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 57: Short stature homeobox 2

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 11 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.
14 A6NJT0 (/ISA) A6NJT0 (/ISA) O15266 (/ISA) O15266 (/ISA) O15266 (/ISA) O15266 (/ISA) O60902 (/ISA) O60902 (/ISA) O60902 (/ISA) O60902 (/ISA)
(4 more)
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.
14 A6NJT0 (/ISM) A6NJT0 (/ISM) O15266 (/ISM) O15266 (/ISM) O15266 (/ISM) O15266 (/ISM) O60902 (/ISM) O60902 (/ISM) O60902 (/ISM) O60902 (/ISM)
(4 more)
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.
12 O15266 (/NAS) O15266 (/NAS) O15266 (/NAS) O15266 (/NAS) O60902 (/NAS) O60902 (/NAS) O60902 (/NAS) O60902 (/NAS) O60902 (/NAS) O60902 (/NAS)
(2 more)
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 O15266 (/IDA) O15266 (/IDA) O15266 (/IDA) O15266 (/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 O15266 (/IMP) O15266 (/IMP) O15266 (/IMP) O15266 (/IMP)
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.
4 O15266 (/TAS) O15266 (/TAS) O15266 (/TAS) O15266 (/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).
4 O15266 (/IPI) O15266 (/IPI) O15266 (/IPI) O15266 (/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.
4 O15266 (/IDA) O15266 (/IDA) O15266 (/IDA) O15266 (/IDA)
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.
4 O15266 (/IMP) O15266 (/IMP) O15266 (/IMP) O15266 (/IMP)
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 P29506 (/IMP)
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 P29506 (/ISS)

