HsaINT0119370 @ hg19
Intron Retention
Gene
ENSG00000178467 | P4HTM
Description
prolyl 4-hydroxylase, transmembrane (endoplasmic reticulum) [Source:HGNC Symbol;Acc:28858]
Coordinates
chr3:49027341-49028347:+
Coord C1 exon
chr3:49027341-49028043
Coord A exon
chr3:49028044-49028265
Coord C2 exon
chr3:49028266-49028347
Length
222 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
GCTGTGCGCCTTTTCCTTAGGTG
3' ss Score
9.66
Exon sequences
Seq C1 exon
AGAGGGCGTCTTCACGCAGGCACCGAGAAGCTCCCACTAGTGTATGCCTTAATGGTGCCGCTCTTGTCCGCGTCTACGCTTGGGACCTTGGCTTCTGACTTGGAGAGTGTACAGCTCTGCCCGACGGCAACCCAGCTTGGGAAGAGAAGCCCCAGCGTGGGCTGGGGCTCAAGGCGCAGGAAGGCCGAGCCCGGCGCGGACGCAGGCGGCTCCGGGCGGGCTCAGCACCCCCAGGCACCGTCTCCTAGTGACCGCGGCGCTCGCGGGCCTGGCGGCCGTTGTCCGGGCGACTGCGCAGCGCGGGCACCCCCGCGGCCCCTCCCCTGGGCGCGCGCGCGACCTGGGTGCCATGGCGGCAGCGGCGGTGACAGGCCAGCGGCCTGAGACCGCGGCGGCCGAGGAGGCCTCGAGGCCGCAGTGGGCGCCGCCAGACCACTGCCAGGCTCAGGCGGCGGCCGGGCTGGGCGACGGCGAGGACGCACCGGTGCGTCCGCTGTGCAAGCCCCGCGGCATCTGCTCGCGCGCCTACTTCCTGGTGCTGATGGTGTTCGTGCACCTGTACCTGGGTAACGTGCTGGCGCTGCTGCTCTTCGTGCACTACAGCAACGGCGACGAAAGCAGCGATCCCGGGCCCCAACACCGTGCCCAGGGCCCCGGGCCCGAGCCCACCTTAGGTCCCCTCACCCGGCTGGAGGGCATCAAG
Seq A exon
GTGAGGACCTCCCTGCCCCGCCGCGCTCCAGGCCCTGCACGGCTGAGCCCGAGAGGACCGGCGCTCAGCCCGGGTCCCCACGCTGCCCCCGGCGCTGCTCTGCGTCGGTCCCGCGCGCTCCCACTCACTCGCCTGCTGTCGCTCTCCGGGCCGGGGCGACTTGGCCCTTCTTGGGCAGCGCGGTCTGGCGCCCCAGCTGCCCGCTGTGCGCCTTTTCCTTAG
Seq C2 exon
GTGGGGCACGAGCGTAAGGTCCAGCTGGTCACCGACAGGGATCACTTCATCCGAACCCTCAGCCTCAAGCCGCTGCTCTTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000178467-P4HTM:NM_177939:1
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=0.537 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGACCACTGCCAGGCTCAG
R:
CGGTGACCAGCTGGACCTTA
Band lengths:
308-530
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)