HsaINT0119374 @ hg19
Intron Retention
Gene
ENSG00000178467 | P4HTM
Description
prolyl 4-hydroxylase, transmembrane (endoplasmic reticulum) [Source:HGNC Symbol;Acc:28858]
Coordinates
chr3:49041531-49042479:+
Coord C1 exon
chr3:49041531-49041693
Coord A exon
chr3:49041694-49042293
Coord C2 exon
chr3:49042294-49042479
Length
600 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
AAATGCCTGCTGCCCACCAGGGT
3' ss Score
4.8
Exon sequences
Seq C1 exon
GAGTGCTGAGTCTGCAGGAGTTCTCCAACATGGACCTTCGGGACTTCCACAAGTACATGAGGAGCCACAAGGCAGAGTCCAGTGAGCTGGTGCGGAACAGCCACCATACCTGGCTCTACCAGGGTGAGGGTGCCCACCACATCATGCGTGCCATCCGCCAGAG
Seq A exon
GTGAGCACCTGAAGCTGTTCTCACTGGAGCAGGGGGAGAAGACTGGGCAGGGCCTCCACAGAAGTCCTTGTCTGGGGCCAAGAGGACAGAATGGATTAACCCATTTGGGATTAAGTTCCATTTGTTAGACCAGGATTGGGACCCACTGAAAGACAGGCAATTAACAAAGGCAAATTAGCCCTCCTTGCAGGCACACAATGGGCAACTGGGGTTAGATAGAGATTGAGCACTTCTTTCTGATTAGATAAATGACCTCTTATCTTTGACCCCTTATCTGACCCCGTCACAGCAGGAAAAGGGTTTTTAAATAAACAACTTTCTTCCAGGGAGGAGGACCTCAGGACTCCCCGCCCCCTTTATTTAGTGGAAATGTCAACATTTCCACATAGCAGGTGTCTCTGTCTTTGGCATCTGAGGGAGAAGGATCATCATGAGTAACCCCCTCCTGCTCTTACAGGGCCAGTCTGAGATGGCTTAAGGGACTTCCAGGGGAGGTGGGTAGGGGCAAAGCTTGTGGCAGGCCTAGGGTCCACCTTGGCCAGCTCCTTCAGATCACCACCTTGCCTGGGGCTGCCCAGCCAAATGCCTGCTGCCCACCAG
Seq C2 exon
GGTGCTGCGCCTCACTCGCCTGTCGCCTGAGATCGTGGAGCTCAGCGAGCCGCTGCAGGTTGTTCGATATGGTGAGGGGGGCCACTACCATGCCCACGTGGACAGTGGGCCTGTGTACCCAGAGACCATCTGCTCCCATACCAAGCTGGTAGCCAACGAGTCTGTACCCTTCGAGACCTCCTGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000178467-P4HTM:NM_177939:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.020 A=NA C2=0.044
Domain overlap (PFAM):
C1:
PF134991=EF-hand_7=PD(14.7=20.0)
A:
NA
C2:
PF136401=2OG-FeII_Oxy_3=PU(30.1=69.8)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGCTGAGTCTGCAGGAGTTC
R:
CAGGAGGTCTCGAAGGGTACA
Band lengths:
344-944
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)