAGCAGAATTTAGTCTTATTTTCACTCATGGAGTCATTACTGTGTCCACAGTTTTCTGCCATAATATCTGAGATAAGCCAAGTTAAGACCATCATGATAGTTCATTGTTGGCATGTCTAACAAAGTTTCTCAAGGAACAATGCAAGTCTAACATCCTCAGCAAAAGGAGGGTCTTGAAATCAATTTACAGAAGTGATAATGAGAAGGACACTGTGTGTTCAGTGCTTGTCACAGGCTAGACCTGATGTGAAGTCCTGGTTCAATAATCTATGCTGACCAATTTCCTTATGCCCGTGAGGTACAGTGATTACCTTTTCCTCATTAGTGATAAATCTGAGGGTCAAACATATCAGAGACCTTGTTCACATTATCCTGCAGGAAGTGAGCTAAAAATGGTGCACATGGGGTTCCTCTTAGTTTAGCAGACTAAGATCAGACCAACTTCCTAAAGGTATGACAGGCAAGAACTAGAAGAAGGCAAATAACTGACTGAGGGAGCACAGAACATGGGAATCAGGACGTCTGACCCAGTCTCGGGTCTTCATCTGCTACGGAAGCTGCTTCCAGTTTGGGTTATCCCTGAGGTCAGCTATCTAGGGCTGAGATCCAGAAGGCTGGTTTGAGGTTGTCCATTTGAGTGGTTGGGATTGGGCAGAGCCTCAGGGAGCCAAGATTCAAAACCTCTCTCCCTTTCCCTCTCCCTCTCCCCCTCCCCCTCCCCCCCTCTCCCTCTCTCAAAG
Seq C2 exon
GCCAAGTGGCTGCGCCTGGCCTCAGGGGGTAGCACCCGTCTGAACATGTTTGAGAACATCAGCCTCATGACCTTGGACACTTTGCAGAAATGCGTCTTCAGCTTCAACAGCAACTGTCAGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000090700:ENSMUST00000165061:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006717=p450=FE(33.1=100)
A:
NA
C2:
PF0006717=p450=FE(8.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATGGGCTCTTGGTGAGTGC
R:
TCCTGACAGTTGCTGTTGAAG
Band lengths:
248-1940
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