Human Gene PUM3 (ENST00000397885.3_7) from GENCODE V47lift37
  Description: pumilio RNA binding family member 3 (from RefSeq NM_014878.5)
Gencode Transcript: ENST00000397885.3_7
Gencode Gene: ENSG00000080608.10_10
Transcript (Including UTRs)
   Position: hg19 chr9:2,804,152-2,844,095 Size: 39,944 Total Exon Count: 18 Strand: -
Coding Region
   Position: hg19 chr9:2,804,331-2,838,507 Size: 34,177 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:2,804,152-2,844,095)mRNA (may differ from genome)Protein (648 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMalacards
MGIOMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: K0020_HUMAN
DESCRIPTION: RecName: Full=Pumilio domain-containing protein KIAA0020; AltName: Full=HBV X-transactivated gene 5 protein; AltName: Full=HBV XAg-transactivated protein 5; AltName: Full=Minor histocompatibility antigen HA-8; Short=HLA-HA8;
SUBCELLULAR LOCATION: Nucleus, nucleolus.
TISSUE SPECIFICITY: Widely expressed.
DOMAIN: The HA-8 region can be cleaved and exposed at the cell surface where it plays a role as a minor histocompatibility HLA- A*0201-restricted antigen.
POLYMORPHISM: The following alleles of HA-8 are known: HA-8R, HA- 8P, HA-8PL, of which only HA-8R leads to specific cytotoxic T lymphocyte (CTL) recognition. The lack of CTL recognition of cells expressing HA-8P may be due to impaired transport associated with antigen processing. The sequence shown is that of HA-8R.
SIMILARITY: Contains 1 PUM-HD domain.
SIMILARITY: Contains 6 pumilio repeats.
SEQUENCE CAUTION: Sequence=BAA02808.1; Type=Erroneous initiation; Sequence=CAI12924.2; Type=Erroneous gene model prediction; Sequence=CAI15123.2; Type=Erroneous gene model prediction;

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: PUM3
Diseases sorted by gene-association score: teeth hard tissue disease (2)

+  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: 24.73 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 429.87 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 -20.0061-0.328 Picture PostScript Text
3' UTR -37.50179-0.209 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
IPR011989 - ARM-like
IPR016024 - ARM-type_fold
IPR012959 - CPL
IPR001313 - Pumilio_RNA-bd_rpt

Pfam Domains:
PF00806 - Pumilio-family RNA binding repeat
PF08144 - CPL (NUC119) domain

SCOP Domains:
48371 - ARM repeat
54928 - RNA-binding domain, RBD

ModBase Predicted Comparative 3D Structure on Q15397
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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 orthologNo orthologNo orthologNo orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0005515 protein binding

Biological Process:
GO:0006417 regulation of translation
GO:0010835 regulation of protein ADP-ribosylation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005730 nucleolus
GO:0005783 endoplasmic reticulum


-  Descriptions from all associated GenBank mRNAs
  BC016137 - Homo sapiens KIAA0020, mRNA (cDNA clone MGC:8749 IMAGE:3908516), complete cds.
AK225953 - Homo sapiens mRNA for KIAA0020 isoform 1 variant, clone: FCC114H06.
D13645 - Homo sapiens KIAA0020 mRNA, complete cds.
AL832245 - Homo sapiens mRNA; cDNA DKFZp686N1277 (from clone DKFZp686N1277).
AL832239 - Homo sapiens mRNA; cDNA DKFZp686H1377 (from clone DKFZp686H1377).
JD549968 - Sequence 530992 from Patent EP1572962.
AK292169 - Homo sapiens cDNA FLJ75307 complete cds.
JD496344 - Sequence 477368 from Patent EP1572962.
JD243608 - Sequence 224632 from Patent EP1572962.
JD506542 - Sequence 487566 from Patent EP1572962.
AF490254 - Homo sapiens XTP5 (XTP5) mRNA, complete cds.
AK315531 - Homo sapiens cDNA, FLJ96597.
AB383708 - Synthetic construct DNA, clone: pF1KSDA0020, Homo sapiens KIAA0020 gene for KIAA0020 protein, complete cds, without stop codon, in Flexi system.
JF432255 - Synthetic construct Homo sapiens clone IMAGE:100073425 KIAA0020 (KIAA0020) gene, encodes complete protein.
KJ898118 - Synthetic construct Homo sapiens clone ccsbBroadEn_07512 KIAA0020 gene, encodes complete protein.
CR456957 - Homo sapiens full open reading frame cDNA clone RZPDo834E0121D for gene KIAA0020, KIAA0020; complete cds, incl. stopcodon.
AY047588 - Homo sapiens KIAA0020 mRNA, partial cds.
AY047589 - Homo sapiens KIAA0020 mRNA, partial cds.
AY047590 - Homo sapiens KIAA0020 mRNA, partial cds.
CU677573 - Synthetic construct Homo sapiens gateway clone IMAGE:100019978 5' read KIAA0020 mRNA.
JD171449 - Sequence 152473 from Patent EP1572962.
JD305857 - Sequence 286881 from Patent EP1572962.
JD360731 - Sequence 341755 from Patent EP1572962.
JD082733 - Sequence 63757 from Patent EP1572962.
JD314821 - Sequence 295845 from Patent EP1572962.
BC020598 - Homo sapiens cDNA clone IMAGE:4715208.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K804, cPERP-C , ENST00000397885.1, ENST00000397885.2, KIAA0020 , NM_014878, PUF-A , PUM3 , PUM3_HUMAN, Q15397, Q547G7, Q5SZY9, Q6IB47, Q96B27, Q96L78, Q96L79, Q96L80, uc318zjd.1, uc318zjd.2, XTP5
UCSC ID: ENST00000397885.3_7
RefSeq Accession: NM_014878.5
Protein: Q15397 (aka K0020_HUMAN or K020_HUMAN)

-  Gene Model Information
  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.