Human Gene RNF17 (ENST00000255324.10_4) from GENCODE V47lift37
  Description: ring finger protein 17, transcript variant 1 (from RefSeq NM_031277.3)
Gencode Transcript: ENST00000255324.10_4
Gencode Gene: ENSG00000132972.19_14
Transcript (Including UTRs)
   Position: hg19 chr13:25,338,307-25,454,059 Size: 115,753 Total Exon Count: 36 Strand: +
Coding Region
   Position: hg19 chr13:25,338,342-25,453,423 Size: 115,082 Coding Exon Count: 35 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene 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 (chr13:25,338,307-25,454,059)mRNA (may differ from genome)Protein (1623 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RNF17_HUMAN
DESCRIPTION: RecName: Full=RING finger protein 17; AltName: Full=Tudor domain-containing protein 4;
FUNCTION: Seems to be involved in regulation of transcriptional activity of MYC. In vitro, inhibits DNA-binding activity of Mad- MAX heterodimers. Can recruit Mad transcriptional repressors (MXD1, MXD3, MXD4 and MXI1) to the cytoplasm. May be involved in spermiogenesis (By similarity).
SUBUNIT: Interacts with MXD1, MXD3, MXD4, MXI1 and PIWIL1. Self- associates (By similarity).
SUBCELLULAR LOCATION: Cytoplasm (By similarity). Nucleus (By similarity). Note=Predominantly found in the cytoplasm. Component of a nuage in male germ cells (an electron-dense spherical cytoplasmic body present in late pachytene and diplotene spermatocytes and in elonging spermatids) (By similarity).
TISSUE SPECIFICITY: Testis specific.
SIMILARITY: Contains 1 RING-type zinc finger.
SIMILARITY: Contains 4 Tudor domains.
SEQUENCE CAUTION: Sequence=AAH64847.1; Type=Erroneous initiation; Sequence=BAA91972.1; Type=Erroneous initiation;

-  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

+  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: 15.93 RPKM in Testis
Total median expression: 16.22 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 -5.9035-0.169 Picture PostScript Text
3' UTR -37.00195-0.190 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
IPR006021 - Staphylococcal_nuclease
IPR002999 - Tudor
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD
IPR017907 - Znf_RING_CS

Pfam Domains:
PF00567 - Tudor domain

SCOP Domains:
54160 - Chromo domain-like
63748 - Tudor/PWWP/MBT
50199 - Staphylococcal nuclease
57850 - RING/U-box
57903 - FYVE/PHD zinc finger
118310 - AN1-like Zinc finger

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2EQK - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q9BXT8
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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 orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding

Biological Process:
GO:0007275 multicellular organism development
GO:0007283 spermatogenesis
GO:0007286 spermatid development
GO:0030154 cell differentiation

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  BC037275 - Homo sapiens cDNA clone IMAGE:5266526, **** WARNING: chimeric clone ****.
BC146822 - Homo sapiens cDNA clone MGC:167101 IMAGE:8860434.
AK302405 - Homo sapiens cDNA FLJ61720 complete cds, highly similar to Homo sapiens ring finger protein 17 (RNF17), mRNA.
AK302435 - Homo sapiens cDNA FLJ61721 complete cds, highly similar to Homo sapiens ring finger protein 17 (RNF17), mRNA.
BC048962 - Homo sapiens cDNA clone IMAGE:4823672, **** WARNING: chimeric clone ****.
BC166669 - Synthetic construct Homo sapiens clone IMAGE:100066395, MGC:195532 ring finger protein 17 (RNF17) mRNA, encodes complete protein.
BC064847 - Homo sapiens ring finger protein 17, mRNA (cDNA clone IMAGE:30387200), complete cds.
AK001907 - Homo sapiens cDNA FLJ11045 fis, clone PLACE1004460.
AF285603 - Homo sapiens ring finger protein 17 short isoform (RNF17) mRNA, complete cds.
AF285602 - Homo sapiens ring finger protein 17 long isoform (RNF17) mRNA, complete cds.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000255324.1, ENST00000255324.2, ENST00000255324.3, ENST00000255324.4, ENST00000255324.5, ENST00000255324.6, ENST00000255324.7, ENST00000255324.8, ENST00000255324.9, NM_031277, Q5T2J9, Q6P1W3, Q9BXT7, Q9BXT8, Q9NUY9, RNF17_HUMAN, TDRD4, uc317frp.1, uc317frp.2
UCSC ID: ENST00000255324.10_4
RefSeq Accession: NM_031277.3
Protein: Q9BXT8 (aka RNF17_HUMAN or RN17_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.