Human Gene PRDM7 (uc010cje.3) Description and Page Index
  Description: Homo sapiens PR domain containing 7 (PRDM7), transcript variant 1, mRNA.
RefSeq Summary (NM_001098173): This gene encodes a member of a family of proteins that may have roles in transcription and other nuclear processes. The encoded protein contains a KRAB (Kruppel-associated box) domain -A box and a SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain and may function as a histone methyltransferase. [provided by RefSeq, Aug 2013]. ##Evidence-Data-START## Transcript exon combination :: AM690991.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1968968, SAMEA2161674 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr16:90,122,974-90,142,338 Size: 19,365 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg19 chr16:90,124,697-90,142,318 Size: 17,622 Coding Exon Count: 10 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:90,122,974-90,142,338)mRNA (may differ from genome)Protein (492 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: PRDM7_HUMAN
DESCRIPTION: RecName: Full=Probable histone-lysine N-methyltransferase PRDM7; EC=2.1.1.43; AltName: Full=PR domain zinc finger protein 7; AltName: Full=PR domain-containing protein 7;
FUNCTION: Probable histone methyltransferase (By similarity).
CATALYTIC ACTIVITY: S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
SUBCELLULAR LOCATION: Nucleus (Potential). Chromosome (Potential).
MISCELLANEOUS: The mouse orthologous protein seems not to exist. According to PubMed:17916234, human PRDM7 and PRDM9 genes, a pair of close paralogs corresponding to a single mouse gene Prdm9, were generated by a recent gene duplication event after the divergence of the ancestors of human and mouse.
SIMILARITY: Contains 1 KRAB-related domain.
SIMILARITY: Contains 1 SET domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PRDM7
CDC HuGE Published Literature: PRDM7
Positive Disease Associations: Heart Failure
Related Studies:
  1. Heart Failure
    , , . [PubMed 0]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 2.14 RPKM in Testis
Total median expression: 2.33 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR 0.00200.000 Picture PostScript Text
3' UTR -568.971723-0.330 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
IPR001909 - Krueppel-associated_box
IPR003655 - Krueppel-associated_box-rel
IPR001214 - SET_dom
IPR019041 - SSXRD_motif

Pfam Domains:
PF01352 - KRAB box
PF09514 - SSXRD motif

SCOP Domains:
109640 - KRAB domain (Kruppel-associated box, Pfam 01352)

ModBase Predicted Comparative 3D Structure on Q9NQW5
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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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003676 nucleic acid binding
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0016740 transferase activity
GO:0018024 histone-lysine N-methyltransferase activity

Biological Process:
GO:0006325 chromatin organization
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0032259 methylation
GO:0034968 histone lysine methylation

Cellular Component:
GO:0005622 intracellular
GO:0005634 nucleus
GO:0005694 chromosome


-  Descriptions from all associated GenBank mRNAs
  AL137711 - Homo sapiens mRNA; cDNA DKFZp434H1323 (from clone DKFZp434H1323).
AF274347 - Homo sapiens PR-domain zinc finger protein 7 isoform A (PRDM7) mRNA, complete cds; alternatively spliced.
AF274348 - Homo sapiens PR-domain zinc finger protein 7 isoform B (PRDM7) mRNA, complete cds; alternatively spliced.
JD317330 - Sequence 298354 from Patent EP1572962.
JD502119 - Sequence 483143 from Patent EP1572962.
JD246613 - Sequence 227637 from Patent EP1572962.
JD136386 - Sequence 117410 from Patent EP1572962.
JD396273 - Sequence 377297 from Patent EP1572962.
JD126026 - Sequence 107050 from Patent EP1572962.
JD554947 - Sequence 535971 from Patent EP1572962.
JD299594 - Sequence 280618 from Patent EP1572962.
JD236351 - Sequence 217375 from Patent EP1572962.
JD557756 - Sequence 538780 from Patent EP1572962.
JD280404 - Sequence 261428 from Patent EP1572962.
JD353919 - Sequence 334943 from Patent EP1572962.
JD391154 - Sequence 372178 from Patent EP1572962.
JD423940 - Sequence 404964 from Patent EP1572962.
JD439676 - Sequence 420700 from Patent EP1572962.
JD539824 - Sequence 520848 from Patent EP1572962.
JD068534 - Sequence 49558 from Patent EP1572962.
JD046623 - Sequence 27647 from Patent EP1572962.
JD317859 - Sequence 298883 from Patent EP1572962.
JD283551 - Sequence 264575 from Patent EP1572962.
JD529297 - Sequence 510321 from Patent EP1572962.
JD518893 - Sequence 499917 from Patent EP1572962.
JD292315 - Sequence 273339 from Patent EP1572962.
AM690993 - Homo sapiens partial mRNA for PRDM7 long isoform, variant 2 (PRDM7_V3 gene).
AM690992 - Homo sapiens partial mRNA for PRDM7 long isoform, variant 2 (PRDM7_V2 gene).
AM690991 - Homo sapiens partial mRNA for PRDM7 long isoform, variant 1 (PRDM7_V1 gene).
BC107033 - Homo sapiens PR domain containing 7, mRNA (cDNA clone IMAGE:40000087), complete cds.
KJ893227 - Synthetic construct Homo sapiens clone ccsbBroadEn_02621 PRDM7 gene, encodes complete protein.
AB527979 - Synthetic construct DNA, clone: pF1KB7533, Homo sapiens PRDM7 gene for PR domain containing protein 7, without stop codon, in Flexi system.

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

Protein Q9NQW5 (Reactome details) participates in the following event(s):

R-HSA-975040 KRAB-ZNF / KAP Interaction
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: A4Q9G8, NM_001098173, NP_001091643, PFM4, PRDM7_HUMAN, Q08EM4, Q9NQW4, Q9NQW5
UCSC ID: uc010cje.3
RefSeq Accession: NM_001098173
Protein: Q9NQW5 (aka PRDM7_HUMAN or PRD7_HUMAN)
CCDS: CCDS45557.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001098173.1
exon count: 10CDS single in 3' UTR: no RNA size: 3284
ORF size: 1479CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2336.00frame shift in genome: no % Coverage: 98.11
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.