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Protocols

HomeoDB specifications

Information


Unique identifier OMICS_24515
Name HomeoDB
Alternative name Homeobox Database
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
  • Vertebrates
    • Danio rerio
    • Gallus gallus

Maintainers


  • person_outline Ying-fu Zhong
  • person_outline Peter Holland

Publications for Homeobox Database

HomeoDB citations

 (12)
library_books

The house spider genome reveals an ancient whole genome duplication during arachnid evolution

2017
BMC Biol
PMCID: 5535294
PMID: 28756775
DOI: 10.1186/s12915-017-0399-x

[…] To identify possible homeobox genes in P. tepidariorum and C. sculpturatus, the complete set of homeodomain sequences from HomeoDB [, ], those identified previously in the scorpion Mesobuthus martensii [], and the P. tepidariorum gene prospero (Accession: BAE87100.1) were BLASTP-searched (version 2.4.0+) [] against the P. […]

library_books

Brain regionalization genes are co opted into shell field patterning in Mollusca

2017
Sci Rep
PMCID: 5511173
PMID: 28710480
DOI: 10.1038/s41598-017-05605-5

[…] Homeodomain amino acid sequences of Gbx, Dlx, Hox1, Hox3, Cdx, and Lhx2/4 were retrieved from the homeobox database (http://homeodb.cbi.pku.edu.cn/) and GenBank (accession numbers provided in Supplementary Fig. ), . Gbx amino acid sequences were used in BLAST searches against the assembled transcr […]

library_books

A sister of NANOG regulates genes expressed in pre implantation human development

2017
Open Biol
PMCID: 5413911
PMID: 28446706
DOI: 10.1098/rsob.170027

[…] Predicted peptide sequences were obtained from NCBI, Ensembl and HomeoDB2 [], and are listed in the electronic supplementary material, file S5. Amino acid sequence alignments were generated using MAFFT v. 7.123b [] and putatively homologous peptide motifs identifie […]

library_books

Dynamics of genomic innovation in the unicellular ancestry of animals

2017
eLife
PMCID: 5560861
PMID: 28726632
DOI: 10.7554/eLife.26036.043

[…] lar holozoans (see taxon sampling above) using the homeobox HMM (PF00046), and restricted the subsequent phylogenetic analysis (see below) to sequences that clustered with known LIM-HD genes from the HomeoDB database in blastp searches ().In the case of the eRF3, eIF4A3, Smg5/6/7 and SRSF1-9 gene families, we queried the genomes/transcriptomes mentioned above using blastp searches of the human ort […]

call_split

A Conserved Structural Signature of the Homeobox Coding DNA in HOX genes

2016
Sci Rep
PMCID: 5064350
PMID: 27739488
DOI: 10.1038/srep35415
call_split See protocol

[…] shold of 0.001, and selected the genes for which the alignment length was at least 140 nucleotides. For other species, the selection was based on the species-specific list of Hox genes present in the Homeobox Database that have sequences in GenBank. We predicted the HRC patterns using a modified sliding tetramer window algorithm. The original sliding tetramer HRC prediction produces four values of […]

call_split

HOX gene complement and expression in the planarian Schmidtea mediterranea

2016
PMCID: 4815179
PMID: 27034770
DOI: 10.1186/s13227-016-0044-8
call_split See protocol

[…] Protein sequences were obtained from the NCBI Entrez protein database as well as individual organism genome sequencing project Web sites and the Homeobox Database (http://homeodb.zoo.ox.ac.uk) []. All protein sequences or GenBank accession numbers are in Additional file : Table S1. www.macgenome.org was used for all Macrostomum lignano genomic […]

Citations

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HomeoDB institution(s)
Department of Zoology, University of Oxford, Oxford, UK
HomeoDB funding source(s)
Supported by a Marie Curie International Incoming Fellowship within the 7th European Community Framework Programme.

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