The name of this superfamily has been modified since the most recent official CATH+ release (v4_3_0). At the point of the last release, this superfamily was named:

"
Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
".

Functional Families

Overview of the Structural Clusters (SC) and Functional Families within this CATH Superfamily. Clusters with a representative structure are represented by a filled circle.
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FunFam 84: paired box protein Pax-9

Please note: GO annotations are assigned to the full protein sequence rather than individual protein domains. Since a given protein can contain multiple domains, it is possible that some of the annotations below come from additional domains that occur in the same protein, but have been classified elsewhere in CATH.

There are 13 GO terms relating to "molecular function"

The search results have been sorted with the annotations that are found most frequently at the top of the list. The results can be filtered by typing text into the search box at the top of the table.
GO Term Annotations Evidence
DNA-binding transcription factor activity, RNA polymerase II-specific GO:0000981
A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a RNA polymerase II-transcribed gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units.
4 P15863 (/ISA) P55771 (/ISA) P55771 (/ISA) P55771 (/ISA)
DNA-binding transcription factor activity, RNA polymerase II-specific GO:0000981
A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a RNA polymerase II-transcribed gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units.
4 P15863 (/ISM) P55771 (/ISM) P55771 (/ISM) P55771 (/ISM)
DNA-binding transcription factor activity, RNA polymerase II-specific GO:0000981
A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a RNA polymerase II-transcribed gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units.
4 P15863 (/NAS) P55771 (/NAS) P55771 (/NAS) P55771 (/NAS)
DNA-binding transcription activator activity, RNA polymerase II-specific GO:0001228
A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a RNA polymerase II-transcribed gene to activate or increase transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units.
3 P09084 (/IDA) P47242 (/IDA) P47242 (/IDA)
DNA-binding transcription factor activity GO:0003700
A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
3 P09084 (/TAS) P47242 (/TAS) P47242 (/TAS)
Protein binding GO:0005515
Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
3 P55771 (/IPI) P55771 (/IPI) P55771 (/IPI)
Sequence-specific DNA binding GO:0043565
Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
3 G5ED14 (/IDA) Q98865 (/IDA) Q98866 (/IDA)
RNA polymerase II regulatory region sequence-specific DNA binding GO:0000977
Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
2 P47242 (/IMP) P47242 (/IMP)
RNA polymerase II regulatory region sequence-specific DNA binding GO:0000977
Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
1 G5ED14 (/IDA)
RNA polymerase II proximal promoter sequence-specific DNA binding GO:0000978
Interacting selectively and non-covalently with a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in the proximal promoter of a gene transcribed by RNA polymerase II. The proximal promoter is in cis with and relatively close to the core promoter.
1 P09084 (/IMP)
DNA-binding transcription activator activity, RNA polymerase II-specific GO:0001228
A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a RNA polymerase II-transcribed gene to activate or increase transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units.
1 P09084 (/IMP)
DNA binding GO:0003677
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
1 Q95139 (/ISS)
DNA-binding transcription factor activity GO:0003700
A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
1 G5ED14 (/ISS)

There are 57 GO terms relating to "biological process"

