Human Gene PHF21B (ENST00000313237.10_13) from GENCODE V47lift37
  Description: PHD finger protein 21B, transcript variant 1 (from RefSeq NM_138415.5)
Gencode Transcript: ENST00000313237.10_13
Gencode Gene: ENSG00000056487.17_18
Transcript (Including UTRs)
   Position: hg19 chr22:45,277,042-45,405,886 Size: 128,845 Total Exon Count: 13 Strand: -
Coding Region
   Position: hg19 chr22:45,278,966-45,405,430 Size: 126,465 Coding Exon Count: 13 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:45,277,042-45,405,886)mRNA (may differ from genome)Protein (531 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PF21B_HUMAN
DESCRIPTION: RecName: Full=PHD finger protein 21B;
SIMILARITY: Contains 1 PHD-type zinc finger.

-  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: 14.27 RPKM in Pituitary
Total median expression: 61.09 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 -265.90456-0.583 Picture PostScript Text
3' UTR -750.901924-0.390 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
IPR011011 - Znf_FYVE_PHD
IPR001965 - Znf_PHD
IPR019787 - Znf_PHD-finger
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF00628 - PHD-finger

SCOP Domains:
57850 - RING/U-box
57903 - FYVE/PHD zinc finger

ModBase Predicted Comparative 3D Structure on Q96EK2
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 DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0003682 chromatin binding
GO:0003712 transcription cofactor activity
GO:0005515 protein binding
GO:0042393 histone binding
GO:0046872 metal ion binding

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

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  BC012187 - Homo sapiens PHD finger protein 21B, mRNA (cDNA clone MGC:20476 IMAGE:4634631), complete cds.
AK091480 - Homo sapiens cDNA FLJ34161 fis, clone FCBBF3014229, highly similar to PHD finger protein 21B.
AX747013 - Sequence 538 from Patent EP1308459.
AK092243 - Homo sapiens cDNA FLJ34924 fis, clone NT2RP7003134, highly similar to PHD finger protein 21B.
AX747427 - Sequence 952 from Patent EP1308459.
AK297317 - Homo sapiens cDNA FLJ60693 complete cds, highly similar to PHD finger protein 21B.
CR456448 - Homo sapiens dJ127B20.3 full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.dJ127B20.3.V2).
CU012999 - Homo sapiens PHF21B, mRNA (cDNA clone IMAGE:100000161), complete cds, with stop codon, in Gateway system.
KJ899988 - Synthetic construct Homo sapiens clone ccsbBroadEn_09382 PHF21B gene, encodes complete protein.
AB489146 - Synthetic construct DNA, clone: pF1KB9546, Homo sapiens PHF21B gene for PHD finger protein 21B, without stop codon, in Flexi system.
CU013287 - Homo sapiens PHF21B, mRNA (cDNA clone IMAGE:100000065), complete cds, without stop codon, in Gateway system.
KU178842 - Homo sapiens PHD finger protein 21B isoform 1 (PHF21B) mRNA, partial cds.
KU178843 - Homo sapiens PHD finger protein 21B isoform 2 (PHF21B) mRNA, partial cds.
KU178844 - Homo sapiens PHD finger protein 21B isoform 3 (PHF21B) mRNA, complete cds, alternatively spliced.
AK299836 - Homo sapiens cDNA FLJ54987 complete cds, highly similar to PHD finger protein 21B.
CU680262 - Synthetic construct Homo sapiens gateway clone IMAGE:100019800 5' read PHF21B mRNA.
AK095777 - Homo sapiens cDNA FLJ38458 fis, clone FEBRA2020406, highly similar to PHD finger protein 21B.
JD219351 - Sequence 200375 from Patent EP1572962.
JD077611 - Sequence 58635 from Patent EP1572962.
JD056276 - Sequence 37300 from Patent EP1572962.
JD144878 - Sequence 125902 from Patent EP1572962.
JD094342 - Sequence 75366 from Patent EP1572962.
JD066270 - Sequence 47294 from Patent EP1572962.
JD089008 - Sequence 70032 from Patent EP1572962.
JD103058 - Sequence 84082 from Patent EP1572962.
JD098004 - Sequence 79028 from Patent EP1572962.
JD518377 - Sequence 499401 from Patent EP1572962.
JD252026 - Sequence 233050 from Patent EP1572962.
JD319023 - Sequence 300047 from Patent EP1572962.
JD286002 - Sequence 267026 from Patent EP1572962.
JD139327 - Sequence 120351 from Patent EP1572962.
JD501444 - Sequence 482468 from Patent EP1572962.
JD486088 - Sequence 467112 from Patent EP1572962.
JD402509 - Sequence 383533 from Patent EP1572962.
JD377022 - Sequence 358046 from Patent EP1572962.
JD535657 - Sequence 516681 from Patent EP1572962.
JD143323 - Sequence 124347 from Patent EP1572962.
JD195750 - Sequence 176774 from Patent EP1572962.
JD150200 - Sequence 131224 from Patent EP1572962.
JD107864 - Sequence 88888 from Patent EP1572962.
JD075801 - Sequence 56825 from Patent EP1572962.
JD322138 - Sequence 303162 from Patent EP1572962.
JD065347 - Sequence 46371 from Patent EP1572962.
JD339628 - Sequence 320652 from Patent EP1572962.
JD316974 - Sequence 297998 from Patent EP1572962.
DQ570584 - Homo sapiens piRNA piR-30696, complete sequence.

-  Other Names for This Gene
  Alternate Gene Symbols: B0QYW3, B0QYW4, B3KRU4, B7Z4F8, ENST00000313237.1, ENST00000313237.2, ENST00000313237.3, ENST00000313237.4, ENST00000313237.5, ENST00000313237.6, ENST00000313237.7, ENST00000313237.8, ENST00000313237.9, KIAA1661, NM_138415, PF21B_HUMAN, Q5TFL2, Q6ICC0, Q96EK2, uc317pjh.1, uc317pjh.2
UCSC ID: ENST00000313237.10_13
RefSeq Accession: NM_138415.5
Protein: Q96EK2 (aka PF21B_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.