HsaINT0123885 @ hg19
Intron Retention
Gene
ENSG00000109118 | PHF12
Description
PHD finger protein 12 [Source:HGNC Symbol;Acc:20816]
Coordinates
chr17:27232271-27234012:-
Coord C1 exon
chr17:27233874-27234012
Coord A exon
chr17:27233536-27233873
Coord C2 exon
chr17:27232271-27233535
Length
338 bp
Sequences
Splice sites
5' ss Seq
TCAGTAAGT
5' ss Score
9.14
3' ss Seq
ACCATCCCCCTTTTTCCCAGGGC
3' ss Score
9.13
Exon sequences
Seq C1 exon
AATACCAAACATTATGAGCTGTTAAACTACAGTGAGCATGGGACAACGGTGGACAATGTGCTGTATTCATGTGACTTCTCGGAGAAGACCCCGCCAACCCCCCCAAGCAGTATTGTTGCCAAAGTGCAGAGTGTCATCA
Seq A exon
GTAAGTTGGAGCAGAGATCTGTGGCCACAAAGCTGAGGCCCCAGTCAGGGTGGTTCTGACTTGCTGCCCATGGTCTGTCTCTTGCCTTCCCAGTCCTATTGGCCAAGCTCTACTTCCTCGTGGGCCCAGGGCAGGCCACAGAGAAGCAAGTGCTGAGTACCCCCATGTGTGTACACACCTGTGGGGACTTCAGACTCCACCAACCCTTTCTGAGCATCCTTCCTCCCTAGTCATGCAGCAGTTGGAATGGGGAGATGCAGGAGCCCAACCTTGGCAAACAGCCCACATGGGTTGGCTGCTCACTGTTCCTCTTCTGTGACCATCCCCCTTTTTCCCAG
Seq C2 exon
GGCGCCGCCGGCACCAGAAACAGGACGAAGAGCCAAGTGAGGAGGCAGCCATGATGAGTTCCCAGGCCCAGGGGCCGCAGCGGAGACCCTGCAATTGCAAAGCCAGCAGCTCGAGCTTGATTGGGGGCAGTGGGGCCGGCTGGGAGGGCACAGCCTTACTGCACCATGGCAGCTACATCAAGCTGGGCTGCCTGCAGTTTGTCTTCAGCATCACTGAGTTTGCGACCAAACAGCCCAAAGGCGATGCCAGCCTGCTGCAGGATGGGGTCTTGGCCGAGAAGCTCTCTCTCAAGCCCCACCAGGGCCCTGTGCTGCGCTCCAACTCTGTTCCTTAGGACTGGCGGCTACCCCGCCACTGGCCTGTACACCCACCCAAGACTCCTGCAATGCAAAAATGTACACAAACCAAGCCCGGGTGTTTTCTATACTCTACCAGAAACCCTTCAACTACAATCTTTGCATGAAATGAAGAAAACCTTTTGACTGTTTTTTAAAAATCCTTTTTCTTTTCTCAAGTTCTAGGGGGCATTTGCACATATATTTGTACTCAACATTTCATGGGAAAGCGGCAGACCTGAGCTGAGGAACAGCGTGGGCAGGGAGGGAAAGACCCAGGGTCTGGACACTTCCTCCAACACAAAACCCTTCCCCACCCACCTCCTGCTCCCTCCCCCTCGCCCACCATTGTAAAATAATCAGAAACTTGTTCTATTTTGTGGCAGTGACAATAGTTTTATATTAAAAGAAAAAATACAGTTTTCATACAGCAAAATCTATACAATATCATTGTTTTATTTAATATAAAGATCGCTACCCACCTTCCTTCCATGGTTCCCACCCTCCACGTTATTTTCCCTTTCTGCAGCGGTTGCACTACAGGTAGCTACTGTGTATTATGGACAAATGAGAAATGAATTCTTTTTCTGGCTGTCCATCTATTTTATTTCAAATAAGGAAAAGTGTATTTGGATTTTGTGTAAATACATCTAGTGATGACATTTTTTCAATGTTTTTAAAAACCGTGTACAGTACTACATGTGGTAGAGCGTTTTCTCAAATTGTCTATTGTAGCAAAAATGTTTTTGTCGTAAACCTGTTTTGTCTCCTTTTTTTGTTCTCTTGCCACTTCTCTCCTCTTCCTCCTGCCCCTGGTTCCCTCCTCTCCTCCCACCCCCACAACCAGTACCAATGTACATAGTAATTGTAATGTTTTAGACTTTACAGAAACTTTCCTGTATTCTGTATATAAAAAACAAAAATACTTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000109118-PHF12:NM_001033561:14
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.170 A=NA C2=0.351
Domain overlap (PFAM):
C1:
PF0049821=FHA=PD(47.7=66.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGCCAAAGTGCAGAGTGTCA
R:
TAAGGAACAGAGTTGGAGCGC
Band lengths:
358-696
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)