HsaINT0128292 @ hg19
Intron Retention
Gene
ENSG00000165688 | PMPCA
Description
peptidase (mitochondrial processing) alpha [Source:HGNC Symbol;Acc:18667]
Coordinates
chr9:139306942-139307344:+
Coord C1 exon
chr9:139306942-139307021
Coord A exon
chr9:139307022-139307261
Coord C2 exon
chr9:139307262-139307344
Length
240 bp
Sequences
Splice sites
5' ss Seq
TCGGTCAGT
5' ss Score
7.03
3' ss Seq
TCCTTATTTATTTTTACTAGTCT
3' ss Score
6.21
Exon sequences
Seq C1 exon
TTCTTATCAATTCAGGATCGAGATATGAAGCGAAATACCTTAGTGGAATTGCTCACTTTTTGGAAAAATTGGCATTTTCG
Seq A exon
GTCAGTACCCAGTTTTGTAATTTTTTAGACTATACTTTTGAAGGATGTTTGAGATTTTTCTTGTCTATAATGGTTATTTTAATAAATTATCAAGTTGCTAAGTTAATGTTAATAAAAGACTTTTAAGTTAAAAGATAATTTTTGTATGTGTGTTAAAAGCAAAAGTAGATTTTAAAAAAAAATTGTGTTTCAGGGATAGCCTGGATTGCTTATTTAGGTTTCCTTATTTATTTTTACTAG
Seq C2 exon
TCTACTGCTCGATTTGACAGCAAAGATGAAATTCTGCTTACGTTGGAAAAGCATGGGGGTATCTGTGACTGCCAGACATCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165688-PMPCA:NM_015160:3
Average complexity
IR-S
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=FE(37.1=100),PF109053=DUF2695=PU(10.0=11.1)
A:
NA
C2:
PF0067515=Peptidase_M16=FE(38.6=100),PF109053=DUF2695=PD(83.3=89.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCAATTCAGGATCGAGATATGAAGCG
R:
TTGATGTCTGGCAGTCACAGA
Band lengths:
156-396
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)