Human Gene ZNF542 (uc010etk.4)
  Description: Homo sapiens zinc finger protein 542 (ZNF542), transcript variant 3, non-coding RNA.
Transcript (Including UTRs)
   Position: hg19 chr19:56,879,490-56,891,196 Size: 11,707 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr19:56,884,619-56,888,549 Size: 3,931 Coding Exon Count: 3 

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

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr19:56,879,490-56,891,196)mRNA (may differ from genome)Protein (146 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Putative zinc finger protein 542;
FUNCTION: May be involved in transcriptional regulation.
SIMILARITY: Belongs to the krueppel C2H2-type zinc-finger protein family.
SIMILARITY: Contains 3 C2H2-type zinc fingers.
SIMILARITY: Contains 1 KRAB domain.
CAUTION: Could be the product of a pseudogene.
SEQUENCE CAUTION: Sequence=CAE45809.1; Type=Erroneous translation; Note=Wrong choice of CDS;

-  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: 2.11 RPKM in Testis
Total median expression: 40.60 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 -206.90504-0.411 Picture PostScript Text
3' UTR -852.872647-0.322 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
IPR007087 - Znf_C2H2
IPR015880 - Znf_C2H2-like
IPR013087 - Znf_C2H2/integrase_DNA-bd

Pfam Domains:
PF00096 - Zinc finger, C2H2 type

SCOP Domains:
57667 - C2H2 and C2HC zinc fingers

ModBase Predicted Comparative 3D Structure on Q5EBM4
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 Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0046872 metal ion binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated

Cellular Component:
GO:0005622 intracellular
GO:0005634 nucleus

-  Descriptions from all associated GenBank mRNAs
  AK297170 - Homo sapiens cDNA FLJ58906 complete cds.
BX640680 - Homo sapiens mRNA; cDNA DKFZp686B2197 (from clone DKFZp686B2197).
BX647919 - Homo sapiens mRNA; cDNA DKFZp686I1219 (from clone DKFZp686I1219).
AK097128 - Homo sapiens cDNA FLJ39809 fis, clone SPLEN2009541, highly similar to Zinc finger protein 542.
AL833621 - Homo sapiens mRNA; cDNA DKFZp686I1273 (from clone DKFZp686I1273).
BC064603 - Homo sapiens zinc finger protein 542, mRNA (cDNA clone IMAGE:5784531), partial cds.
BC089419 - Homo sapiens zinc finger protein 542, mRNA (cDNA clone IMAGE:3078727).
JD195759 - Sequence 176783 from Patent EP1572962.
JD440042 - Sequence 421066 from Patent EP1572962.
JD274415 - Sequence 255439 from Patent EP1572962.
JD208113 - Sequence 189137 from Patent EP1572962.
JD090393 - Sequence 71417 from Patent EP1572962.
JD305012 - Sequence 286036 from Patent EP1572962.
LF366739 - JP 2014500723-A/174242: Polycomb-Associated Non-Coding RNAs.
JD097712 - Sequence 78736 from Patent EP1572962.
AB464766 - Synthetic construct DNA, clone: pF1KB9609, Homo sapiens ZNF542 gene for zinc finger protein 542, without stop codon, in Flexi system.
KJ901159 - Synthetic construct Homo sapiens clone ccsbBroadEn_10553 ZNF542 gene, encodes complete protein.
LF366740 - JP 2014500723-A/174243: Polycomb-Associated Non-Coding RNAs.
JD553542 - Sequence 534566 from Patent EP1572962.
JD503009 - Sequence 484033 from Patent EP1572962.
JD501721 - Sequence 482745 from Patent EP1572962.
JD248089 - Sequence 229113 from Patent EP1572962.
JD274547 - Sequence 255571 from Patent EP1572962.
JD274548 - Sequence 255572 from Patent EP1572962.
JD450726 - Sequence 431750 from Patent EP1572962.
JD085207 - Sequence 66231 from Patent EP1572962.
JD250131 - Sequence 231155 from Patent EP1572962.
JD111791 - Sequence 92815 from Patent EP1572962.
JD355687 - Sequence 336711 from Patent EP1572962.
JD543004 - Sequence 524028 from Patent EP1572962.
JD213380 - Sequence 194404 from Patent EP1572962.
JD463293 - Sequence 444317 from Patent EP1572962.
JD295438 - Sequence 276462 from Patent EP1572962.
JD331155 - Sequence 312179 from Patent EP1572962.
JD421222 - Sequence 402246 from Patent EP1572962.
JD414819 - Sequence 395843 from Patent EP1572962.
AK130322 - Homo sapiens cDNA FLJ26812 fis, clone PRS06281.
JD206556 - Sequence 187580 from Patent EP1572962.
JD357364 - Sequence 338388 from Patent EP1572962.
JD243477 - Sequence 224501 from Patent EP1572962.
JD067971 - Sequence 48995 from Patent EP1572962.
JD166466 - Sequence 147490 from Patent EP1572962.
JD382186 - Sequence 363210 from Patent EP1572962.
JD284696 - Sequence 265720 from Patent EP1572962.
JD237124 - Sequence 218148 from Patent EP1572962.
JD350749 - Sequence 331773 from Patent EP1572962.
JD043122 - Sequence 24146 from Patent EP1572962.
JD093447 - Sequence 74471 from Patent EP1572962.
JD425578 - Sequence 406602 from Patent EP1572962.
JD527490 - Sequence 508514 from Patent EP1572962.
JD243337 - Sequence 224361 from Patent EP1572962.
JD518412 - Sequence 499436 from Patent EP1572962.
JD045178 - Sequence 26202 from Patent EP1572962.
JD281599 - Sequence 262623 from Patent EP1572962.
JD517085 - Sequence 498109 from Patent EP1572962.
JD221363 - Sequence 202387 from Patent EP1572962.
JD301385 - Sequence 282409 from Patent EP1572962.
MA602316 - JP 2018138019-A/174242: Polycomb-Associated Non-Coding RNAs.
MA602317 - JP 2018138019-A/174243: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: B3KUG2, B4DLV1, NR_024057, Q5EBM4, Q6N061, uc010etk.3, ZN542_HUMAN
UCSC ID: uc010etk.4
RefSeq Accession: NR_024057
Protein: Q5EBM4 (aka ZN542_HUMAN)

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NR_024057.2
exon count: 5CDS single in 3' UTR: no RNA size: 3612
ORF size: 441CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 728.00frame shift in genome: no % Coverage: 99.45
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.