MmuINT0122936 @ mm9
Intron Retention
Gene
ENSMUSG00000026926 | Pmpca
Description
peptidase (mitochondrial processing) alpha [Source:MGI Symbol;Acc:MGI:1918568]
Coordinates
chr2:26249038-26250689:+
Coord C1 exon
chr2:26249038-26249100
Coord A exon
chr2:26249101-26250544
Coord C2 exon
chr2:26250545-26250689
Length
1444 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGG
5' ss Score
8.92
3' ss Seq
TTGCGGTGTTTGGTCCTCAGGTG
3' ss Score
9.76
Exon sequences
Seq C1 exon
GTTCGAGAAATGGTAGAAATCATCACAAAGGAGTTTATCTTGATGGGCAGGACGGTGGATTTG
Seq A exon
GTAAGGCCTGGAGCATCCTGTGCACCTGATGTAGCAAGTCACTCGGCTGAAAGAGCCACAGGCTGAGCCTCCCTAGTGCCTCCCCGAGGGCAGTGTCCCTCTCTTGAGTTGTTCCTACAGAATGGCCATGCGCTAAAGCATCATTGTACAAGACAGACAATAATGCGGGGATTTTTCCCAGGCCTTTCTTGGCTCCATTTTATGTTGGAACCCAAGTTTGTGTTGACTTTTTTTTTGGAAATGAAGTTTCTATGTTGTGGGCTGTCTGTCTGTCCTGGAACTTGCTCTGTAGACCAGGCTGGTCTTGAACTCAGAGCCACCTGATTGGCTTCCCAACTACTGGGATTAAAGGTATACACTACCACTGCCTGGCTGTCTTTTAGTTAATGTTTGGAAATTTTGTTACTTCCTGGGCCAGAGCTTATAAAAGCAAGGTGATTTCCTTGAGCATGCATTTTTGTCTTTCAGCATAGTGCAAGTTTTCTTCAGTGGTCAGATACCACATCCTGGCTTTTTAAGGAGGAAAAGGCAACATTATTGAAAAAATAAAAATCTGCTTAAAAATGAAAACTACTGCAAAGCAAAGCAATTAATGCATATGCATGTCTCTGACCTCAGCTCTCAGGAAGGAGAGGTAGGAGGTGATGAGTTCAAGGTCAGCCTAAAGTAATGTGTAATAAGACTGACTGGGTCTGGGAGTATGGCTCAGTGGTAGAGAGCTTACTAAGTATGCTCAAGACCCTGGGGTTCACCCCCAGCACAGCCAAAATTAATGCTCTATATTTCCACTAATATCTTGATAAAATACTTTCCACTAAAGTCAGATCTGTTGAGATAAATGTACAGTATTAAGTGTCTGCCTGAAATCGCATAAGTCTTAAATAACTTGTGTTAAGACAAAGACTCATGAGATAGCCAAGCTGGCCTCAAGCTTACAGTCCTCTTGCCCTGCCTCCTCCTGAGAGCTTGCGTACAGGCGAGCGCCCACACACCCAGCTTGCTCTGTCCCTTGTGGTCCTGATTCTTTGGTGCTACATTTGAGGTTCACACCTGGCCAGAGGCTCAATGTTGATTCTGCTGCCTCCTTGGTAGCACCAGGTGATAGTAGCCTGGGTCCTCTGTTTAGGACACTGACCACCAGAATCTTTGCTTCATCAACAACTTCGGGTTGCCCGTGCAGCCAGGCGTGGCTTCCTGATGCATGTTGCTCTCCTGTGATCCAGACAAGCAGCAGAGATTGGACATGTGTTTCTGTCCCGGTGTGATGAAGGCTTTTCCAATGTAGTTCCTCCCATGCTCGGAGTGTGCCAGACTGGAAACCAGACTGGGACAGCCCCTCCACTCTACTCATCTTTGGGCACATGGAGATTTCTTTGCTGAGACATGTTTGGGTCAGCCCCTCTTGAGCCAGCTGTCGAGGTGACTTGCGGTGTTTGGTCCTCAG
Seq C2 exon
GTGGAGCTAGAGCGGGCCAAGACACAGCTCATGTCCATGCTCATGATGAACCTGGAGTCCAGGCCTGTGATTTTTGAGGATGTGGGGAGGCAGGTGTTGGCTACACATTCAAGAAAGCTGCCCCACGAGCTATGTACACTCATTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026926-Pmpca:NM_173180:11
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.067 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0519316=Peptidase_M16_C=PD(10.5=46.5)
A:
NA
C2:
PF0519316=Peptidase_M16_C=PD(4.5=18.4)
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:
TCGAGAAATGGTAGAAATCATCACA
R:
GAATGAGTGTACATAGCTCGTGGG
Band lengths:
206-1650
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: