Human Gene ZSCAN5B (uc010ygh.2) Description and Page Index
  Description: Homo sapiens zinc finger and SCAN domain containing 5B (ZSCAN5B), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr19:56,701,058-56,704,421 Size: 3,364 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr19:56,701,196-56,704,421 Size: 3,226 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsGene AllelesRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Model InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:56,701,058-56,704,421)mRNA (may differ from genome)Protein (495 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaBioGPSCGAP
EnsemblEntrez GeneExonPrimerGeneCardsHGNCHPRD
LynxMGIneXtProtPubMedStanford SOURCETreefam
UniProtKB

-  Comments and Description Text from UniProtKB
  ID: ZSA5B_HUMAN
DESCRIPTION: RecName: Full=Zinc finger and SCAN domain-containing protein 5B;
FUNCTION: May be involved in transcriptional regulation (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity).
SIMILARITY: Contains 5 C2H2-type zinc fingers.
SIMILARITY: Contains 1 SCAN box domain.

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 1.59 RPKM in Testis
Total median expression: 3.06 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 -20.51138-0.149 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
IPR008916 - Retrov_capsid_C
IPR003309 - Tscrpt_reg_SCAN
IPR007087 - Znf_C2H2
IPR015880 - Znf_C2H2-like
IPR013087 - Znf_C2H2/integrase_DNA-bd

Pfam Domains:
PF00096 - Zinc finger, C2H2 type
PF02023 - SCAN domain
PF12874 - Zinc-finger of C2H2 type
PF13912 - C2H2-type zinc finger

SCOP Domains:
48695 - Multiheme cytochromes
57667 - C2H2 and C2HC zinc fingers

ModBase Predicted Comparative 3D Structure on A6NJL1
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 orthologGenome Browser
Gene Details    Gene Details
Gene Sorter    Gene Sorter
     SGD
     Protein Sequence
     Alignment

-  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:0003700 transcription factor activity, sequence-specific DNA 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

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
 

-  Other Names for This Gene
  Alternate Gene Symbols: A6NJL1, NM_001080456, NP_001073925, ZSA5B_HUMAN
UCSC ID: uc010ygh.2
RefSeq Accession: NM_001080456
Protein: A6NJL1 (aka ZSA5B_HUMAN)
CCDS: CCDS46203.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001080456.2
exon count: 4CDS single in 3' UTR: no RNA size: 1626
ORF size: 1488CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3164.00frame shift in genome: no % Coverage: 100.00
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.