Human Gene PCIF1 (uc002xqs.3) Description and Page Index
  Description: Homo sapiens PDX1 C-terminal inhibiting factor 1 (PCIF1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr20:44,563,317-44,576,662 Size: 13,346 Total Exon Count: 17 Strand: +
Coding Region
   Position: hg19 chr20:44,567,639-44,576,394 Size: 8,756 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:44,563,317-44,576,662)mRNA (may differ from genome)Protein (704 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: PCIF1_HUMAN
DESCRIPTION: RecName: Full=Phosphorylated CTD-interacting factor 1;
FUNCTION: May play a role in transcription elongation or in coupling transcription to pre-mRNA processing through its association with the phosphorylated C-terminal domain (CTD) of RNAPII largest subunit.
SUBUNIT: Interacts with the phosphorylated C-terminal domain (CTD) of RNAPII largest subunit.
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Ubiquitous.
DOMAIN: The WW domain is sufficient for direct and specific interaction with the phosphorylated CTD of RNAPII largest subunit.
SIMILARITY: Contains 1 WW domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PCIF1
CDC HuGE Published Literature: PCIF1
Positive Disease Associations: Cholesterol, HDL , Triglycerides
Related Studies:
  1. Cholesterol, HDL
    Sekar Kathiresan et al. Nature genetics 2009, Common variants at 30 loci contribute to polygenic dyslipidemia., Nature genetics. [PubMed 19060906]
  2. Triglycerides
    Sekar Kathiresan et al. Nature genetics 2009, Common variants at 30 loci contribute to polygenic dyslipidemia., Nature genetics. [PubMed 19060906]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 35.08 RPKM in Uterus
Total median expression: 1020.01 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -149.24314-0.475 Picture PostScript Text
3' UTR -87.72268-0.327 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR022035 - PCIF1_WW
IPR001202 - WW_Rsp5_WWP

Pfam Domains:
PF00397 - WW domain
PF12237 - Phosphorylated CTD interacting factor 1 WW domain

SCOP Domains:
51045 - WW domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help

2JX8
- NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q9H4Z3
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserNo orthologNo ortholog
Gene Details  Gene Details  
Gene Sorter  Gene Sorter  
  EnsemblFlyBase  
  Protein SequenceProtein Sequence  
  AlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0010923 negative regulation of phosphatase activity

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0015630 microtubule cytoskeleton
GO:0045171 intercellular bridge


-  Descriptions from all associated GenBank mRNAs
  AK299435 - Homo sapiens cDNA FLJ61655 complete cds, highly similar to Phosphorylated CTD-interacting factor 1.
AB050014 - Homo sapiens mRNA for posphorylated CTD interacting factor PCIF1, complete cds.
AK056553 - Homo sapiens cDNA FLJ31991 fis, clone NT2RP7009097.
BC010005 - Homo sapiens PDX1 C-terminal inhibiting factor 1, mRNA (cDNA clone MGC:15106 IMAGE:4131938), complete cds.
BC013365 - Homo sapiens PDX1 C-terminal inhibiting factor 1, mRNA (cDNA clone MGC:16205 IMAGE:3640928), complete cds.
JD207312 - Sequence 188336 from Patent EP1572962.
JD462108 - Sequence 443132 from Patent EP1572962.
JD129668 - Sequence 110692 from Patent EP1572962.
JD278435 - Sequence 259459 from Patent EP1572962.
JD143127 - Sequence 124151 from Patent EP1572962.
JD166959 - Sequence 147983 from Patent EP1572962.
JD409839 - Sequence 390863 from Patent EP1572962.
JD136987 - Sequence 118011 from Patent EP1572962.
EU832663 - Synthetic construct Homo sapiens clone HAIB:100067692; DKFZo008G0431 chromosome 20 open reading frame 67 protein (C20orf67) gene, encodes complete protein.
AB385560 - Synthetic construct DNA, clone: pF1KB8004, Homo sapiens C20orf67 gene for phosphorylated CTD-interacting factor 1, complete cds, without stop codon, in Flexi system.
EU832741 - Synthetic construct Homo sapiens clone HAIB:100067770; DKFZo004G0432 chromosome 20 open reading frame 67 protein (C20orf67) gene, encodes complete protein.
AL137473 - Homo sapiens mRNA; cDNA DKFZp434E1723 (from clone DKFZp434E1723).
JD174262 - Sequence 155286 from Patent EP1572962.
JD357314 - Sequence 338338 from Patent EP1572962.
JD500841 - Sequence 481865 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: C20orf67, E1P5P1, NM_022104, NP_071387, PCIF1_HUMAN, Q54AB9, Q9H4Z3, Q9NT85
UCSC ID: uc002xqs.3
RefSeq Accession: NM_022104
Protein: Q9H4Z3 (aka PCIF1_HUMAN or PCF1_HUMAN)
CCDS: CCDS13388.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_022104.3
exon count: 17CDS single in 3' UTR: no RNA size: 2703
ORF size: 2115CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3993.00frame shift in genome: no % Coverage: 99.78
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.