HsaINT0119375 @ hg19
Intron Retention
Gene
ENSG00000178467 | P4HTM
Description
prolyl 4-hydroxylase, transmembrane (endoplasmic reticulum) [Source:HGNC Symbol;Acc:28858]
Coordinates
chr3:49043210-49043620:+
Coord C1 exon
chr3:49043210-49043300
Coord A exon
chr3:49043301-49043496
Coord C2 exon
chr3:49043497-49043620
Length
196 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGG
5' ss Score
9.33
3' ss Seq
CACCACCCTGCTGCCCACAGAGT
3' ss Score
7.8
Exon sequences
Seq C1 exon
CTACATGACAGTGCTGTTTTATTTGAACAACGTCACTGGTGGGGGCGAGACTGTTTTCCCTGTAGCAGATAACAGAACCTACGATGAAATG
Seq A exon
GTAAGGGTCAACTGGGCTATTACTCTTGTGGGCTGGCAGGGGCTTAGACAAGTGAAGTACACACCTCTCCAGGTCTAAGGATGTGGGCCCAAATTATTCCTTGGGCATATCTGGTTGGTTTCCCTTTGGTCACCCTTGGCTGGCCTGGCCATAGAGTGGGGACAGGTTGAACACCCCACCACCCTGCTGCCCACAG
Seq C2 exon
AGTCTGATTCAGGATGACGTGGACCTCCGTGACACACGGAGGCACTGTGACAAGGGAAACCTGCGTGTCAAGCCCCAACAGGGCACAGCAGTCTTCTGGTACAACTACCTGCCTGATGGGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000178467-P4HTM:NM_177939:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.010 A=NA C2=0.159
Domain overlap (PFAM):
C1:
PF136401=2OG-FeII_Oxy_3=FE(20.5=100)
A:
NA
C2:
PF136401=2OG-FeII_Oxy_3=FE(38.7=100)
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:
TACATGACAGTGCTGTTTTATTTGA
R:
CCCATCAGGCAGGTAGTTGTAC
Band lengths:
210-406
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)