Human Gene ZCCHC17 (uc001bsp.1) Description and Page Index
  Description: Homo sapiens zinc finger, CCHC domain containing 17 (ZCCHC17), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr1:31,769,842-31,837,780 Size: 67,939 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr1:31,782,946-31,837,040 Size: 54,095 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:31,769,842-31,837,780)mRNA (may differ from genome)Protein (241 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtPubMedStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: NO40_HUMAN
DESCRIPTION: RecName: Full=Nucleolar protein of 40 kDa; Short=pNO40; AltName: Full=Pnn-interacting nucleolar protein; AltName: Full=Putative S1 RNA-binding domain protein; Short=PS1D protein; AltName: Full=Zinc finger CCHC domain-containing protein 17;
SUBUNIT: Interacts with PNN. Associates with the 60S ribosomal subunit (By similarity).
SUBCELLULAR LOCATION: Nucleus, nucleolus.
SIMILARITY: Contains 1 CCHC-type zinc finger.
SIMILARITY: Contains 1 S1 motif domain.
SEQUENCE CAUTION: Sequence=AAF36171.1; Type=Frameshift; Positions=48;

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 54.10 RPKM in Brain - Spinal cord (cervical c-1)
Total median expression: 1002.55 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 -40.90136-0.301 Picture PostScript Text
3' UTR -261.00740-0.353 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
IPR012340 - NA-bd_OB-fold
IPR016027 - NA-bd_OB-fold-like
IPR003029 - Rbsml_prot_S1_RNA-bd_dom
IPR022967 - RNA-binding_domain_S1
IPR001878 - Znf_CCHC

Pfam Domains:
PF00575 - S1 RNA binding domain

SCOP Domains:
50249 - Nucleic acid-binding proteins

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

2CQO
- NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q9NP64
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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0046872 metal ion binding

Cellular Component:
GO:0005634 nucleus
GO:0005730 nucleolus


-  Descriptions from all associated GenBank mRNAs
  AK022506 - Homo sapiens cDNA FLJ12444 fis, clone NT2RM1000187, weakly similar to PUTATIVE PRE-MRNA SPLICING FACTOR ATP-DEPENDENT RNA HELICASE SPAC10F6.02C.
LF383912 - JP 2014500723-A/191415: Polycomb-Associated Non-Coding RNAs.
AK024049 - Homo sapiens cDNA FLJ13987 fis, clone Y79AA1001963, weakly similar to PUTATIVE PRE-MRNA SPLICING FACTOR ATP-DEPENDENT RNA HELICASE SPAC10F6.02C.
AK307478 - Homo sapiens cDNA, FLJ97426.
AF151085 - Homo sapiens HSPC251 mRNA, complete cds.
AK302248 - Homo sapiens cDNA FLJ60949 complete cds, highly similar to Nucleolar protein of 40 kDa.
AK001929 - Homo sapiens cDNA FLJ11067 fis, clone PLACE1004902, weakly similar to PUTATIVE PRE-MRNA SPLICING FACTOR ATP-DEPENDENT RNA HELICASE SPAC10F6.02C.
LF356827 - JP 2014500723-A/164330: Polycomb-Associated Non-Coding RNAs.
AK302343 - Homo sapiens cDNA FLJ52942 complete cds, highly similar to Nucleolar protein of 40 kDa.
BC050609 - Homo sapiens zinc finger, CCHC domain containing 17, mRNA (cDNA clone MGC:60064 IMAGE:6527025), complete cds.
BC007446 - Homo sapiens zinc finger, CCHC domain containing 17, mRNA (cDNA clone MGC:4523 IMAGE:3009823), complete cds.
AF151077 - Homo sapiens HSPC243 mRNA, complete cds.
BC000685 - Homo sapiens zinc finger, CCHC domain containing 17, mRNA (cDNA clone IMAGE:3347946), partial cds.
AF247661 - Homo sapiens LDC4 mRNA, complete cds.
AB528355 - Synthetic construct DNA, clone: pF1KB6968, Homo sapiens ZCCHC17 gene for zinc finger, CCHC domain containing 17, without stop codon, in Flexi system.
DQ893246 - Synthetic construct clone IMAGE:100005876; FLH195580.01X; RZPDo839D12152D zinc finger, CCHC domain containing 17 (ZCCHC17) gene, encodes complete protein.
DQ896575 - Synthetic construct Homo sapiens clone IMAGE:100011035; FLH195576.01L; RZPDo839D12151D zinc finger, CCHC domain containing 17 (ZCCHC17) gene, encodes complete protein.
KJ893936 - Synthetic construct Homo sapiens clone ccsbBroadEn_03330 ZCCHC17 gene, encodes complete protein.
LF356819 - JP 2014500723-A/164322: Polycomb-Associated Non-Coding RNAs.
LF356815 - JP 2014500723-A/164318: Polycomb-Associated Non-Coding RNAs.
LF356813 - JP 2014500723-A/164316: Polycomb-Associated Non-Coding RNAs.
JD206308 - Sequence 187332 from Patent EP1572962.
JD470747 - Sequence 451771 from Patent EP1572962.
JD324158 - Sequence 305182 from Patent EP1572962.
JD243493 - Sequence 224517 from Patent EP1572962.
JD499249 - Sequence 480273 from Patent EP1572962.
JD486859 - Sequence 467883 from Patent EP1572962.
JD247372 - Sequence 228396 from Patent EP1572962.
JD529534 - Sequence 510558 from Patent EP1572962.
JD392637 - Sequence 373661 from Patent EP1572962.
JD075773 - Sequence 56797 from Patent EP1572962.
JD316891 - Sequence 297915 from Patent EP1572962.
JD055972 - Sequence 36996 from Patent EP1572962.
JD150130 - Sequence 131154 from Patent EP1572962.
JD336739 - Sequence 317763 from Patent EP1572962.
JD236634 - Sequence 217658 from Patent EP1572962.
JD503231 - Sequence 484255 from Patent EP1572962.
MA619489 - JP 2018138019-A/191415: Polycomb-Associated Non-Coding RNAs.
MA592404 - JP 2018138019-A/164330: Polycomb-Associated Non-Coding RNAs.
MA592396 - JP 2018138019-A/164322: Polycomb-Associated Non-Coding RNAs.
MA592392 - JP 2018138019-A/164318: Polycomb-Associated Non-Coding RNAs.
MA592390 - JP 2018138019-A/164316: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: D3DPN4, HSPC243, HSPC251, LDC4, NM_016505, NO40_HUMAN, NP_057589, PS1D, Q6PKH4, Q9NP64, Q9NYG4, Q9P0M8
UCSC ID: uc001bsp.1
RefSeq Accession: NM_016505
Protein: Q9NP64 (aka NO40_HUMAN)
CCDS: CCDS341.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_016505.2
exon count: 8CDS single in 3' UTR: no RNA size: 1602
ORF size: 726CDS single in intron: no Alignment % ID: 99.94
txCdsPredict score: 1637.00frame shift in genome: no % Coverage: 100.00
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.