RnoINT0114293 @ rn6
Intron Retention
Gene
ENSRNOG00000026775 | Pmpca
Description
peptidase, mitochondrial processing alpha subunit [Source:RGD Symbol;Acc:727897]
Coordinates
chr3:3837385-3837969:+
Coord C1 exon
chr3:3837385-3837648
Coord A exon
chr3:3837649-3837876
Coord C2 exon
chr3:3837877-3837969
Length
228 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACT
5' ss Score
9.01
3' ss Seq
ATGTGTCTGGTTGGTTCTAGGTG
3' ss Score
10.42
Exon sequences
Seq C1 exon
GCTGCTTTTAGGGAGAACACGGTGGGCCTGCACCGGTTTTGTCCTGTAGAGAACATAGGGAAGATTGACCGAGAAGTGCTGCATTCCTACCTGAAGAACTACTACACCCCCGACCGCATGGTGCTTGCTGGAGTGGGCGTGGAGCATGAGCACCTGGTCGAATGTGCCAGAAAGTACCTCCTGGGAGTGCAGCCTGCCTGGGGAGCTCCGGGAGCTGTGGATGTTGACAGCTCAGTGGCACAGTACACGGGGGGGATCATCAAG
Seq A exon
GTAACTGGGCAGGAAAACTCTCAGGACTTGTGCCATGTATTCTCTGGGTATGTGCTTTGATGAACATGTTTATACTTCTTAGTGTACAATCCAGCACTTAGCAGTATGAACACATCCCATGTTCAAAGCAAGAGGTGACAGGGCTGAGGTCACCTGGTGTCTGGTTGAGTGTGGCTGTTTTCATACTAGAAGTTTGCTGGCCTTATTGATGTGTCTGGTTGGTTCTAG
Seq C2 exon
GTGGAGAGAGACATGTCAAATGTCAGCCTTGGCCCCACCCCGATTCCAGAGCTCACACATATCATGGTGGGGCTAGAGAGCTGCTCCTTCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000026775:ENSRNOT00000031607:7
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:
PF0067515=Peptidase_M16=PD(9.9=17.0),PF0519316=Peptidase_M16_C=PU(33.5=76.1)
A:
NA
C2:
PF0519316=Peptidase_M16_C=FE(15.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCACCGGTTTTGTCCTGTAG
R:
ATGTGTGAGCTCTGGAATCGG
Band lengths:
296-524
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]