Human Gene PAGR1 (uc002dug.4)
  Description: Homo sapiens PAXIP1 associated glutamate-rich protein 1 (PAGR1), mRNA.
RefSeq Summary (NM_024516): C16ORF53 (PA1) is a component of a Set1-like multiprotein histone methyltransferase complex (Cho et al., 2007 [PubMed 17500065]).[supplied by OMIM, May 2008]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data because no single transcript was available for the full length of the gene. The extent of this transcript is supported by transcript alignments.
Transcript (Including UTRs)
   Position: hg19 chr16:29,827,528-29,833,816 Size: 6,289 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr16:29,827,847-29,831,075 Size: 3,229 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:29,827,528-29,833,816)mRNA (may differ from genome)Protein (254 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
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H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PAGR1_HUMAN
DESCRIPTION: RecName: Full=PAXIP1-associated glutamate-rich protein 1; AltName: Full=PAXIP1-associated protein 1; AltName: Full=PTIP-associated protein 1;
SUBUNIT: Interacts with PAXIP1/PTIP; the interaction is direct and is required for the association with the rest of the PTIP complex. Component of the MLL2/MLL3 complex (also named ASCOM complex), at least composed of MLL2/ALR or MLL3, ASH2L, RBBP5, WDR5, NCOA6, DPY30, KDM6A, PAXIP1/PTIP, PAGR1 and alpha- and beta-tubulin.
INTERACTION: Q6ZW49:PAXIP1; NbExp=5; IntAct=EBI-2372223, EBI-743225;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


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

+  Common Gene Haplotype Alleles
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+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -165.70319-0.519 Picture PostScript Text
3' UTR -1088.022741-0.397 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
  Pfam Domains:
PF15364 - PAXIP1-associated-protein-1 C term PTIP binding protein

ModBase Predicted Comparative 3D Structure on Q9BTK6
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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 orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0030331 estrogen receptor binding

Biological Process:
GO:0006281 DNA repair
GO:0006310 DNA recombination
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006974 cellular response to DNA damage stimulus
GO:0033148 positive regulation of intracellular estrogen receptor signaling pathway
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:1902808 positive regulation of cell cycle G1/S phase transition

Cellular Component:
GO:0005634 nucleus
GO:0035097 histone methyltransferase complex
GO:0044666 MLL3/4 complex


-  Descriptions from all associated GenBank mRNAs
  AK226151 - Homo sapiens mRNA for hypothetical protein LOC112476 variant, clone: fk13667.
EF195235 - Homo sapiens PTIP-associated 1 protein mRNA, complete cds.
BC003640 - Homo sapiens chromosome 16 open reading frame 53, mRNA (cDNA clone MGC:4606 IMAGE:3356565), complete cds.
CU678552 - Synthetic construct Homo sapiens gateway clone IMAGE:100018613 5' read C16orf53 mRNA.
HQ447362 - Synthetic construct Homo sapiens clone IMAGE:100070683; CCSB003927_02 chromosome 16 open reading frame 53 (C16orf53) gene, encodes complete protein.
KJ894681 - Synthetic construct Homo sapiens clone ccsbBroadEn_04075 C16orf53 gene, encodes complete protein.
JD367860 - Sequence 348884 from Patent EP1572962.
JD271751 - Sequence 252775 from Patent EP1572962.
JD151034 - Sequence 132058 from Patent EP1572962.
JD146326 - Sequence 127350 from Patent EP1572962.
JD253042 - Sequence 234066 from Patent EP1572962.
JD409860 - Sequence 390884 from Patent EP1572962.
JD168879 - Sequence 149903 from Patent EP1572962.
AK026112 - Homo sapiens cDNA: FLJ22459 fis, clone HRC10045.
AK310168 - Homo sapiens cDNA, FLJ17210.
AK301130 - Homo sapiens cDNA FLJ54179 complete cds.
AK298238 - Homo sapiens cDNA FLJ53437 complete cds, highly similar to Major vault protein.
AJ291366 - Homo sapiens partial mRNA for major vault protein (MVP gene), splice variant 1.
AJ291367 - Homo sapiens partial mRNA for major vault protein (MVP gene) and upstream open reading frame (uORF), splice variant 2.
X79882 - Homo sapiens lrp mRNA.
HM005570 - Homo sapiens clone HTL-S-30 testicular secretory protein Li 30 mRNA, complete cds.
AK293302 - Homo sapiens cDNA FLJ54588 complete cds, highly similar to Major vault protein.
AK302052 - Homo sapiens cDNA FLJ53371 complete cds, highly similar to Major vault protein.
BC015623 - Homo sapiens major vault protein, mRNA (cDNA clone MGC:22969 IMAGE:4843712), complete cds.
JD564341 - Sequence 545365 from Patent EP1572962.
JD319342 - Sequence 300366 from Patent EP1572962.
JD383859 - Sequence 364883 from Patent EP1572962.
JD420981 - Sequence 402005 from Patent EP1572962.
JD420980 - Sequence 402004 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9BTK6 (Reactome details) participates in the following event(s):

R-HSA-5617472 Activation of anterior HOX genes in hindbrain development during early embryogenesis
R-HSA-5619507 Activation of HOX genes during differentiation
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: A2ICR6, C16orf53, NM_024516, NP_078792, PA1, PAGR1_HUMAN, Q9BTK6
UCSC ID: uc002dug.4
RefSeq Accession: NM_024516
Protein: Q9BTK6 (aka PAGR1_HUMAN)
CCDS: CCDS10655.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_024516.3
exon count: 3CDS single in 3' UTR: no RNA size: 3843
ORF size: 765CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1630.00frame shift in genome: no % Coverage: 99.53
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
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.