HsaINT0123714 @ hg19
Intron Retention
Gene
ENSG00000087157 | PGS1
Description
phosphatidylglycerophosphate synthase 1 [Source:HGNC Symbol;Acc:30029]
Coordinates
chr17:76394333-76395618:+
Coord C1 exon
chr17:76394333-76394432
Coord A exon
chr17:76394433-76395428
Coord C2 exon
chr17:76395429-76395618
Length
996 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGT
5' ss Score
9.65
3' ss Seq
TTTTCTCTGTCCGTGTTCAGGCC
3' ss Score
11.62
Exon sequences
Seq C1 exon
GTGGACTGCCTGGAAAGTACTCTAGAAAAGTCACTCCAAGCAAAGTTTCCTTCAAATCTCAAGGTCTCCATTCTCTTAGACTTCACGCGGGGCTCACGAG
Seq A exon
GTAGGTGGCATGCAAGCCTGGCCCCTCCTGCTTCCTGTGTCAGATCCTCAGTCCCAAGAGGGGTTACTGTCACCCCCTCATCCCCAGGCAGAGTCAAGGCTATTTGAAGATCATCCAAGCTGGCCCAGGGCTGCCTGATTGTGTGAGTTAGGATTTTTTTCTTCAGCAAGTGACTGAAAGCCCAACTAAAAACAGCTTAGGCAGGAGCCGAGTGCAGTGGCATGCCCTGTAGTCCCACTTGCGTGGGAGGCTGAGGTGGGAGGATTGCTTGAGCCAGGAGTTTGAGTCCAGCCTGGGCAACATAGCCAGACTTTGTCTCATGAAAAACTGCCTTAGGCAAAAAGACTTTTTGTGGACTCCTGTGACTGATCTGCTTTGGGTGGCTTGTGATTTGGGGTTTGGCCGTGTCACCAGGATTCATCCCCTAGCTGTTTCCTTTGGGCTGGCTTCCTTCTCAGGCTCTGTGTGGTGGCCCCTGGTGGCTTAGGCTTGTCTCCCCATGACACCTTGTCTTTTGGAAGAGTCTGATTCCATGAGAATCGGGTCAAAGCTCCTGACTGGCCTGACGGTGGCATGCCCAGCTGGGAGCTTGGAGTGTGCCGAGTAGCCCAGCCCAGGCCTGCGTGCTCCCTCATGGAGCTGGGGGTGAGGGGCAAGGTGGGTAGGGTCGTCTTCACCCAGAGCAGAAATGCTGCGAGTGGGTGGGGTAGTGCCCCAGGAGAAGGTTGGGTGCAGTTACCAGGAGAAGGGTGAATGGGTGCTGTGTGGCAAGAAGAGCAGGCGTCTGCCACGCTGAGGACTTCAGGCCTGAGACATGGCCAGCATGCAGGACAGAGGTTGGCCTGGAAGTCCTCTGGCTAGGAGTAGCCCCAGCTGGTGTGACTGATTCAGGTGGACGGCACAGGTGAAGGCGAGGCCACGTGGAGGTGGCTCCTCATTGGGGGCAGGACGCCTTCCTGTTGTGAGTCAGGTGCCGTTTTCTCTGTCCGTGTTCAG
Seq C2 exon
GCCGGAAGAACTCCCGCACAATGCTGCTCCCACTCCTGCGGAGGTTCCCAGAGCAGGTCCGAGTCTCCCTCTTTCACACGCCGCACCTCCGTGGGCTGCTTCGGCTCCTCATCCCTGAGCGCTTCAACGAGACCATCGGCCTCCAGCACATTAAGGTGTACCTCTTCGACAACAGCGTCATCTTGAGCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000087157-PGS1:NM_024419:4
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=0.000
Domain overlap (PFAM):
C1:
PF130911=PLDc_2=PU(23.8=91.2)
A:
NA
C2:
PF130911=PLDc_2=FE(39.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGACTGCCTGGAAAGTACTCT
R:
CGCTCAAGATGACGCTGTTGT
Band lengths:
288-1284
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)