HsaINT0119373 @ hg19
Intron Retention
Gene
ENSG00000178467 | P4HTM
Description
prolyl 4-hydroxylase, transmembrane (endoplasmic reticulum) [Source:HGNC Symbol;Acc:28858]
Coordinates
chr3:49039933-49041693:+
Coord C1 exon
chr3:49039933-49040029
Coord A exon
chr3:49040030-49041530
Coord C2 exon
chr3:49041531-49041693
Length
1501 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGC
5' ss Score
9.44
3' ss Seq
ATGGTGGGTGCCCTGTGCAGGAG
3' ss Score
6.04
Exon sequences
Seq C1 exon
GTTCTGGCCCAGACTCGCCTGGGAAATGGATGGTGGATGACTCCAGAGAGCATTCAGGAGATGTACGCCGCGATCAAGGCTGACCCTGATGGTGACG
Seq A exon
GTGAGCTCACACCTCTGCACAGTCCTATCCCCGTGAGCCTCCTGCCCACTCCCAGGTGCACAATTTTGAAAACTTGGGCCCTTCCCCCACAGCCAGGCAGCCTCTCTGCACCCCTTTATAGTGGCCAGAGATGGGGAGGTGAAGATCCAGCCTTGCTTTTTACCCCTGGGAAGTAGGCAGGCAGCCAGGCCCCCCGTTCCCCTTGGTGATGGTCTCGAGGGCAGTTCTTGGAGACCCTTTTGATAACATCAGGCAGAGTTGAGAGCCTGGGGACAGGAAGTAGGGCTGCTAGTTGGCAGAGAACAGAGTGGGTGGAGCAGGAGCAAGGCGACAGTGAGGCCAGCTAGAGCTTGGCTGTTTACCCTGCTCCATCCATCTCTCCAGCCAGACACGAGGTCCACCCCAGCAGACAGCTTCCCTGGTCTAAGTGAGATCTCCCTTGCCTTCCTCTTGTCCACCTGGAGTCATGCCGAAGCGCCTAAAATGGTAGTGCTGCTACCTGTGCTAACTGCTGGGGAGGGGTGGGCAGGGAAGCTGTCATGCAAGTGGTGCCCCCTCTGGTAATAACTCTCAGGAGGTTTCTGAGGTGTGGTCATCACCCTCATGCCCAAATTCTGGACCAAGAGAGGAAGATACAGCAGTTAGAAAGGACTTGGAACAGTGGCTTTGCGGCTGGTGAACCAGAGTGAAGAATCTGGCCGTGACCTGTGGCTGGATGGCTGCCACACTGCTATAGGCCCCAGAACAGAGGTGGTGACAGTCTCACAGCCCTTGAATGTCCCCCACCCTCAGAGGAATCTGGGCCAAAGAGTGGAAGGTGATGTCCTTGGGTCAGCCAGAATAACATGGAGCAAAGATACCAACTACTCTTCCAGAACCCCAAGAGGGTAGAACCCCTGCTTAATGGTTTGAGCAGGGACAGTGGAGAATGTTCTCATGAGAGGGGGTGGCCTGACTTTCGTTGCTAAGGTGGGCTGGTAACGCAGTAGGCAGGGCTGGCGAAGTAGGTTCCACCCAGGATGAAACCTGGGGTCATGAGGAACTCCCCGGGGGCTGGCCCTGCTTGCACCCTGGCGTATGTATGTAAGGCCCTGGATGAGGCCCAGCACTGCCTGCTCTCTCCTCACCCTCCACAGGCCGGAGAGTGGCCACCACTCTATATAGCCAGGCTGGAAGGCCAGGGTCCTGGCCATATGGCTCAAGCTTCCTTTGGAGAACCTTCTCTGGCCACTCTAATAGGGGGTGGGCCTCTTTCTTCTTAGGGCCAAATTAGGGCTTAAACTGAGAAAAGGAACTGCTCTGGGTCTTCCTGTAAGGCCTGATGTGACAGAAACCAGGTTCATCTGACCCAAAAGTCCAGGTGGGGGACAAGTGTACAAGGCCCCTCAGTGCCTGAGGTCAGGGGCTGCTGCTGCCTTTGGGGTAGGTAGGGAAGTGCAGCCTGCCACTGTTGCCTCCCAATATGGGCTTGGTGGGCATTGATGGTGGGTGCCCTGTGCAG
Seq C2 exon
GAGTGCTGAGTCTGCAGGAGTTCTCCAACATGGACCTTCGGGACTTCCACAAGTACATGAGGAGCCACAAGGCAGAGTCCAGTGAGCTGGTGCGGAACAGCCACCATACCTGGCTCTACCAGGGTGAGGGTGCCCACCACATCATGCGTGCCATCCGCCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000178467-P4HTM:NM_177939:4
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.042 A=NA C2=0.020
Domain overlap (PFAM):
C1:
PF134991=EF-hand_7=FE(42.7=100)
A:
NA
C2:
PF134991=EF-hand_7=PD(14.7=20.0)
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:
GTTCTGGCCCAGACTCGC
R:
CGGATGGCACGCATGATGT
Band lengths:
254-1755
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)