HsaINT0128287 @ hg19
Intron Retention
Gene
ENSG00000165688 | PMPCA
Description
peptidase (mitochondrial processing) alpha [Source:HGNC Symbol;Acc:18667]
Coordinates
chr9:139305116-139306651:+
Coord C1 exon
chr9:139305116-139305191
Coord A exon
chr9:139305192-139306448
Coord C2 exon
chr9:139306449-139306651
Length
1257 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
GGCCGCTTTCTCTGTTTTAGGTT
3' ss Score
12.76
Exon sequences
Seq C1 exon
GCAAGATGGCGGCTGTGGTGCTGGCGGCGACGCGGTTGCTGCGGGGCTCGGGTTCTTGGGGCTGTTCGCGGCTGAG
Seq A exon
GTGAGCCAAAGGCGAACCAGGCTTCGGCCTGGGGCGGGGGCGGCTCGAGTCTTTCTGGACGCTCCGTCTTCGGTTTCTACAGGTGACATGGCGCCCGTGGGACGGGCTCGCACTTCGGGACACTGGTGTCCCCGAGGCGACGGGGGCCCTGCCTTGCTTTGCGCCTCGAGCCCGGGGACGCAGTCCCATCTGTCTCTCCTCTCCCCGGCTGCTGGGTCCTCTCCCCCCCTCACTTCCCGGGTCGACGGGCCTTCTCCGAGGCCATGCCTCATATTTGCCCCCGCGCTTCACCTACCGCGTGCTCCTTCAGGAGGCTGAGCCGGTGGGGGCCCAGCTCTGTTAGACCCGCAGGGTTCTGACACCAGGGTCCAGGCTCTCGGTTGCTGCGGTCTGTCCGTTGATCTCTGACGTTTAAGAACCCTTTCCGTACCCACCGCTCCTCCCACCCAAGTGACCGGGCCTGCCTTTCCCCACGCTGGAACTTTGTTCCGACAGCACAGGCGTCGCCCCTCCCCACACAACGAGCGCCGTTTCAGGGGTGCGGAGGTGCTGCCTCCAGGAGATGGATACAGGCTGGAGCGTAAACAAAATATCGGCAGTCGCGTAAATGCTTTGGAGTAAACAAGCAGCCTTTCATGATAGAAAATAGCAGGAAAGACTAGACTGGTGAGGGATAGTCCTCCATCAGGGTGACATTTAAGGGAAGAGCTGAAGAATGAAAGAAGGGGTAGGCATGGGCAAAGGGCAAGCCCTGGAACGGTGAAGAAGCTTTGGGGTTGATGAGTCAAATGTGTTCCAGGAATTGACAAGAATCAGTGTGACCAGGACCTATGGGAGTGTGGGGGTTCAAGAGATGAGTTTGGAGAGGGAGACAGAGGCCAAGTCACACCCCGCCTTCGGACCAGGTTAATAAGGGATATGGCTTTTATCCAAGACTTCGGTGGTGCTGTTGGAGGGCAGAGCTGTTAAGTGCTTTATGTGTACAAACTGCACTTAGAGTGAGTTACTGTTAATAAGCCCTGTTTTTACAGAGATAGCAACTAAGACCCAAAGGACGGAACCAGCTTGCTCCAGGTCCCGTGGCTGAGCCTTTGTTGTCAGCCTCTGCTTTGTCTTCCAAAGTCTGTAGAAATAAGTCCTGTAGAAAGGCAGATGCTCACTTTTAACCCAGACAAAACATAACTAACCGCACCTAACAGGTCATCACAGGTTTGTTGTCTCAAGCCTGTTGTAACTGGGCCGCTTTCTCTGTTTTAG
Seq C2 exon
GTTTGGACCTCCTGCGTACAGACGGTTTAGTAGTGGTGGTGCCTATCCCAACATCCCCCTCTCTTCTCCCTTACCTGGAGTACCCAAGCCTGTTTTTGCTACAGTTGATGGACAGGAAAAGTTTGAAACCAAAGTAACCACATTGGATAATGGGCTTCGCGTGGCATCTCAGAATAAGTTTGGACAGTTTTGTACAGTAGGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165688-PMPCA:NM_015160:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0067515=Peptidase_M16=PU(21.4=21.7)
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:
CAAGATGGCGGCTGTGGTG
R:
TTCCTACTGTACAAAACTGTCCA
Band lengths:
278-1535
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)