HsaINT0128294 @ hg19
Intron Retention
Gene
ENSG00000165688 | PMPCA
Description
peptidase (mitochondrial processing) alpha [Source:HGNC Symbol;Acc:18667]
Coordinates
chr9:139309005-139310843:+
Coord C1 exon
chr9:139309005-139309099
Coord A exon
chr9:139309100-139310742
Coord C2 exon
chr9:139310743-139310843
Length
1643 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGG
5' ss Score
6.34
3' ss Seq
GCCTTTGGGTTCTCTTGCAGATG
3' ss Score
11.71
Exon sequences
Seq C1 exon
AGACACCACCATGTATGCTGTGTCTGCTGATAGCAAAGGCTTGGACACGGTGGTTGCCTTACTGGCTGATGTGGTTCTGCAGCCCCGGCTAACAG
Seq A exon
GTGTGGATCCCAGCCGCTGGCGTTTGAGGTGGGCTTGGACATAGGGAAGACCGGAAAGGTTTGCAGAAGCCCTGTAGCCATGAGGGAGAGCACCATGTAATTGGAGCTTTAGGCCAACACAAAGTGACAGCGAGATCTCATAAGAAATAGCGCTGGGGCTGGGCATGGTGGCTCACACCTGGAATCCCAGGACTTTGGGAGGCTCAGGCAGGCAAATCGCTTGAGCCCAGGAGTTTGAGACCAGCCTGGGCAACATGGTGAAACCCTGTCTCTACAAAAAAGATACAAGAATTAGCTGGCTGTGGTTGCTTACACTTAGAGTCCTAGCTACTCGGGAGGCTGAGGTAGGAAGATCGTTTGAGCCTGGGAGGTTGAGGCTGCAGTGAGCCATGATTGTGCCACTGCCCTCCAGCCTGGGCAACAGAGTGAGGCTTTGTCTCAAAAAAAGAAAGAAAGGAAAAAGAAATAGTGCTAGTAGCCAGGCGTGCTGGCTCACGCCTGTAATCCCGGCATTTAGGGATGTAGAGATGGGAGGATCACTTCAGCCCAGGAGTTCGAGACCAGTCTGAGCAACATAGCAAGACTCTGTTCTCCACAAAAAGGAAAAAAAACCCACTGGTGATTGTAAAAGTCCTTAGTGTTTGAGAGAATGTGTATTTGAGACATCTGTGCCCTCATCCCTGTGGGATGTTTTTAGCGAAATTGGTTCTTTGATTTCGGAAGGGCACCTCGGACCGTCTTTAAACAAGTGGAATGGTGTGTGCCAGAAATTTCCATTTCACTGTTTCCATTACCCTCCTCAGCCTTGCAGATGGCAGGACTTTGAGTCCCTGTCAGGGGTGGACCAGGAGAGGGGAACGTTGGCTTTTCCAGATACCCTAAGGGTGCAGTTTCACAGCAGCTTGCGCTTGGTGTTCAAAGGCTACAGTCCCACGTTAAGATCTTGTGGTCACAACTGATGAAAGGCGCCCTTGACATCTGTCTGTGCCTCTGTTTCTTTTTGGAGATAGAGTCTGTCTCTGTCACCCAGGCTGGAATGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCACCTCCCAGGTTCAAGTGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGCGCCCGCCACCGCGCCCAGTTAATTTTTGTATTTTTAGTAGAGATGGGGTTTCACAGTGCTGGCCAGGCTGGTCTTGAACTCCTGACCTCAGGTGATCCACCCACCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCACCCAGCGTGTGCCTCTGTTTCTAAGCACCTTCATGTCTGGTCTCGTGTCCTCACAGCAGCACTTGGGACAGACAGGTCCAGTGTCTTCGGTGCCTTTCACCAGCAAGGAAGCCAGGGCTTAGCAGGCTCACGTGGCTGCTTCATGGCTGAGGCGGGATGTGAGGCCCAGGTCCCCTAGCTCCTGCTCCCTGTAGCAGTCCCCCTCACTCACACAAGCACCCAGTCTGCCCCTAGATGAAGGCAGAGGTGACTGCCAACAGCCACCAACAGGCGACACTCAGGCCAGCACACAAGCTGTGGGTCACTGCTGTGTTCCTCATCTCTGCCTGTGCAGACTCAGCCCTGGCCTTTGGGTTCTCTTGCAG
Seq C2 exon
ATGAAGAAGTCGAGATGACGCGGATGGCGGTCCAGTTTGAGCTGGAGGACCTGAACCTGCGGCCTGACCCAGAGCCACTTCTCACCGAGATGATTCATGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165688-PMPCA:NM_015160:5
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.115
Domain overlap (PFAM):
C1:
PF0067515=Peptidase_M16=FE(21.2=100)
A:
NA
C2:
PF0067515=Peptidase_M16=FE(21.9=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:
AGACACCACCATGTATGCTGTG
R:
AATCATCTCGGTGAGAAGTGGC
Band lengths:
190-1833
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)