Human Gene ZNF554 (ENST00000317243.10_4) from GENCODE V47lift37
  Description: zinc finger protein 554 (from RefSeq NM_001102651.2)
Gencode Transcript: ENST00000317243.10_4
Gencode Gene: ENSG00000172006.12_7
Transcript (Including UTRs)
   Position: hg19 chr19:2,819,866-2,836,733 Size: 16,868 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr19:2,820,070-2,834,850 Size: 14,781 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:2,819,866-2,836,733)mRNA (may differ from genome)Protein (538 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ZN554_HUMAN
DESCRIPTION: RecName: Full=Zinc finger protein 554;
FUNCTION: May be involved in transcriptional regulation.
SUBCELLULAR LOCATION: Nucleus (Probable).
SIMILARITY: Belongs to the krueppel C2H2-type zinc-finger protein family.
SIMILARITY: Contains 8 C2H2-type zinc fingers.
SIMILARITY: Contains 1 KRAB domain.
SEQUENCE CAUTION: Sequence=AAH00113.1; 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: 4.89 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 127.04 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -110.70204-0.543 Picture PostScript Text
3' UTR -744.501883-0.395 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
PF01352 - KRAB box
PF13894 - C2H2-type zinc finger
PF13912 - C2H2-type zinc finger

SCOP Domains:
109640 - KRAB domain (Kruppel-associated box)
57667 - beta-beta-alpha zinc fingers
57716 - Glucocorticoid receptor-like (DNA-binding domain)
57783 - Zinc beta-ribbon
57802 - Rubredoxin-like
57889 - Cysteine-rich domain
57903 - FYVE/PHD zinc finger

ModBase Predicted Comparative 3D Structure on Q86TJ5
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 Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
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
GO:0006357 regulation of transcription from RNA polymerase II promoter

Cellular Component:
GO:0005622 intracellular
GO:0005634 nucleus
GO:0005730 nucleolus


