Human Gene ZNF546 (ENST00000347077.9_9) from GENCODE V47lift37

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Description: zinc finger protein 546, transcript variant 1 (from RefSeq NM_178544.5)
Gencode Transcript: ENST00000347077.9_9
Gencode Gene: ENSG00000187187.14_14
Transcript (Including UTRs)
Position: hg19 chr19:40,502,967-40,526,945 Size: 23,979 Total Exon Count: 7 Strand: +
Coding Region
Position: hg19 chr19:40,504,234-40,521,688 Size: 17,455 Coding Exon Count: 5

Page Index	Sequence and Links	UniProtKB Comments	Primers	Gene Alleles	RNA-Seq Expression
RNA Structure	Protein Structure	Other Species	GO Annotations	mRNA Descriptions	Pathways
Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr19:40,502,967-40,526,945)			mRNA (may differ from genome)		Protein (836 aa)
Gene Sorter	Genome Browser	Other Species FASTA	Gene interactions	Table Schema	AlphaFold
BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards	HGNC
MGI	PubMed	Reactome	UniProtKB	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: ZN546_HUMAN DESCRIPTION: RecName: Full=Zinc finger protein 546; AltName: Full=Zinc finger protein 49; FUNCTION: May be involved in transcriptional regulation. SUBCELLULAR LOCATION: Nucleus (Probable). SIMILARITY: Belongs to the krueppel C2H2-type zinc-finger protein family. SIMILARITY: Contains 22 C2H2-type zinc fingers. SIMILARITY: Contains 1 KRAB domain.

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.
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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

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 9.73 RPKM in Testis Total median expression: 62.84 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-63.10	232	-0.272	Picture	PostScript	Text
3' UTR	-1475.70	5257	-0.281	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
PF13912 - C2H2-type zinc finger

SCOP Domains:
109640 - KRAB domain (Kruppel-associated box)
46689 - Homeodomain-like
52166 - Ribosomal protein L4
55550 - SH2 domain
57667 - beta-beta-alpha zinc fingers
57716 - Glucocorticoid receptor-like (DNA-binding domain)
57783 - Zinc beta-ribbon
57802 - Rubredoxin-like
57889 - Cysteine-rich domain

ModBase Predicted Comparative 3D Structure on Q86UE3


Front	Top	Side

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No 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:0003700 transcription factor activity, sequence-specific 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

