HsaINT0123886 @ hg19
Intron Retention
Gene
ENSG00000109118 | PHF12
Description
PHD finger protein 12 [Source:HGNC Symbol;Acc:20816]
Coordinates
chr17:27277083-27278508:-
Coord C1 exon
chr17:27277913-27278508
Coord A exon
chr17:27277265-27277912
Coord C2 exon
chr17:27277083-27277264
Length
648 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGA
5' ss Score
10.06
3' ss Seq
CCGTTTGTATGTGTGTGCAGCAA
3' ss Score
7.58
Exon sequences
Seq C1 exon
CGGGTGGCTTTGCGGGCGCTCGCGGTAAGTTTGCGCCAAGTGCGCGGCAGCCGGGACGCAGACGGCGGCGGCGGCGAGAGGCGGAGCCCGGGGACCACCCCCCATCACCCTCCCCCCAGTCACCTCACGTACCACAACCTCACGTAACCTCTCACCCCCCCTCCGATACCCCCAGCCCCGGGATGGCAGCGCCCGCCAGCCTTCCCGGCCGGACCGGCTGTCGCCAGTGCCGGCTTTAGCCTGTGGGACTAGGCCCCGCCGAGGCCTGACCCCCGGAGCCGGGACCCACTGTGCAGCCAGCAGCCGGGCCGGGACTGAGGGGCCGCTCCCCCCTCGCGGCCCGTCGGGAGGACGCTGTCGTCCCGGGGACTGGGGGCCGGGGGGTGGGGGGGAGCCAGGGCGAGGAAGTCGGGACCCGTATTGGGAAAAAAGCGGGGCCGGGGTCAGGAGCGCCCCCTCCCCTCACCTCCCCCCTCCCCCCGGGGTTGGGGGGGCCGGAGCAGAGAGCACCCAGCCCGGGAGGTGGATGAATGTGGGAGAAAATGGAGACCAAGACGATCGTGTACGACTTGGACACATCAGGGGGGCTGATGGAG
Seq A exon
GTAAGAGTGGCCCTCCTCATCTCCTTCCTCCAGCGCCGGGAGGGAACCTCCGCCCTCCGCCCCACAAAGCCAGTCCTAAACTCGAAGCGCCTAGATGGCCGAGGGAGGGGGATTCTTCCTCACCTAGCCTCTCCCTCCCCTCTTTGCAATTTAGGGGGCTGAGCTCAGCCTCCGAGGACGTTTGCAGCAGTTTCACCTACCCGCCGCCCTCGATTCGCTCTCCCGAGGCGCCAGCCCACTCCATCTCGTTGCACCGGCAGGCCTCCCCACCCCCTTCTTGTTGGCCCCTTTGTGCTTCCCCCAGCACGTCCGGGTACCGGGCTTTGGGCCTCTCCCGAGCGGGTCTTTGGAGTCCCCCACTGTCCATACAAGGAAGTGGCAAGAAGGGAACCGCGCACCCTCTTCCCATCCCCCTACCCTTGATCCTCCCCATTTGGAAGAAGCTGTTCTCGTTGTTGTGCTGCAGGAACGCGGTTAGGGTGGGCTCCCCCTGGTTCCGGGGGCTGAGAGATTCTGGGAGCAGCCTGGATGGGAGGAAGAAGGACAAAAGGGGGGAGAGGGGTGGGTGACGGAGAAACCGCGCCGGGGGGGCGACGGACCGCCCGGGAGCTCCGAGTGTGCACACACGCCGTTTGTATGTGTGTGCAG
Seq C2 exon
CAAATCCAAGCTCTGCTGGCTCCCCCCAAGACGGACGAGGCAGAAAAGCGCAGTCGGAAGCCTGAGAAGGAGCCCCGGAGAAGCGGCAGGGCCACCAACCACGACAGCTGCGATAGCTGCAAGGAAGGTGGAGATCTCCTGTGCTGCGACCACTGCCCGGCTGCCTTCCACCTCCAGTGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000109118-PHF12:NM_020889:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.049 A=NA C2=0.567
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF137711=zf-HC5HC2H=PU(95.2=96.7),PF144461=Prok-RING_1=PU(91.2=50.8)
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:
GAGCCGGGACCCACTGTG
R:
GAGCCAGCAGAGCTTGGATTT
Band lengths:
343-991
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)