There are 47 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
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).
12 O15266 (/TAS) O15266 (/TAS) O15266 (/TAS) O15266 (/TAS) O60902 (/TAS) O60902 (/TAS) O60902 (/TAS) O60902 (/TAS) O60902 (/TAS) O60902 (/TAS)
(2 more)
Nervous system development GO:0007399
The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
8 O60902 (/TAS) O60902 (/TAS) O60902 (/TAS) O60902 (/TAS) O60902 (/TAS) O60902 (/TAS) O60902 (/TAS) O60902 (/TAS)
Heart development GO:0007507
The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
8 O60902 (/TAS) O60902 (/TAS) O60902 (/TAS) O60902 (/TAS) O60902 (/TAS) O60902 (/TAS) O60902 (/TAS) O60902 (/TAS)
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).
4 O15266 (/TAS) O15266 (/TAS) O15266 (/TAS) O15266 (/TAS)
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.
4 O15266 (/IMP) O15266 (/IMP) O15266 (/IMP) O15266 (/IMP)
Ossification GO:0001503
The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
2 B0S5T0 (/IMP) Q3B7G6 (/IMP)
Heart development GO:0007507
The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
2 E9QBI3 (/IMP) Q7SZN8 (/IMP)
Regulation of heart contraction GO:0008016
Any process that modulates the frequency, rate or extent of heart contraction. Heart contraction is the process in which the heart decreases in volume in a characteristic way to propel blood through the body.
2 E9QBI3 (/IMP) Q7SZN8 (/IMP)
Cell population proliferation GO:0008283
The multiplication or reproduction of cells, resulting in the expansion of a cell population.
2 B0S5T0 (/IMP) Q3B7G6 (/IMP)
Bone mineralization GO:0030282
The deposition of hydroxyapatite, a form of calcium phosphate with the formula Ca10(PO4)6(OH)2, in bone tissue.
2 B0S5T0 (/IMP) Q3B7G6 (/IMP)
Multicellular organism reproduction GO:0032504
The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
2 O96616 (/HEP) Q9VX20 (/HEP)
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.
2 B0S5T0 (/IGI) Q3B7G6 (/IGI)
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.
2 B0S5T0 (/IMP) Q3B7G6 (/IMP)
Cartilage condensation GO:0001502
The condensation of mesenchymal cells that have been committed to differentiate into chondrocytes.
1 O08934 (/IMP)
Osteoblast differentiation GO:0001649
The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.
1 P70390 (/IMP)
Positive regulation of mesenchymal cell proliferation GO:0002053
The process of activating or increasing the rate or extent of mesenchymal cell proliferation. Mesenchymal cells are loosely organized embryonic cells.
1 P70390 (/IMP)
Chondrocyte differentiation GO:0002062
The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte. A chondrocyte is a polymorphic cell that forms cartilage.
1 P70390 (/IMP)
Chondrocyte development GO:0002063
The process whose specific outcome is the progression of a chondrocyte over time, from its commitment to its mature state. Chondrocyte development does not include the steps involved in committing a chondroblast to a chondrocyte fate.
1 P70390 (/IMP)
Heart valve development GO:0003170
The progression of a heart valve over time, from its formation to the mature structure. A heart valve is a structure that restricts the flow of blood to different regions of the heart and forms from an endocardial cushion.
1 P70390 (/IMP)
Cardiac atrium morphogenesis GO:0003209
The process in which the cardiac atrium is generated and organized. A cardiac atrium receives blood from a vein and pumps it to a cardiac ventricle.
1 P70390 (/IMP)
Regulation of transcription, DNA-templated GO:0006355
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
1 P29506 (/IMP)
Regulation of transcription, DNA-templated GO:0006355
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
1 P29506 (/ISS)
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 O08934 (/IMP)
Neuroblast fate determination GO:0007400
The cell fate determination process in which a cell becomes capable of differentiating autonomously into a neuroblast cell regardless of its environment; upon determination, the cell fate cannot be reversed. An example of this process is found in Mus musculus.
1 P29506 (/IMP)
Synapse assembly GO:0007416
The aggregation, arrangement and bonding together of a set of components to form a synapse. This process ends when the synapse is mature (functional).
1 P29506 (/IMP)
Synaptic target recognition GO:0008039
The process in which a neuronal cell in a multicellular organism interprets signals produced by potential target cells, with which it may form synapses.
1 P29506 (/IMP)
Regulation of gene expression GO:0010468
Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
1 O08934 (/IMP)
Dorsal spinal cord development GO:0021516
The process whose specific outcome is the progression of the dorsal region of the spinal cord over time, from its formation to the mature structure. The dorsal region of the mature spinal cord contains neurons that process and relay sensory input.
1 O08934 (/IMP)
Olfactory bulb interneuron differentiation GO:0021889
The process in which a neuroblast acquires specialized features of an interneuron residing in the olfactory bulb.
1 O08934 (/IMP)
Embryonic limb morphogenesis GO:0030326
The process, occurring in the embryo, by which the anatomical structures of the limb are generated and organized. A limb is an appendage of an animal used for locomotion or grasping.
1 P70390 (/IMP)
Regulation of chondrocyte differentiation GO:0032330
Any process that modulates the frequency, rate or extent of chondrocyte differentiation.
1 P70390 (/IMP)
Embryonic forelimb morphogenesis GO:0035115
The process, occurring in the embryo, by which the anatomical structures of the forelimb are generated and organized. The forelimbs are the front limbs of an animal, e.g. the arms of a human.
1 P70390 (/IMP)
Common myeloid progenitor cell proliferation GO:0035726
The multiplication or reproduction of common myeloid progenitor cells, resulting in the expansion of a cell population. A common myeloid progenitor cell is a progenitor cell committed to the myeloid lineage.
1 O08934 (/IMP)
Locomotion GO:0040011
Self-propelled movement of a cell or organism from one location to another.
1 P29506 (/IMP)
Regulation of cell differentiation GO:0045595
Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features.
1 O08934 (/IMP)
Positive regulation of smoothened signaling pathway GO:0045880
Any process that activates or increases the frequency, rate or extent of smoothened signaling.
1 P70390 (/IMP)
Synaptic vesicle transport GO:0048489
The directed movement of synaptic vesicles.
1 P29506 (/IMP)
Embryonic digestive tract morphogenesis GO:0048557
The process in which the anatomical structures of the digestive tract are generated and organized during embryonic development. The digestive tract is the anatomical structure through which food passes and is processed.
1 P70390 (/IMP)
Embryonic morphogenesis GO:0048598
The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants.
1 P70390 (/IMP)
Positive regulation of skeletal muscle fiber development GO:0048743
Any process that activates, maintains or increases the rate of skeletal muscle fiber development. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast.
1 P70390 (/IMP)
Regulation of axonogenesis GO:0050770
Any process that modulates the frequency, rate or extent of axonogenesis, the generation of an axon, the long process of a neuron.
1 P29506 (/IMP)
Positive regulation of axonogenesis GO:0050772
Any process that activates or increases the frequency, rate or extent of axonogenesis.
1 P70390 (/IMP)
Regulation of synapse structure or activity GO:0050803
Any process that modulates the physical form or the activity of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell).
1 P29506 (/IMP)
Embryonic skeletal joint morphogenesis GO:0060272
The process in which the anatomical structures of skeletal joints are generated and organized during the embryonic phase. A skeletal joint is the connecting structure between the bones of the skeleton.
1 P70390 (/IMP)
Cartilage development involved in endochondral bone morphogenesis GO:0060351
The process whose specific outcome is the progression of the cartilage that will provide a scaffold for mineralization of endochondral bones.
1 P70390 (/IMP)
Muscle tissue morphogenesis GO:0060415
The process in which the anatomical structures of muscle tissue are generated and organized. Muscle tissue consists of a set of cells that are part of an organ and carry out a contractive function.
1 P70390 (/IMP)
Regulation of branching morphogenesis of a nerve GO:2000172
Any process that modulates the frequency, rate or extent of branching morphogenesis of a nerve.
1 P70390 (/IMP)

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
Nucleoplasm GO:0005654
That part of the nuclear content other than the chromosomes or the nucleolus.
8 A0A024R385 (/IDA) A0A024R385 (/IDA) A0A024R385 (/IDA) A0A024R385 (/IDA) O15266 (/IDA) O15266 (/IDA) O15266 (/IDA) O15266 (/IDA)
Intracellular membrane-bounded organelle GO:0043231
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
8 A0A024R385 (/IDA) A0A024R385 (/IDA) A0A024R385 (/IDA) A0A024R385 (/IDA) O15266 (/IDA) O15266 (/IDA) O15266 (/IDA) O15266 (/IDA)
Extracellular space GO:0005615
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
2 O96616 (/HDA) Q9VX20 (/HDA)
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 P29506 (/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 P29506 (/NAS)
Axon GO:0030424
The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
1 P29506 (/IDA)