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 66: Paired mesoderm homeobox protein 1

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
HMG box domain binding GO:0071837
Interacting selectively and non-covalently with an HMG box domain, a protein domain that consists of three helices in an irregular array. HMG-box domains are found in one or more copies in HMG-box proteins, which form a large, diverse family involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin.
23 P63013 (/IPI) P63013 (/IPI) P63013 (/IPI) P63013 (/IPI) P63013 (/IPI) P63013 (/IPI) P63013 (/IPI) P63013 (/IPI) P63013 (/IPI) P63013 (/IPI)
(13 more)
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.
22 P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA)
(12 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.
22 P54821 (/ISA) P54821 (/ISA) P54821 (/ISA) P54821 (/ISA) P54821 (/ISA) P54821 (/ISA) P54821 (/ISA) P54821 (/ISA) P54821 (/ISA) P54821 (/ISA)
(12 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.
22 P54821 (/ISM) P54821 (/ISM) P54821 (/ISM) P54821 (/ISM) P54821 (/ISM) P54821 (/ISM) P54821 (/ISM) P54821 (/ISM) P54821 (/ISM) P54821 (/ISM)
(12 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.
22 P54821 (/NAS) P54821 (/NAS) P54821 (/NAS) P54821 (/NAS) P54821 (/NAS) P54821 (/NAS) P54821 (/NAS) P54821 (/NAS) P54821 (/NAS) P54821 (/NAS)
(12 more)
DNA-binding transcription repressor activity, RNA polymerase II-specific GO:0001227
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 repress or decrease transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units.
22 P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA)
(12 more)
DNA binding GO:0003677
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
22 P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA)
(12 more)
Transcription coactivator activity GO:0003713
A protein or a member of a complex that interacts specifically and non-covalently with a DNA-bound DNA-binding transcription factor to activate the transcription of specific genes. Coactivators often act by altering chromatin structure and modifications. For example, one class of transcription coregulators modifies chromatin structure through covalent modification of histones. A second ATP-dependent class modifies the conformation of chromatin. Another type of coregulator activity is the bridging of a DNA-binding transcription factor to the basal transcription machinery. The Mediator complex, which bridges transcription factors and RNA polymerase, is also a transcription coactivator.
22 P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA)
(12 more)
Transcription coactivator activity GO:0003713
A protein or a member of a complex that interacts specifically and non-covalently with a DNA-bound DNA-binding transcription factor to activate the transcription of specific genes. Coactivators often act by altering chromatin structure and modifications. For example, one class of transcription coregulators modifies chromatin structure through covalent modification of histones. A second ATP-dependent class modifies the conformation of chromatin. Another type of coregulator activity is the bridging of a DNA-binding transcription factor to the basal transcription machinery. The Mediator complex, which bridges transcription factors and RNA polymerase, is also a transcription coactivator.
16 P54821 (/TAS) P54821 (/TAS) P54821 (/TAS) P54821 (/TAS) P54821 (/TAS) P54821 (/TAS) P54821 (/TAS) P54821 (/TAS) P54821 (/TAS) P54821 (/TAS)
(6 more)
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.
6 Q99811 (/NAS) Q99811 (/NAS) Q99811 (/NAS) Q99811 (/NAS) Q99811 (/NAS) Q99811 (/NAS)
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 Q21836 (/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.
1 Q06348 (/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 Q06348 (/IMP)

