Human Gene RP11-566D24.2 (uc002adw.1)
  Description: Homo sapiens zinc finger protein 280D (RP11-566D24.2), transcript variant 2, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr15:56,945,019-57,210,697 Size: 265,679 Total Exon Count: 24 Strand: -
Coding Region
   Position: hg19 chr15:56,945,691-57,017,112 Size: 71,422 Coding Exon Count: 18 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:56,945,019-57,210,697)mRNA (may differ from genome)Protein (788 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsGeneNetworkH-INV
LynxMGIPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: H0YL38_HUMAN
DESCRIPTION: SubName: Full=Zinc finger protein 280D;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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


+  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: 6.38 RPKM in Cervix - Endocervix
Total median expression: 158.92 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
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -557.721605-0.347 Picture PostScript Text
3' UTR -175.50672-0.261 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
IPR025243 - DUF4195
IPR007087 - Znf_C2H2
IPR015880 - Znf_C2H2-like

Pfam Domains:
PF13836 - Domain of unknown function (DUF4195)
PF13912 - C2H2-type zinc finger

SCOP Domains:
57667 - C2H2 and C2HC zinc fingers

ModBase Predicted Comparative 3D Structure on H0YL38
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 Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding


-  Descriptions from all associated GenBank mRNAs
  LF208550 - JP 2014500723-A/16053: Polycomb-Associated Non-Coding RNAs.
BC040532 - Homo sapiens zinc finger protein 280D, mRNA (cDNA clone IMAGE:5261474).
BX641000 - Homo sapiens mRNA; cDNA DKFZp686H13148 (from clone DKFZp686H13148); complete cds.
AB046804 - Homo sapiens KIAA1584 mRNA for KIAA1584 protein.
BC130451 - Homo sapiens zinc finger protein 280D, mRNA (cDNA clone MGC:163323 IMAGE:40146482), complete cds.
BC136412 - Homo sapiens zinc finger protein 280D, mRNA (cDNA clone MGC:168023 IMAGE:9020400), complete cds.
BX640707 - Homo sapiens mRNA; cDNA DKFZp686F11161 (from clone DKFZp686F11161); complete cds.
AK295159 - Homo sapiens cDNA FLJ56078 complete cds, highly similar to Suppressor of hairy wing homolog 4.
AK289739 - Homo sapiens cDNA FLJ76213 complete cds, highly similar to Homo sapiens suppressor of hairy wing homolog 4 (Drosophila) (SUHW4), transcript variant 2, mRNA.
AM392650 - Synthetic construct Homo sapiens clone IMAGE:100002534 for hypothetical protein (SUHW4 gene).
AM393745 - Synthetic construct Homo sapiens clone IMAGE:100002533 for hypothetical protein (SUHW4 gene).
BX640637 - Homo sapiens mRNA; cDNA DKFZp779P138 (from clone DKFZp779P138); complete cds.
BC036541 - Homo sapiens cDNA clone IMAGE:4829311.
AK310882 - Homo sapiens cDNA, FLJ17924.
BC064359 - Homo sapiens zinc finger protein 280D, mRNA (cDNA clone IMAGE:5531919), complete cds.
BC053649 - Homo sapiens zinc finger protein 280D, mRNA (cDNA clone IMAGE:5538785), complete cds.
MA444127 - JP 2018138019-A/16053: Polycomb-Associated Non-Coding RNAs.
AK000093 - Homo sapiens cDNA FLJ20086 fis, clone COL03629.
AB385484 - Synthetic construct DNA, clone: pF1KA1584, Homo sapiens SUHW4 gene for suppressor of hairy wing homolog 4, complete cds, without stop codon, in Flexi system.
AK025073 - Homo sapiens cDNA: FLJ21420 fis, clone COL04105.
LF377622 - JP 2014500723-A/185125: Polycomb-Associated Non-Coding RNAs.
JD082130 - Sequence 63154 from Patent EP1572962.
BC015382 - Homo sapiens zinc finger protein 280D, mRNA (cDNA clone IMAGE:4413086), complete cds.
LF377617 - JP 2014500723-A/185120: Polycomb-Associated Non-Coding RNAs.
MA613199 - JP 2018138019-A/185125: Polycomb-Associated Non-Coding RNAs.
MA613194 - JP 2018138019-A/185120: Polycomb-Associated Non-Coding RNAs.
AK056606 - Homo sapiens cDNA FLJ32044 fis, clone NTONG2000985.
AK096657 - Homo sapiens cDNA FLJ39338 fis, clone OCBBF2017899.
JD188769 - Sequence 169793 from Patent EP1572962.
JD337632 - Sequence 318656 from Patent EP1572962.
JD310708 - Sequence 291732 from Patent EP1572962.
JD361556 - Sequence 342580 from Patent EP1572962.
JD524341 - Sequence 505365 from Patent EP1572962.
JD363450 - Sequence 344474 from Patent EP1572962.
BC063546 - Homo sapiens cDNA clone IMAGE:4755015, partial cds.
JD425213 - Sequence 406237 from Patent EP1572962.
JD071512 - Sequence 52536 from Patent EP1572962.
JD338945 - Sequence 319969 from Patent EP1572962.
JD062124 - Sequence 43148 from Patent EP1572962.
JD565120 - Sequence 546144 from Patent EP1572962.
JD358517 - Sequence 339541 from Patent EP1572962.
JD414105 - Sequence 395129 from Patent EP1572962.
JD438120 - Sequence 419144 from Patent EP1572962.
JD313457 - Sequence 294481 from Patent EP1572962.
JD345819 - Sequence 326843 from Patent EP1572962.
JD179797 - Sequence 160821 from Patent EP1572962.
JD129840 - Sequence 110864 from Patent EP1572962.
JD223184 - Sequence 204208 from Patent EP1572962.
JD476369 - Sequence 457393 from Patent EP1572962.
JD196042 - Sequence 177066 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: BC036541, H0YL38, H0YL38_HUMAN, NM_001002843, NP_001002843, ZNF280D
UCSC ID: uc002adw.1
RefSeq Accession: NM_001002843
Protein: H0YL38

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: BC036541.1
exon count: 24CDS single in 3' UTR: no RNA size: 4811
ORF size: 2367CDS single in intron: no Alignment % ID: 99.94
txCdsPredict score: 4014.50frame shift in genome: no % Coverage: 96.53
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.