Descriptions from all associated GenBank mRNAs


	AK122968 - Homo sapiens cDNA FLJ16707 fis, clone UTERU2003321, highly similar to Zinc finger protein 546. AK292528 - Homo sapiens cDNA FLJ75134 complete cds, highly similar to Homo sapiens zinc finger protein 546 (ZNF546), mRNA. BC045649 - Homo sapiens zinc finger protein 546, mRNA (cDNA clone MGC:43537 IMAGE:5268795), complete cds. JD312636 - Sequence 293660 from Patent EP1572962. CU692284 - Synthetic construct Homo sapiens gateway clone IMAGE:100020964 5' read ZNF546 mRNA. KJ900618 - Synthetic construct Homo sapiens clone ccsbBroadEn_10012 ZNF546 gene, encodes complete protein. DQ578180 - Homo sapiens piRNA piR-46292, complete sequence. LF367215 - JP 2014500723-A/174718: Polycomb-Associated Non-Coding RNAs. DQ586080 - Homo sapiens piRNA piR-53192, complete sequence. AK172809 - Homo sapiens cDNA FLJ23970 fis, clone HEP17024. JD314886 - Sequence 295910 from Patent EP1572962. JD314887 - Sequence 295911 from Patent EP1572962. JD032199 - Sequence 13223 from Patent EP1572962. JD032199 - Sequence 13223 from Patent EP1572962. JD314886 - Sequence 295910 from Patent EP1572962. JD314887 - Sequence 295911 from Patent EP1572962. JD032199 - Sequence 13223 from Patent EP1572962. DQ580339 - Homo sapiens piRNA piR-48451, complete sequence. JD328282 - Sequence 309306 from Patent EP1572962. JD314886 - Sequence 295910 from Patent EP1572962. JD314887 - Sequence 295911 from Patent EP1572962. LF367214 - JP 2014500723-A/174717: Polycomb-Associated Non-Coding RNAs. LF367213 - JP 2014500723-A/174716: Polycomb-Associated Non-Coding RNAs. DQ572057 - Homo sapiens piRNA piR-40169, complete sequence. JD298714 - Sequence 279738 from Patent EP1572962. JD183791 - Sequence 164815 from Patent EP1572962. DQ575435 - Homo sapiens piRNA piR-43547, complete sequence. JD412739 - Sequence 393763 from Patent EP1572962. JD512694 - Sequence 493718 from Patent EP1572962. JD202833 - Sequence 183857 from Patent EP1572962. JD184192 - Sequence 165216 from Patent EP1572962. JD093071 - Sequence 74095 from Patent EP1572962. JD561424 - Sequence 542448 from Patent EP1572962. JD281991 - Sequence 263015 from Patent EP1572962. JD230079 - Sequence 211103 from Patent EP1572962. JD269647 - Sequence 250671 from Patent EP1572962. JD185468 - Sequence 166492 from Patent EP1572962. JD149601 - Sequence 130625 from Patent EP1572962. JD313045 - Sequence 294069 from Patent EP1572962. JD512691 - Sequence 493715 from Patent EP1572962. JD047496 - Sequence 28520 from Patent EP1572962. JD147075 - Sequence 128099 from Patent EP1572962. JD355897 - Sequence 336921 from Patent EP1572962. JD179622 - Sequence 160646 from Patent EP1572962. JD122167 - Sequence 103191 from Patent EP1572962. JD158934 - Sequence 139958 from Patent EP1572962. JD158933 - Sequence 139957 from Patent EP1572962. JD158932 - Sequence 139956 from Patent EP1572962. JD208726 - Sequence 189750 from Patent EP1572962. JD208725 - Sequence 189749 from Patent EP1572962. JD469758 - Sequence 450782 from Patent EP1572962. JD482719 - Sequence 463743 from Patent EP1572962. JD486887 - Sequence 467911 from Patent EP1572962. JD112120 - Sequence 93144 from Patent EP1572962. JD112121 - Sequence 93145 from Patent EP1572962. JD488598 - Sequence 469622 from Patent EP1572962. JD402710 - Sequence 383734 from Patent EP1572962. JD164712 - Sequence 145736 from Patent EP1572962. JD417767 - Sequence 398791 from Patent EP1572962. JD258503 - Sequence 239527 from Patent EP1572962. JD377299 - Sequence 358323 from Patent EP1572962. JD529571 - Sequence 510595 from Patent EP1572962. JD169975 - Sequence 150999 from Patent EP1572962. JD306696 - Sequence 287720 from Patent EP1572962. JD056552 - Sequence 37576 from Patent EP1572962. JD382043 - Sequence 363067 from Patent EP1572962. JD094649 - Sequence 75673 from Patent EP1572962. JD349728 - Sequence 330752 from Patent EP1572962. JD088839 - Sequence 69863 from Patent EP1572962. JD358582 - Sequence 339606 from Patent EP1572962. DQ584921 - Homo sapiens piRNA piR-52033, complete sequence. JD459707 - Sequence 440731 from Patent EP1572962. JD562564 - Sequence 543588 from Patent EP1572962. JD243050 - Sequence 224074 from Patent EP1572962. JD098232 - Sequence 79256 from Patent EP1572962. JD090319 - Sequence 71343 from Patent EP1572962. JD175368 - Sequence 156392 from Patent EP1572962. JD300550 - Sequence 281574 from Patent EP1572962. JD474950 - Sequence 455974 from Patent EP1572962. JD474951 - Sequence 455975 from Patent EP1572962. AF087985 - Homo sapiens full length insert cDNA clone YW29F03. MA602792 - JP 2018138019-A/174718: Polycomb-Associated Non-Coding RNAs. MA602791 - JP 2018138019-A/174717: Polycomb-Associated Non-Coding RNAs. MA602790 - JP 2018138019-A/174716: Polycomb-Associated Non-Coding RNAs.

Biochemical and Signaling Pathways


	Reactome (by CSHL, EBI, and GO) Protein Q86UE3 (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: A8K913, ENST00000347077.1, ENST00000347077.2, ENST00000347077.3, ENST00000347077.4, ENST00000347077.5, ENST00000347077.6, ENST00000347077.7, ENST00000347077.8, NM_178544, Q86UE3, uc317xls.1, uc317xls.2, ZN546_HUMAN, ZNF49 UCSC ID: ENST00000347077.9_9 RefSeq Accession: NM_178544.5 Protein: Q86UE3 (aka ZN546_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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