There are 28 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
Negative regulation of transcription by RNA polymerase II GO:0000122
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription mediated by RNA polymerase II.
44 P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA)
(34 more)
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.
23 P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI)
(13 more)
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.
23 P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI)
(13 more)
Inner ear morphogenesis GO:0042472
The process in which the anatomical structures of the inner ear are generated and organized. The inner ear is the structure in vertebrates that contains the organs of balance and hearing. It consists of soft hollow sensory structures (the membranous labyrinth) containing fluid (endolymph) surrounded by fluid (perilymph) and encased in a bony cavity (the bony labyrinth). It consists of two chambers, the sacculus and utriculus, from which arise the cochlea and semicircular canals respectively.
23 P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI)
(13 more)
Middle ear morphogenesis GO:0042474
The process in which the anatomical structures of the middle ear are generated and organized. The middle ear is the air-filled cavity within the skull of vertebrates that lies between the outer ear and the inner ear. It is linked to the pharynx (and therefore to outside air) via the Eustachian tube and in mammals contains the three ear ossicles, which transmit auditory vibrations from the outer ear (via the tympanum) to the inner ear (via the oval window).
23 P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI)
(13 more)
Positive regulation of smoothened signaling pathway GO:0045880
Any process that activates or increases the frequency, rate or extent of smoothened signaling.
23 P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI)
(13 more)
Embryonic cranial skeleton morphogenesis GO:0048701
The process in which the anatomical structures of the cranial skeleton are generated and organized during the embryonic phase.
23 P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI)
(13 more)
Embryonic skeletal system morphogenesis GO:0048704
The process in which the anatomical structures of the skeleton are generated and organized during the embryonic phase.
23 P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI)
(13 more)
Artery morphogenesis GO:0048844
The process in which the anatomical structures of arterial blood vessels are generated and organized. Arteries are blood vessels that transport blood from the heart to the body and its organs.
23 P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI)
(13 more)
Cartilage development GO:0051216
The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
23 P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI) P63013 (/IGI)
(13 more)
Negative regulation of transcription by RNA polymerase II GO:0000122
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription mediated by RNA polymerase II.
22 P63013 (/ISO) P63013 (/ISO) P63013 (/ISO) P63013 (/ISO) P63013 (/ISO) P63013 (/ISO) P63013 (/ISO) P63013 (/ISO) P63013 (/ISO) P63013 (/ISO)
(12 more)
Middle ear morphogenesis GO:0042474
The process in which the anatomical structures of the middle ear are generated and organized. The middle ear is the air-filled cavity within the skull of vertebrates that lies between the outer ear and the inner ear. It is linked to the pharynx (and therefore to outside air) via the Eustachian tube and in mammals contains the three ear ossicles, which transmit auditory vibrations from the outer ear (via the tympanum) to the inner ear (via the oval window).
22 P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP)
(12 more)
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.
22 P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA)
(12 more)
Neuron fate determination GO:0048664
The process in which a cell becomes capable of differentiating autonomously into a neuron regardless of its environment; upon determination, the cell fate cannot be reversed.
22 P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA)
(12 more)
Embryonic cranial skeleton morphogenesis GO:0048701
The process in which the anatomical structures of the cranial skeleton are generated and organized during the embryonic phase.
22 P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP)
(12 more)
Embryonic skeletal system morphogenesis GO:0048704
The process in which the anatomical structures of the skeleton are generated and organized during the embryonic phase.
22 P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP)
(12 more)
Artery morphogenesis GO:0048844
The process in which the anatomical structures of arterial blood vessels are generated and organized. Arteries are blood vessels that transport blood from the heart to the body and its organs.
22 P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP)
(12 more)
Cartilage development GO:0051216
The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
22 P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP)
(12 more)
Roof of mouth development GO:0060021
The biological process whose specific outcome is the progression of the roof of the mouth from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The roof of the mouth is the partition that separates the nasal and oral cavities.
22 P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP)
(12 more)
Regulation of neuron projection regeneration GO:0070570
Any process that modulates the rate, frequency or extent of neuron projection regeneration, the regrowth of neuronal processes such as axons or dendrites following their loss or damage.
22 P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP) P63013 (/IMP)
(12 more)
Neuronal stem cell population maintenance GO:0097150
Any process in by an organism or tissue maintains a population of neuronal stem cells.
22 P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA)
(12 more)
Regulation of transcription, DNA-templated GO:0006355
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
6 Q99811 (/NAS) Q99811 (/NAS) Q99811 (/NAS) Q99811 (/NAS) Q99811 (/NAS) Q99811 (/NAS)
Cranial skeletal system development GO:1904888
The process whose specific outcome is the progression of a cranial skeletal system over time, from its formation to the mature structure. The cranial skeletal system is the skeletal subdivision of the head, and includes the skull (cranium plus mandible), pharyngeal and/or hyoid apparatus.
3 F1Q7Y7 (/IMP) Q6P295 (/IMP) Q7T373 (/IMP)
Positive regulation of gene expression GO:0010628
Any process that increases 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.
2 F1Q7Y7 (/IMP) Q6P295 (/IMP)
Epithelial to mesenchymal transition GO:0001837
A transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
1 Q7T373 (/IMP)
Heart looping GO:0001947
The tube morphogenesis process in which the primitive heart tube loops asymmetrically. This looping brings the primitive heart chambers into alignment preceding their future integration. Heart looping begins with dextral-looping and ends when the main regional divisions of the mature heart and primordium of the great arterial trunks become established preceeding septation.
1 Q7T373 (/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 Q06348 (/IMP)
Atrial cardiac muscle cell action potential GO:0086014
An action potential that occurs in an atrial cardiac muscle cell.
1 Q7T373 (/IMP)

There are 5 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.
23 P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA) P63013 (/IDA)
(13 more)
Nucleoplasm GO:0005654
That part of the nuclear content other than the chromosomes or the nucleolus.
22 P63013 (/ISO) P63013 (/ISO) P63013 (/ISO) P63013 (/ISO) P63013 (/ISO) P63013 (/ISO) P63013 (/ISO) P63013 (/ISO) P63013 (/ISO) P63013 (/ISO)
(12 more)
Cytosol GO:0005829
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
22 P63013 (/ISO) P63013 (/ISO) P63013 (/ISO) P63013 (/ISO) P63013 (/ISO) P63013 (/ISO) P63013 (/ISO) P63013 (/ISO) P63013 (/ISO) P63013 (/ISO)
(12 more)
Nucleoplasm GO:0005654
That part of the nuclear content other than the chromosomes or the nucleolus.
19 G3V2N3 (/IDA) G3V2N3 (/IDA) G3V2N3 (/IDA) P54821 (/IDA) P54821 (/IDA) P54821 (/IDA) P54821 (/IDA) P54821 (/IDA) P54821 (/IDA) P54821 (/IDA)
(9 more)
Cytosol GO:0005829
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
19 G3V2N3 (/IDA) G3V2N3 (/IDA) G3V2N3 (/IDA) P54821 (/IDA) P54821 (/IDA) P54821 (/IDA) P54821 (/IDA) P54821 (/IDA) P54821 (/IDA) P54821 (/IDA)
(9 more)