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:

"
Homeodomain-like
".

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 73: Putative LIM/homeobox protein Lhx3

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 16 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
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).
7 P36200 (/IPI) P36200 (/IPI) P50481 (/IPI) Q969G2 (/IPI) Q969G2 (/IPI) Q969G2 (/IPI) Q969G2 (/IPI)
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.
6 Q969G2 (/ISA) Q969G2 (/ISA) Q969G2 (/ISA) Q969G2 (/ISA) Q9UBR4 (/ISA) Q9UBR4 (/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.
6 Q969G2 (/ISM) Q969G2 (/ISM) Q969G2 (/ISM) Q969G2 (/ISM) Q9UBR4 (/ISM) Q9UBR4 (/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.
6 Q969G2 (/NAS) Q969G2 (/NAS) Q969G2 (/NAS) Q969G2 (/NAS) Q9UBR4 (/NAS) Q9UBR4 (/NAS)
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.
6 Q969G2 (/IDA) Q969G2 (/IDA) Q969G2 (/IDA) Q969G2 (/IDA) Q9UBR4 (/IDA) Q9UBR4 (/IDA)
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.
4 Q969G2 (/IC) Q969G2 (/IC) Q969G2 (/IC) Q969G2 (/IC)
Methyl-CpG binding GO:0008327
Interacting selectively and non-covalently with a methylated cytosine/guanine dinucleotide.
4 Q969G2 (/IDA) Q969G2 (/IDA) Q969G2 (/IDA) Q969G2 (/IDA)
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 A2ALD8 (/IDA) Q9UBR4 (/IDA) Q9UBR4 (/IDA)
RNA polymerase II transcription factor binding GO:0001085
Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II.
2 Q9UBR4 (/IPI) Q9UBR4 (/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.
2 P50481 (/ISO) P53776 (/ISO)
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 A2ALD8 (/IDA)
RNA polymerase II transcription factor binding GO:0001085
Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II.
1 P50481 (/ISO)
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 P50481 (/ISO)
DNA binding GO:0003677
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
1 O97581 (/IDA)
Methyl-CpG binding GO:0008327
Interacting selectively and non-covalently with a methylated cytosine/guanine dinucleotide.
1 P53776 (/ISO)
Methyl-CpG binding GO:0008327
Interacting selectively and non-covalently with a methylated cytosine/guanine dinucleotide.
1 P53776 (/ISS)

There are 22 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
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.
8 A2ALD8 (/IDA) P50481 (/IDA) Q969G2 (/IDA) Q969G2 (/IDA) Q969G2 (/IDA) Q969G2 (/IDA) Q9UBR4 (/IDA) Q9UBR4 (/IDA)
Ventral spinal cord interneuron specification GO:0021521
The process in which a cell becomes capable of differentiating autonomously into a ventral spinal cord interneuron in an environment that is neutral with respect to the developmental pathway.
3 A1L270 (/IGI) B0S5S7 (/IGI) Q90421 (/IGI)
Positive regulation of transcription, DNA-templated GO:0045893
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
3 O97581 (/ISS) Q9UBR4 (/ISS) Q9UBR4 (/ISS)
Placenta development GO:0001890
The process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
2 P50481 (/IGI) P53776 (/IGI)
Motor neuron axon guidance GO:0008045
The process in which the migration of an axon growth cone of a motor neuron is directed to a specific target site in response to a combination of attractive and repulsive cues.
2 P50481 (/IGI) P53776 (/IGI)
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.
2 Q9UBR4 (/TAS) Q9UBR4 (/TAS)
Medial motor column neuron differentiation GO:0021526
The process in which differentiating motor neurons in the neural tube acquire the specialized structural and/or functional features of medial motor column neurons. Medial motor column neurons are generated at all rostrocaudal levels and send axons to the axial muscles (medial group) and to the body wall muscles (lateral group). Differentiation includes the processes involved in commitment of a cell to a specific fate.
2 P50481 (/IGI) P53776 (/IGI)
Lung development GO:0030324
The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
2 G3V8E3 (/IEP) G3V9E7 (/IEP)
Negative regulation of apoptotic process GO:0043066
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
2 P50481 (/IMP) P53776 (/IMP)
Positive regulation of transcription, DNA-templated GO:0045893
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
2 O97581 (/IDA) P50481 (/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.
2 P50481 (/ISO) P53776 (/ISO)
Inner ear development GO:0048839
The process whose specific outcome is the progression of the inner ear over time, from its formation to the mature structure.
2 Q9UBR4 (/IEP) Q9UBR4 (/IEP)
Regulation of transcription, DNA-templated GO:0006355
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
1 O97581 (/IDA)
Multicellular organism development GO:0007275
The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
1 Q9HBU2 (/NAS)
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.
1 P53776 (/IMP)
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 P50481 (/IMP)
Spinal cord motor neuron cell fate specification GO:0021520
The process in which a cell becomes capable of differentiating autonomously into a motor neuron in an environment that is neutral with respect to the developmental pathway.
1 P50481 (/IGI)
Ventral spinal cord interneuron specification GO:0021521
The process in which a cell becomes capable of differentiating autonomously into a ventral spinal cord interneuron in an environment that is neutral with respect to the developmental pathway.
1 P50481 (/IDA)
Spinal cord association neuron differentiation GO:0021527
The process in which neuroepithelial cells in the neural tube acquire specialized structural and/or functional features of association neurons. Association neurons are cells located in the dorsal portion of the spinal cord that integrate sensory input. Differentiation includes the processes involved in commitment of a cell to a specific fate.
1 P50481 (/IDA)
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 P50481 (/IMP)
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 P50481 (/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 P50481 (/IGI)

There are 6 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
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 Q9UBR4 (/TAS) Q9UBR4 (/TAS)
Nucleoplasm GO:0005654
That part of the nuclear content other than the chromosomes or the nucleolus.
2 P50481 (/TAS) P53776 (/TAS)
Cell GO:0005623
The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
1 P53412 (/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 O97581 (/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 P50481 (/ISO)
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.
1 P50481 (/IDA)
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