Human Gene ZNF253 (ENST00000589717.2_4) from GENCODE V47lift37

JavaScript is disabled in your web browser

You must have JavaScript enabled in your web browser to use the Genome Browser

Description: zinc finger protein 253, transcript variant 1 (from RefSeq NM_021047.3)
Gencode Transcript: ENST00000589717.2_4
Gencode Gene: ENSG00000256771.5_12
Transcript (Including UTRs)
Position: hg19 chr19:19,976,691-20,005,483 Size: 28,793 Total Exon Count: 4 Strand: +
Coding Region
Position: hg19 chr19:19,976,806-20,003,556 Size: 26,751 Coding Exon Count: 4

Page Index	Sequence and Links	UniProtKB Comments	Primers	CTD	Gene Alleles
RNA-Seq Expression	Microarray 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 (chr19:19,976,691-20,005,483)			mRNA (may differ from genome)		Protein (499 aa)
Gene Sorter	Genome Browser	Other Species FASTA	Gene interactions	Table Schema	AlphaFold
BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards	HGNC
MGI	OMIM	PubMed	Reactome	UniProtKB	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: ZN253_HUMAN DESCRIPTION: RecName: Full=Zinc finger protein 253; AltName: Full=Bone marrow zinc finger 1; Short=BMZF-1; AltName: Full=Zinc finger protein 411; FUNCTION: May function as a transcription factor. Seem to have a transcriptional repression activity. SUBCELLULAR LOCATION: Nucleus (Probable). TISSUE SPECIFICITY: Expressed in bone marrow and in monocytic and immature erythroid cell lines. SIMILARITY: Belongs to the krueppel C2H2-type zinc-finger protein family. SIMILARITY: Contains 11 C2H2-type zinc fingers. SIMILARITY: Contains 1 KRAB domain. SEQUENCE CAUTION: Sequence=AAH14148.2; Type=Erroneous initiation; Sequence=BAC11257.1; 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 D019327 Copper Sulfate D005557 Formaldehyde D024483 Vitamin K 3

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: 4.31 RPKM in Brain - Cerebellar Hemisphere Total median expression: 100.54 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

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-29.70	115	-0.258	Picture	PostScript	Text
3' UTR	-456.40	1927	-0.237	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)
57667 - beta-beta-alpha zinc fingers
57716 - Glucocorticoid receptor-like (DNA-binding domain)
82919 - Zn-finger domain of Sec23/24
57783 - Zinc beta-ribbon
57802 - Rubredoxin-like
63393 - RNA polymerase subunits
57889 - Cysteine-rich domain
57903 - FYVE/PHD zinc finger
161219 - CHY zinc finger-like

ModBase Predicted Comparative 3D Structure on O75346


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:0008270 zinc ion 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 GO:0045892 negative regulation of transcription, DNA-templated Cellular Component: GO:0005622 intracellular GO:0005634 nucleus