The search results have been sorted with the annotations that are found most frequently at the top of the list. The results can be filtered by typing text into the search box at the top of the table.
GO Term Annotations Evidence
Regulation of transcription, DNA-templated GO:0006355
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
3 P09084 (/TAS) P47242 (/TAS) P47242 (/TAS)
Animal organ morphogenesis GO:0009887
Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
3 P09084 (/TAS) P47242 (/TAS) P47242 (/TAS)
Pectoral fin development GO:0033339
The process whose specific outcome is the progression of the pectoral fin over time, from its formation to the mature structure.
3 A0A2R8PYI0 (/IMP) A0A2R8Q5G5 (/IMP) B0S7C8 (/IMP)
Negative regulation of transcription, DNA-templated GO:0045892
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
3 P55771 (/IDA) P55771 (/IDA) P55771 (/IDA)
Positive regulation of transcription by RNA polymerase II GO:0045944
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
3 P09084 (/IDA) P47242 (/IDA) P47242 (/IDA)
Positive regulation of transcription by RNA polymerase II GO:0045944
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
3 P09084 (/IGI) P47242 (/IGI) P47242 (/IGI)
Embryonic skeletal system development GO:0048706
The process, occurring during the embryonic phase, whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure.
3 A0A2R8PYI0 (/IMP) A0A2R8Q5G5 (/IMP) B0S7C8 (/IMP)
Endoderm development GO:0007492
The process whose specific outcome is the progression of the endoderm over time, from its formation to the mature structure. The endoderm is the innermost germ layer that develops into the gastrointestinal tract, the lungs and associated tissues.
2 P47242 (/IMP) P47242 (/IMP)
Odontogenesis GO:0042476
The process whose specific outcome is the progression of a tooth or teeth over time, from formation to the mature structure(s). A tooth is any hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food.
2 P47242 (/IGI) P47242 (/IGI)
Regulation of odontogenesis GO:0042481
Any process that modulates the frequency, rate or extent of the formation and development of a tooth or teeth.
2 P47242 (/IGI) P47242 (/IGI)
Negative regulation of transcription, DNA-templated GO:0045892
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
2 P47242 (/ISO) P47242 (/ISO)
Hard palate development GO:0060022
The biological process whose specific outcome is the progression of the hard palate from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. The hard palate is the anterior portion of the palate consisting of bone and mucous membranes.
2 Q98865 (/IMP) Q98866 (/IMP)
Face morphogenesis GO:0060325
The process in which the anatomical structures of the face are generated and organized. The face is the ventral division of the head.
2 P47242 (/IGI) P47242 (/IGI)
Cellular response to growth factor stimulus GO:0071363
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a growth factor stimulus.
2 P47242 (/IDA) P47242 (/IDA)
Skeletal system development GO:0001501
The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
1 P09084 (/IGI)
Skeletal system development GO:0001501
The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
1 P09084 (/IMP)
Skeletal system development GO:0001501
The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
1 P15863 (/TAS)
Cell fate specification GO:0001708
The process involved in the specification of cell identity. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.
1 G5ED14 (/IMP)
Cell fate determination GO:0001709
A process involved in cell fate commitment. Once determination has taken place, a cell becomes committed to differentiate down a particular pathway regardless of its environment.
1 Q95139 (/ISS)
Somitogenesis GO:0001756
The formation of mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo.
1 P09084 (/IMP)
Neuron migration GO:0001764
The characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature.
1 Q95139 (/ISS)
Nematode larval development GO:0002119
The process whose specific outcome is the progression of the nematode larva over time, from its formation to the mature structure. Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew.
1 G5ED14 (/IMP)
Transcription by RNA polymerase II GO:0006366
The synthesis of RNA from a DNA template by RNA polymerase II (RNAP II), originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
1 P15863 (/TAS)
Pattern specification process GO:0007389
Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate.
1 P09084 (/IMP)
Axonogenesis GO:0007409
De novo generation of a long process of a neuron, including the terminal branched region. Refers to the morphogenesis or creation of shape or form of the developing axon, which carries efferent (outgoing) action potentials from the cell body towards target cells.
1 Q95139 (/ISS)
Axon guidance GO:0007411
The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
1 Q95139 (/ISS)
Brain development GO:0007420
The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
1 Q95139 (/ISS)
Salivary gland morphogenesis GO:0007435
The process in which the anatomical structures of the salivary gland are generated and organized.
1 Q95139 (/ISS)
Larval somatic muscle development GO:0007526
The process whose specific outcome is the progression of the larval somatic muscle over time, from its formation to the mature structure.
1 P23757 (/IMP)
Cell population proliferation GO:0008283
The multiplication or reproduction of cells, resulting in the expansion of a cell population.
1 P09084 (/IMP)
Negative regulation of cell population proliferation GO:0008285
Any process that stops, prevents or reduces the rate or extent of cell proliferation.
1 Q95139 (/ISS)
Embryo development ending in birth or egg hatching GO:0009792