-  Descriptions from all associated GenBank mRNAs
  AK299752 - Homo sapiens cDNA FLJ58790 complete cds, highly similar to Homo sapiens zinc finger protein 554 (ZNF554), mRNA.
BC047777 - Homo sapiens zinc finger protein 554, mRNA (cDNA clone MGC:54281 IMAGE:6187000), complete cds.
AK092136 - Homo sapiens cDNA FLJ34817 fis, clone NT2NE2007967, weakly similar to ZINC FINGER PROTEIN 84.
AX747373 - Sequence 898 from Patent EP1308459.
BC000113 - Homo sapiens zinc finger protein 554, mRNA (cDNA clone IMAGE:3352566), partial cds.
JD476014 - Sequence 457038 from Patent EP1572962.
JD139481 - Sequence 120505 from Patent EP1572962.
CU690506 - Synthetic construct Homo sapiens gateway clone IMAGE:100021481 5' read ZNF554 mRNA.
KJ900019 - Synthetic construct Homo sapiens clone ccsbBroadEn_09413 ZNF554 gene, encodes complete protein.
JD433148 - Sequence 414172 from Patent EP1572962.
JD270781 - Sequence 251805 from Patent EP1572962.
JD125100 - Sequence 106124 from Patent EP1572962.
JD394461 - Sequence 375485 from Patent EP1572962.
JD490882 - Sequence 471906 from Patent EP1572962.
JD532867 - Sequence 513891 from Patent EP1572962.
JD173754 - Sequence 154778 from Patent EP1572962.
AK027860 - Homo sapiens cDNA FLJ14954 fis, clone PLACE3000169, highly similar to Homo sapiens zinc finger protein 554 (ZNF554), mRNA.
JD312378 - Sequence 293402 from Patent EP1572962.
JD528490 - Sequence 509514 from Patent EP1572962.
JD236683 - Sequence 217707 from Patent EP1572962.
JD235104 - Sequence 216128 from Patent EP1572962.
JD541183 - Sequence 522207 from Patent EP1572962.
JD180764 - Sequence 161788 from Patent EP1572962.
JD080386 - Sequence 61410 from Patent EP1572962.
JD493897 - Sequence 474921 from Patent EP1572962.
JD156808 - Sequence 137832 from Patent EP1572962.
JD156809 - Sequence 137833 from Patent EP1572962.
JD115743 - Sequence 96767 from Patent EP1572962.
JD492049 - Sequence 473073 from Patent EP1572962.
JD513530 - Sequence 494554 from Patent EP1572962.
JD321261 - Sequence 302285 from Patent EP1572962.
JD321259 - Sequence 302283 from Patent EP1572962.
JD321260 - Sequence 302284 from Patent EP1572962.
JD388849 - Sequence 369873 from Patent EP1572962.
JD388852 - Sequence 369876 from Patent EP1572962.
JD388850 - Sequence 369874 from Patent EP1572962.
JD388851 - Sequence 369875 from Patent EP1572962.
JD542283 - Sequence 523307 from Patent EP1572962.
JD084889 - Sequence 65913 from Patent EP1572962.
JD516207 - Sequence 497231 from Patent EP1572962.
JD110237 - Sequence 91261 from Patent EP1572962.
JD083776 - Sequence 64800 from Patent EP1572962.
JD240029 - Sequence 221053 from Patent EP1572962.
JD131586 - Sequence 112610 from Patent EP1572962.
JD156308 - Sequence 137332 from Patent EP1572962.
JD535659 - Sequence 516683 from Patent EP1572962.
JD072822 - Sequence 53846 from Patent EP1572962.
JD467912 - Sequence 448936 from Patent EP1572962.
JD308286 - Sequence 289310 from Patent EP1572962.
JD255802 - Sequence 236826 from Patent EP1572962.
JD425916 - Sequence 406940 from Patent EP1572962.
JD345138 - Sequence 326162 from Patent EP1572962.
JD223962 - Sequence 204986 from Patent EP1572962.
JD397354 - Sequence 378378 from Patent EP1572962.
JD252067 - Sequence 233091 from Patent EP1572962.
JD337345 - Sequence 318369 from Patent EP1572962.
JD224645 - Sequence 205669 from Patent EP1572962.
JD348957 - Sequence 329981 from Patent EP1572962.
JD181150 - Sequence 162174 from Patent EP1572962.
JD373765 - Sequence 354789 from Patent EP1572962.
JD148223 - Sequence 129247 from Patent EP1572962.
JD249694 - Sequence 230718 from Patent EP1572962.
KJ900262 - Synthetic construct Homo sapiens clone ccsbBroadEn_09656 ZNF555 gene, encodes complete protein.
JD194818 - Sequence 175842 from Patent EP1572962.
JD136074 - Sequence 117098 from Patent EP1572962.
JD415020 - Sequence 396044 from Patent EP1572962.
JD415021 - Sequence 396045 from Patent EP1572962.
JD414967 - Sequence 395991 from Patent EP1572962.
JD120604 - Sequence 101628 from Patent EP1572962.
JD379770 - Sequence 360794 from Patent EP1572962.
JD163227 - Sequence 144251 from Patent EP1572962.
JD312190 - Sequence 293214 from Patent EP1572962.
JD346673 - Sequence 327697 from Patent EP1572962.
JD346675 - Sequence 327699 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q86TJ5 (Reactome details) participates in the following event(s):

R-HSA-975040 KRAB-ZNF / KAP Interaction
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000317243.1, ENST00000317243.2, ENST00000317243.3, ENST00000317243.4, ENST00000317243.5, ENST00000317243.6, ENST00000317243.7, ENST00000317243.8, ENST00000317243.9, NM_001102651, Q86TJ5, Q8NAT3, Q9BWN3, uc317qes.1, uc317qes.2, ZN554_HUMAN
UCSC ID: ENST00000317243.10_4
RefSeq Accession: NM_001102651.2
Protein: Q86TJ5 (aka ZN554_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.