Human Gene ZFP90 (ENST00000563169.7_4) from GENCODE V47lift37
  Description: ZFP90 zinc finger protein, transcript variant 1 (from RefSeq NM_133458.4)
Gencode Transcript: ENST00000563169.7_4
Gencode Gene: ENSG00000184939.16_7
Transcript (Including UTRs)
   Position: hg19 chr16:68,573,194-68,601,034 Size: 27,841 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr16:68,573,696-68,598,601 Size: 24,906 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:68,573,194-68,601,034)mRNA (may differ from genome)Protein (636 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ZFP90_HUMAN
DESCRIPTION: RecName: Full=Zinc finger protein 90 homolog; Short=Zfp-90; AltName: Full=Zinc finger protein 756;
FUNCTION: May function as a repressor or silencer protein, and most likely exerts its repressing activity upon zinc-dependent binding to DNA. May be involved in proper spermatogenesis by repressing the expression of genes unnecessary or incompatible with the maintenance of a haploid cell state (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity).
SIMILARITY: Belongs to the krueppel C2H2-type zinc-finger protein family.
SIMILARITY: Contains 13 C2H2-type zinc fingers.
SIMILARITY: Contains 1 KRAB domain.
SEQUENCE CAUTION: Sequence=AX721106; Type=Frameshift; Positions=341, 358, 370; Sequence=BAB71228.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAG53759.1; Type=Miscellaneous discrepancy; Note=Intron retention;

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: ZFP90
Diseases sorted by gene-association score: spastic paraplegia, optic atrophy, and neuropathy (11)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 8.46 RPKM in Pituitary
Total median expression: 259.78 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 -105.40224-0.471 Picture PostScript Text
3' UTR -644.202433-0.265 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
PF13913 - zinc-finger of a C2HC-type

SCOP Domains:
109640 - KRAB domain (Kruppel-associated box)
54001 - Cysteine proteinases
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 Q8TF47
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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 DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0046872 metal ion binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0043392 negative regulation of DNA binding
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045893 positive regulation of transcription, DNA-templated

