Human Gene ZNF541 (uc002phg.5)
  Description: Homo sapiens zinc finger protein 541 (ZNF541), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr19:48,023,942-48,059,113 Size: 35,172 Total Exon Count: 15 Strand: -
Coding Region
   Position: hg19 chr19:48,024,481-48,059,113 Size: 34,633 Coding Exon Count: 15 

Page IndexSequence and LinksCTDGene AllelesRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther NamesModel Information
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr19:48,023,942-48,059,113)mRNA (may differ from genome)Protein (1346 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsH-INV

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 20.93 RPKM in Testis
Total median expression: 30.68 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
3' UTR -201.12539-0.373 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
  Pfam Domains:
PF00096 - Zinc finger, C2H2 type
PF01448 - ELM2 domain
PF12874 - Zinc-finger of C2H2 type
PF13912 - C2H2-type zinc finger

SCOP Domains:
46689 - Homeodomain-like
57667 - C2H2 and C2HC zinc fingers

ModBase Predicted Comparative 3D Structure on Q9H0D2-3
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     

-  Descriptions from all associated GenBank mRNAs
  AL136846 - Homo sapiens mRNA; cDNA DKFZp434I1930 (from clone DKFZp434I1930).
AL833862 - Homo sapiens mRNA; cDNA DKFZp434J1526 (from clone DKFZp434J1526).
JD434209 - Sequence 415233 from Patent EP1572962.
BC101050 - Homo sapiens zinc finger protein 541, mRNA (cDNA clone MGC:119518 IMAGE:40008070), complete cds.
BC101051 - Homo sapiens zinc finger protein 541, mRNA (cDNA clone MGC:119519 IMAGE:40008071), complete cds.
BC101052 - Homo sapiens zinc finger protein 541, mRNA (cDNA clone MGC:119520 IMAGE:40008072), complete cds.
BC101053 - Homo sapiens zinc finger protein 541, mRNA (cDNA clone MGC:119521 IMAGE:40008073), complete cds.
JD368564 - Sequence 349588 from Patent EP1572962.
JD402202 - Sequence 383226 from Patent EP1572962.
JD243424 - Sequence 224448 from Patent EP1572962.
JD110515 - Sequence 91539 from Patent EP1572962.
JD520730 - Sequence 501754 from Patent EP1572962.
JD188438 - Sequence 169462 from Patent EP1572962.
JD484791 - Sequence 465815 from Patent EP1572962.
AK314169 - Homo sapiens cDNA, FLJ94882.
JD176961 - Sequence 157985 from Patent EP1572962.
JD227519 - Sequence 208543 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001277075, NP_001264004, Q9H0D2-3, uc002phg.4
UCSC ID: uc002phg.5
RefSeq Accession: NM_001277075
Protein: Q9H0D2-3, splice isoform of Q9H0D2 CCDS: CCDS46133.2

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_001277075.1
exon count: 15CDS single in 3' UTR: no RNA size: 4599
ORF size: 4041CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 8282.00frame shift in genome: no % Coverage: 99.59
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.