# HISTORY 25 Mar 2016: Updated by: TOUCHUP-v1.15 15 Mar 2016: Updated by: TOUCHUP-v1.14 # molecular_function 20140811: Eukaryota_PTN000960546 has function core promoter proximal region sequence-specific DNA binding (GO:0000987) 20140805: Eukaryota_PTN000960546 has function transcription factor activity, sequence-specific DNA binding (GO:0003700) 20140815: Eukaryota_PTN000960546 has function protein homodimerization activity (GO:0042803) # cellular_component 20140805: Eukaryota_PTN000960546 is found in nucleus (GO:0005634) # biological_process 20140813: Eukaryota_PTN000960546 participates in sex differentiation (GO:0007548) 20140815: Boreoeutheria_PTN000268655 participates in brain development (GO:0007420) 20140805: Teleostei_PTN000268826 participates in determination of left/right symmetry (GO:0007368) # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES This family, the doublesex and Mab-3 related transcription factor family, is present in the animals, not within the plants, fungi, or bacteria. While it seems to have been present early within the animals, it looks like it has undergone duplications separately within the Bilateria (includes C. elegans and D. melanogaster) and within the Chordata. Deuterostomia_PTN001389452 - Dmrt2 clade ------------------------------------- Within this clade, the evolution looks simple except within the fish, where it has been characterized in D. rerio that there is a duplication (PMID:18358846, PMID:19789708) where Dmrt2a is more similar to the rest of the clade and is characterized as regulating somitogenesis, similarly to the mouse Dmrt2, while D. rerio Dmrtf2b is somewhat more divergent and is characterized as regulating generation of left/right asymmetry. The relative position of the fish sequences within this group does not look correct. Currently the two Takifugu and the two D. rerio sequences are shown under a speciation node, with individual duplication nodes in each species. However, examination of the MSA specifically for the fish sequences suggests that D. rerio dmrt2a and Takifugu DMRT2 are more similar to each other than either is to D. rerio Dmrt2b and Takifugu TAKRU_TAKRU_H2VDM4. Thus, it appears to me that there should be a duplication node at the top of the fish, so that D. rerio Dmrt2a and Takifugu DMRT2 are paired and likewise the other two fish sequences. Note: Successfully challenged TAS annotations to the BP terms "male gonad development (GO:0008584)" and "sex determination (GO:0007530)" for DMRT2 and also DMRT1 from PMID:10332030 (Raymond CS et al. 1999. A region of human chromosome 9p required for testis development contains two genes related to known sexual regulators. Hum Mol Genet. 1999 Jun;8(6):989-96.) Under Deuterostomia_PTN000268690 and a duplication node, there are four subclades, most of which are entirely vertebrate. Euteleostomi_PTN001389461 - Dmrt3 clade ------------------------------------- This is a vertebrate specific clade, which appears to have roles in regulation of spinal cord neuron specification and odontogenesis, as well as in regulation of sex differentiation. Euteleostomi_PTN001389471 - Dmrt1 clade ------------------------------------- This is a vertebrate specific clade, which appears to have opposing roles in regulation of meiosis versus mitosis in male versus female germ cells, as well as in regulation of sex differentiation. Euteleostomi_PTN000268631 - Dmrta1 ------------------------------------- This is a vertebrate specific clade which has roles in regulation of sex differentiation. Euteleostomi_PTN000268715 - contains Dmrtb1 and multiple mammalian duplications ------------------------------------- Amniota_PTN000268739 - Dmrtb1 - This group appears to have lost DNA binding ability. - Mammalia_PTN000268757 contains multiple vertebrate duplications. In the mouse, there is Dmrtc1c1 & Dmrtc1c2, Dmrtc1b, and Dmrtc2, of which only Dmrtc2 is experimentally characterized. Ecdysozoa_PTN000960581 (D mel & C el) - DROME_dsx, Ce dmd-9, dmd-7, dmd-4, dmd-5 ------------------------------------- This group contains the namesake Drosophila Dsx gene as well as a bunch of duplications in C. elegans. Eumetazoa_PTN001389555 - C elegans mab-3 & dmd-3 ----------------------------------- This clade is primarily composed of Bilateria_PTN000960594, which mostly C elegans genes: dmd-8, mab-23, dmd-6, mab-3, dmd-3, dmd-10, dmd-11. Of these, mab-3 and dmd-3 are both experimentally characterized as being involved in male specific differentiation processes. Eumetazoa_PTN001389568 (4 seqs: 1 Ixodes, 2 Nematostella, 1 Trichoplax) ------------------------------------- This "clade" looks like partial sequences (with two copies of the Nematostella one), so I suspect their placement at this location within the tree may be erroneous. root_PTN001389548 - all but one of these looks like a partial sequence # REFERENCE Annotation inferences using phylogenetic trees The goal of the GO Reference Genome Project, described in PMID 19578431, is to provide accurate, complete and consistent GO annotations for all genes in twelve model organism genomes. To this end, GO curators are annotating evolutionary trees from the PANTHER database with GO terms describing molecular function, biological process and cellular component. GO terms based on experimental data from the scientific literature are used to annotate ancestral genes in the phylogenetic tree by sequence similarity (ISS), and unannotated descendants of these ancestral genes are inferred to have inherited these same GO annotations by descent. The annotations are done using a tool called PAINT (Phylogenetic Annotation and INference Tool).