Human Gene ZC3H12B (uc010nko.3) Description and Page Index
  Description: Homo sapiens zinc finger CCCH-type containing 12B (ZC3H12B), mRNA.
RefSeq Summary (NM_001010888): The protein encoded by this gene belongs to a family of CCCH-type zinc finger proteins that are involved in the proinflammatory activation of macrophages. The exact function of this family member is unknown, but it is thought to function as a ribonuclease. [provided by RefSeq, May 2010]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments. ##Evidence-Data-START## Transcript exon combination :: BC140767.1, SRR1803616.1654.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA2142348, SAMEA2144120 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on conservation, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chrX:64,708,615-64,727,767 Size: 19,153 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chrX:64,708,682-64,723,089 Size: 14,408 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:64,708,615-64,727,767)mRNA (may differ from genome)Protein (836 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIOMIM
PubMedStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: E9PAJ6_HUMAN
DESCRIPTION: SubName: Full=Probable ribonuclease ZC3H12B;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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: 2.32 RPKM in Pituitary
Total median expression: 49.78 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 -10.2067-0.152 Picture PostScript Text
3' UTR -1290.304678-0.276 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
IPR021869 - RNase_Zc3h12
IPR000571 - Znf_CCCH

Pfam Domains:
PF11977 - Zc3h12a-like Ribonuclease NYN domain

ModBase Predicted Comparative 3D Structure on E9PAJ6
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 orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Descriptions from all associated GenBank mRNAs
  KJ904207 - Synthetic construct Homo sapiens clone ccsbBroadEn_13601 ZC3H12B gene, encodes complete protein.
BC140767 - Homo sapiens zinc finger CCCH-type containing 12B, mRNA (cDNA clone MGC:176444 IMAGE:9021635), complete cds.
BC171781 - Homo sapiens zinc finger CCCH-type containing 12B, mRNA (cDNA clone MGC:198496 IMAGE:9054435), complete cds.
BX647241 - Homo sapiens mRNA; cDNA DKFZp686I0949 (from clone DKFZp686I0949).
LF211580 - JP 2014500723-A/19083: Polycomb-Associated Non-Coding RNAs.
LF381522 - JP 2014500723-A/189025: Polycomb-Associated Non-Coding RNAs.
AK091685 - Homo sapiens cDNA FLJ34366 fis, clone FEBRA2016583.
LF381523 - JP 2014500723-A/189026: Polycomb-Associated Non-Coding RNAs.
MA447157 - JP 2018138019-A/19083: Polycomb-Associated Non-Coding RNAs.
MA617099 - JP 2018138019-A/189025: Polycomb-Associated Non-Coding RNAs.
MA617100 - JP 2018138019-A/189026: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: E9PAJ6, E9PAJ6_HUMAN, NM_001010888, NP_001010888
UCSC ID: uc010nko.3
RefSeq Accession: NM_001010888
Protein: E9PAJ6 CCDS: CCDS48131.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001010888.3
exon count: 5CDS single in 3' UTR: no RNA size: 7273
ORF size: 2511CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5201.00frame shift in genome: no % Coverage: 99.77
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.