Cellular Component:
GO:0005622 intracellular
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  BC040871 - Homo sapiens zinc finger protein 90 homolog (mouse), mRNA (cDNA clone IMAGE:5588865), with apparent retained intron.
BC140886 - Homo sapiens zinc finger protein 90 homolog (mouse), mRNA (cDNA clone MGC:176563 IMAGE:9021754), complete cds.
BC140887 - Homo sapiens zinc finger protein 90 homolog (mouse), mRNA (cDNA clone MGC:176564 IMAGE:9021755), complete cds.
AX721146 - Sequence 106 from Patent WO0220754.
AX721106 - Sequence 66 from Patent WO0220754.
AK316251 - Homo sapiens cDNA, FLJ79150 complete cds, highly similar to Zinc finger protein 90.
AK074332 - Homo sapiens cDNA FLJ23752 fis, clone HEP16659, highly similar to ZINC FINGER PROTEIN 90.
AK304152 - Homo sapiens cDNA FLJ59115 complete cds, highly similar to Zinc finger protein 90.
BC040486 - Homo sapiens zinc finger protein 90 homolog (mouse), mRNA (cDNA clone IMAGE:5271431).
KC249978 - Homo sapiens FOXP3-interacting KRAB domain-containing protein (FIK) mRNA, complete cds.
JD126042 - Sequence 107066 from Patent EP1572962.
JD484933 - Sequence 465957 from Patent EP1572962.
LF384442 - JP 2014500723-A/191945: Polycomb-Associated Non-Coding RNAs.
JD264083 - Sequence 245107 from Patent EP1572962.
AK122847 - Homo sapiens cDNA FLJ16463 fis, clone BRHIP2011616, highly similar to Zinc finger protein 90.
AB075834 - Homo sapiens mRNA for KIAA1954 protein.
AK126167 - Homo sapiens cDNA FLJ44179 fis, clone THYMU2038189.
LF374232 - JP 2014500723-A/181735: Polycomb-Associated Non-Coding RNAs.
JD314818 - Sequence 295842 from Patent EP1572962.
JD049076 - Sequence 30100 from Patent EP1572962.
AK056596 - Homo sapiens cDNA FLJ32034 fis, clone NTONG2000334, highly similar to ZINC FINGER PROTEIN 90.
JD314816 - Sequence 295840 from Patent EP1572962.
JD314817 - Sequence 295841 from Patent EP1572962.
BC033165 - Homo sapiens zinc finger protein 90 homolog (mouse), mRNA (cDNA clone IMAGE:4544629), partial cds.
LF374233 - JP 2014500723-A/181736: Polycomb-Associated Non-Coding RNAs.
JD314879 - Sequence 295903 from Patent EP1572962.
JD314877 - Sequence 295901 from Patent EP1572962.
JD314878 - Sequence 295902 from Patent EP1572962.
JD440367 - Sequence 421391 from Patent EP1572962.
JD314875 - Sequence 295899 from Patent EP1572962.
AK123121 - Homo sapiens cDNA FLJ41126 fis, clone BRACE2015995.
JD088582 - Sequence 69606 from Patent EP1572962.
JD267262 - Sequence 248286 from Patent EP1572962.
JD348153 - Sequence 329177 from Patent EP1572962.
JD369451 - Sequence 350475 from Patent EP1572962.
JD077754 - Sequence 58778 from Patent EP1572962.
JD210237 - Sequence 191261 from Patent EP1572962.
JD122389 - Sequence 103413 from Patent EP1572962.
JD052170 - Sequence 33194 from Patent EP1572962.
JD315779 - Sequence 296803 from Patent EP1572962.
JD113806 - Sequence 94830 from Patent EP1572962.
JD185661 - Sequence 166685 from Patent EP1572962.
JD359307 - Sequence 340331 from Patent EP1572962.
JD146338 - Sequence 127362 from Patent EP1572962.
JD226355 - Sequence 207379 from Patent EP1572962.
JD222845 - Sequence 203869 from Patent EP1572962.
JD551999 - Sequence 533023 from Patent EP1572962.
JD275484 - Sequence 256508 from Patent EP1572962.
JD353859 - Sequence 334883 from Patent EP1572962.
JD266454 - Sequence 247478 from Patent EP1572962.
JD468121 - Sequence 449145 from Patent EP1572962.
JD169592 - Sequence 150616 from Patent EP1572962.
JD169593 - Sequence 150617 from Patent EP1572962.
JD306274 - Sequence 287298 from Patent EP1572962.
JD125549 - Sequence 106573 from Patent EP1572962.
JD395369 - Sequence 376393 from Patent EP1572962.
JD441922 - Sequence 422946 from Patent EP1572962.
JD175614 - Sequence 156638 from Patent EP1572962.
JD331805 - Sequence 312829 from Patent EP1572962.
JD182550 - Sequence 163574 from Patent EP1572962.
JD351045 - Sequence 332069 from Patent EP1572962.
JD512882 - Sequence 493906 from Patent EP1572962.
JD097795 - Sequence 78819 from Patent EP1572962.
JD051469 - Sequence 32493 from Patent EP1572962.
JD101244 - Sequence 82268 from Patent EP1572962.
JD269120 - Sequence 250144 from Patent EP1572962.
JD514363 - Sequence 495387 from Patent EP1572962.
JD183618 - Sequence 164642 from Patent EP1572962.
JD359381 - Sequence 340405 from Patent EP1572962.
JD369436 - Sequence 350460 from Patent EP1572962.
JD073627 - Sequence 54651 from Patent EP1572962.
JD323390 - Sequence 304414 from Patent EP1572962.
JD382033 - Sequence 363057 from Patent EP1572962.
JD201714 - Sequence 182738 from Patent EP1572962.
JD541408 - Sequence 522432 from Patent EP1572962.
JD250489 - Sequence 231513 from Patent EP1572962.
JD494881 - Sequence 475905 from Patent EP1572962.
JD244811 - Sequence 225835 from Patent EP1572962.
MA620019 - JP 2018138019-A/191945: Polycomb-Associated Non-Coding RNAs.
MA609809 - JP 2018138019-A/181735: Polycomb-Associated Non-Coding RNAs.
MA609810 - JP 2018138019-A/181736: Polycomb-Associated Non-Coding RNAs.

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

Protein Q8TF47 (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: B2RU00, B3KVE7, ENST00000563169.1, ENST00000563169.2, ENST00000563169.3, ENST00000563169.4, ENST00000563169.5, ENST00000563169.6, KIAA1954, L7S2P3, NM_133458, Q49AD1, Q8TF47, Q96MQ6, uc325rqi.1, uc325rqi.2, ZFP90_HUMAN, ZNF756
UCSC ID: ENST00000563169.7_4
RefSeq Accession: NM_001305203.2
Protein: Q8TF47 (aka ZFP90_HUMAN or ZF90_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.