Descriptions from all associated GenBank mRNAs


	BC053607 - Homo sapiens zinc finger protein 253, mRNA (cDNA clone IMAGE:6012910), with apparent retained intron. BC014148 - Homo sapiens zinc finger protein 253, mRNA (cDNA clone IMAGE:3353658), partial cds. BC065572 - Homo sapiens zinc finger protein 253, mRNA (cDNA clone MGC:75229 IMAGE:6171141), complete cds. AK074757 - Homo sapiens cDNA FLJ90276 fis, clone NT2RP1000271, moderately similar to ZINC FINGER PROTEIN 85. BC125063 - Homo sapiens zinc finger protein 253, mRNA (cDNA clone MGC:149673 IMAGE:40117279), complete cds. BC125064 - Homo sapiens zinc finger protein 253, mRNA (cDNA clone MGC:149674 IMAGE:40117289), complete cds. KJ899241 - Synthetic construct Homo sapiens clone ccsbBroadEn_08635 ZNF253 gene, encodes complete protein. AF038951 - Homo sapiens DNA-binding protein mRNA, complete cds. CU688076 - Synthetic construct Homo sapiens gateway clone IMAGE:100021800 5' read ZNF253 mRNA. KJ902902 - Synthetic construct Homo sapiens clone ccsbBroadEn_12296 ZNF253 gene, encodes complete protein. AK074872 - Homo sapiens cDNA FLJ90391 fis, clone NT2RP2005535, moderately similar to ZINC FINGER PROTEIN 85. JD314877 - Sequence 295901 from Patent EP1572962. JD314878 - Sequence 295902 from Patent EP1572962. JD314871 - Sequence 295895 from Patent EP1572962. JD314877 - Sequence 295901 from Patent EP1572962. LF340536 - JP 2014500723-A/148039: Polycomb-Associated Non-Coding RNAs. JD330509 - Sequence 311533 from Patent EP1572962. JD330511 - Sequence 311535 from Patent EP1572962. JD330510 - Sequence 311534 from Patent EP1572962. DQ570709 - Homo sapiens piRNA piR-30821, complete sequence. JD037677 - Sequence 18701 from Patent EP1572962. JD330509 - Sequence 311533 from Patent EP1572962. JD330511 - Sequence 311535 from Patent EP1572962. JD330510 - Sequence 311534 from Patent EP1572962. DQ570709 - Homo sapiens piRNA piR-30821, complete sequence. JD037677 - Sequence 18701 from Patent EP1572962. JD314870 - Sequence 295894 from Patent EP1572962. JD330509 - Sequence 311533 from Patent EP1572962. JD330511 - Sequence 311535 from Patent EP1572962. JD330510 - Sequence 311534 from Patent EP1572962. DQ570709 - Homo sapiens piRNA piR-30821, complete sequence. JD037677 - Sequence 18701 from Patent EP1572962. JD314877 - Sequence 295901 from Patent EP1572962. JD330509 - Sequence 311533 from Patent EP1572962. JD330511 - Sequence 311535 from Patent EP1572962. JD330510 - Sequence 311534 from Patent EP1572962. DQ570709 - Homo sapiens piRNA piR-30821, complete sequence. JD037677 - Sequence 18701 from Patent EP1572962. JD103622 - Sequence 84646 from Patent EP1572962. JD314877 - Sequence 295901 from Patent EP1572962. JD314878 - Sequence 295902 from Patent EP1572962. JD330513 - Sequence 311537 from Patent EP1572962. JD330514 - Sequence 311538 from Patent EP1572962. JD330515 - Sequence 311539 from Patent EP1572962. JD330516 - Sequence 311540 from Patent EP1572962. JD066994 - Sequence 48018 from Patent EP1572962. JD314877 - Sequence 295901 from Patent EP1572962. JD304608 - Sequence 285632 from Patent EP1572962. JD172093 - Sequence 153117 from Patent EP1572962. JD558585 - Sequence 539609 from Patent EP1572962. JD273927 - Sequence 254951 from Patent EP1572962. JD326153 - Sequence 307177 from Patent EP1572962. JD154233 - Sequence 135257 from Patent EP1572962. JD154234 - Sequence 135258 from Patent EP1572962. JD262358 - Sequence 243382 from Patent EP1572962. JD165906 - Sequence 146930 from Patent EP1572962. JD295737 - Sequence 276761 from Patent EP1572962. JD295738 - Sequence 276762 from Patent EP1572962. JD295739 - Sequence 276763 from Patent EP1572962. JD492142 - Sequence 473166 from Patent EP1572962. JD246344 - Sequence 227368 from Patent EP1572962. JD352795 - Sequence 333819 from Patent EP1572962. JD396967 - Sequence 377991 from Patent EP1572962. JD409739 - Sequence 390763 from Patent EP1572962. JD256020 - Sequence 237044 from Patent EP1572962. BC022891 - Homo sapiens zinc finger protein 253, mRNA (cDNA clone IMAGE:4658943), with apparent retained intron. JD490085 - Sequence 471109 from Patent EP1572962. JD176246 - Sequence 157270 from Patent EP1572962. JD205318 - Sequence 186342 from Patent EP1572962. JD333254 - Sequence 314278 from Patent EP1572962. JD333255 - Sequence 314279 from Patent EP1572962. JD490158 - Sequence 471182 from Patent EP1572962. JD415017 - Sequence 396041 from Patent EP1572962. JD346772 - Sequence 327796 from Patent EP1572962. JD330886 - Sequence 311910 from Patent EP1572962. MA576113 - JP 2018138019-A/148039: Polycomb-Associated Non-Coding RNAs.

Biochemical and Signaling Pathways


	Reactome (by CSHL, EBI, and GO) Protein O75346 (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: A4FVA7, BMZF1, ENST00000589717.1, NM_021047, O75346, Q0P6G3, Q6P0L2, Q8NCA3, Q8NCF9, uc326uet.1, uc326uet.2, ZN253_HUMAN, ZNF411 UCSC ID: ENST00000589717.2_4 RefSeq Accession: NM_021047.3 Protein: O75346 (aka ZN253_HUMAN or Z253_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.