The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell.
1 G5ED14 (/IMP)
Dorsal/ventral axis specification GO:0009950
The establishment, maintenance and elaboration of the dorsal/ventral axis. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism.
1 Q95139 (/ISS)
Anterior/posterior pattern specification GO:0009952
The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
1 Q95139 (/ISS)
Dorsal/ventral pattern formation GO:0009953
The regionalization process in which the areas along the dorsal/ventral axis are established that will lead to differences in cell differentiation. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism.
1 Q95139 (/ISS)
Pituitary gland development GO:0021983
The progression of the pituitary gland over time from its initial formation until its mature state. The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands.
1 Q95139 (/ISS)
Cell differentiation GO:0030154
The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
1 Q95139 (/ISS)
Regulation of cell migration GO:0030334
Any process that modulates the frequency, rate or extent of cell migration.
1 Q95139 (/ISS)
Forebrain development GO:0030900
The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
1 Q95139 (/ISS)
Vulval development GO:0040025
The process whose specific outcome is the progression of the egg-laying organ of female and hermaphrodite nematodes over time, from its formation to the mature structure. In nematodes, the vulva is formed from ventral epidermal cells during larval stages to give rise to a fully formed vulva in the adult.
1 G5ED14 (/IMP)
Eye photoreceptor cell development GO:0042462
Development of a photoreceptor, a sensory cell in the eye that reacts to the presence of light. They usually contain a pigment that undergoes a chemical change when light is absorbed, thus stimulating a nerve.
1 Q95139 (/ISS)
Camera-type eye development GO:0043010
The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.
1 Q95139 (/ISS)
CD4-positive, alpha-beta T cell differentiation GO:0043367
The process in which a relatively unspecialized T cell acquires specialized features of a mature CD4-positive, alpha-beta T cell.
1 P09084 (/IMP)
CD8-positive, alpha-beta T cell differentiation GO:0043374
The process in which a relatively unspecialized T cell acquires specialized features of a mature CD8-positive, alpha-beta T cell.
1 P09084 (/IMP)
Nematode male tail tip morphogenesis GO:0045138
The process in which the anatomical structure of the adult male tail tip is generated and organized. In some species of rhabitid nematodes, the male tail tip undergoes a morphological change such that the most posterior hypodermal cells in the tail (hyp8-11 in C. elegans) fuse and retract anteriorly, changing the shape of the tail from a pointed, tapered cone, or spike, to a rounded, blunt dome.
1 G5ED14 (/IMP)
Cell fate commitment GO:0045165
The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field.
1 Q95139 (/ISS)
Negative regulation of neuron differentiation GO:0045665
Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation.
1 Q95139 (/ISS)
Positive regulation of transcription by RNA polymerase II GO:0045944
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
1 G5ED14 (/IMP)
Positive regulation of transcription by RNA polymerase II GO:0045944
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
1 Q95139 (/ISS)
Thymus development GO:0048538
The process whose specific outcome is the progression of the thymus over time, from its formation to the mature structure. The thymus is a symmetric bi-lobed organ involved primarily in the differentiation of immature to mature T cells, with unique vascular, nervous, epithelial, and lymphoid cell components.
1 P09084 (/IGI)
Dendrite morphogenesis GO:0048813
The process in which the anatomical structures of a dendrite are generated and organized.
1 P23757 (/IMP)
Regulation of neurogenesis GO:0050767
Any process that modulates the frequency, rate or extent of neurogenesis, the generation of cells in the nervous system.
1 Q95139 (/ISS)
Parathyroid gland development GO:0060017
The process whose specific outcome is the progression of the parathyroid gland over time, from its formation to the mature structure. The parathyroid gland is an organ specialised for secretion of parathyroid hormone.
1 P09084 (/IGI)
Uterus development GO:0060065
The reproductive developmental process whose specific outcome is the progression of the uterus over time, from its formation to the mature structure.
1 G5ED14 (/IMP)
Bone morphogenesis GO:0060349
The process in which bones are generated and organized.
1 P09084 (/IMP)
Sclerotome development GO:0061056
The progression of the sclerotome over time, from its initial formation to the mature structure. The sclerotome is the portion of the somite that will give rise to a vertebra.
1 P09084 (/IEP)
Sclerotome development GO:0061056
The progression of the sclerotome over time, from its initial formation to the mature structure. The sclerotome is the portion of the somite that will give rise to a vertebra.
1 P47236 (/NAS)

There are 3 GO terms relating to "cellular component"

The search results have been sorted with the annotations that are found most frequently at the top of the list. The results can be filtered by typing text into the search box at the top of the table.
GO Term Annotations Evidence
Transcription factor complex GO:0005667
A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.
3 P09084 (/TAS) P47242 (/TAS) P47242 (/TAS)
Nucleus GO:0005634
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
2 G5ED14 (/IDA) P23757 (/IDA)
Nucleus GO:0005634
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
1 Q95139 (/ISS)
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