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.
« Back to all FunFams

FunFam 84: Homeobox protein Hox-D13

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 26 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
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.
13 G5EFY5 (/IDA) G5EGL1 (/IDA) P31271 (/IDA) Q92826 (/IDA) Q92826 (/IDA) Q92826 (/IDA) Q92826 (/IDA) Q92826 (/IDA) Q92826 (/IDA) Q92826 (/IDA)
(3 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 P31271 (/ISA) P35453 (/ISA) Q92826 (/ISA) Q92826 (/ISA) Q92826 (/ISA) Q92826 (/ISA) Q92826 (/ISA) Q92826 (/ISA) Q92826 (/ISA) Q92826 (/ISA)
(2 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 P31271 (/ISM) P35453 (/ISM) Q92826 (/ISM) Q92826 (/ISM) Q92826 (/ISM) Q92826 (/ISM) Q92826 (/ISM) Q92826 (/ISM) Q92826 (/ISM) Q92826 (/ISM)
(2 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 P31271 (/NAS) P35453 (/NAS) Q92826 (/NAS) Q92826 (/NAS) Q92826 (/NAS) Q92826 (/NAS) Q92826 (/NAS) Q92826 (/NAS) Q92826 (/NAS) Q92826 (/NAS)
(2 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.
10 Q92826 (/IC) Q92826 (/IC) Q92826 (/IC) Q92826 (/IC) Q92826 (/IC) Q92826 (/IC) Q92826 (/IC) Q92826 (/IC) Q92826 (/IC) Q92826 (/IC)
Methyl-CpG binding GO:0008327
Interacting selectively and non-covalently with a methylated cytosine/guanine dinucleotide.
10 Q92826 (/IDA) Q92826 (/IDA) Q92826 (/IDA) Q92826 (/IDA) Q92826 (/IDA) Q92826 (/IDA) Q92826 (/IDA) Q92826 (/IDA) Q92826 (/IDA) Q92826 (/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.
4 P24344 (/ISS) P35453 (/ISS) Q5EU41 (/ISS) Q9IA17 (/ISS)
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.
3 P79724 (/IDA) Q6W990 (/IDA) Q6W990 (/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 P24344 (/ISS) Q5EU41 (/ISS) Q9IA17 (/ISS)
DNA binding GO:0003677
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
3 P35453 (/IDA) P70217 (/IDA) P70217 (/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.
2 P70217 (/IDA) P70217 (/IDA)
Enhancer sequence-specific DNA binding GO:0001158
Interacting selectively and non-covalently with a specific sequence of DNA that is part of an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter.
2 P70217 (/IDA) P70217 (/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.
2 P70217 (/IDA) P70217 (/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.
2 P70217 (/ISO) P70217 (/ISO)
DNA binding GO:0003677
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
2 P70217 (/ISO) P70217 (/ISO)
DNA binding GO:0003677
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
2 P31271 (/TAS) P35453 (/TAS)
Chromatin binding GO:0003682
Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
2 P70217 (/IDA) P70217 (/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.
2 P70217 (/IDA) P70217 (/IDA)
Sequence-specific double-stranded DNA binding GO:1990837
Interacting selectively and non-covalently with double-stranded 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 P70217 (/ISO) P70217 (/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 P35453 (/IMP)
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).
1 P70321 (/IPI)
Methyl-CpG binding GO:0008327
Interacting selectively and non-covalently with a methylated cytosine/guanine dinucleotide.
1 P70321 (/ISO)
Methyl-CpG binding GO:0008327
Interacting selectively and non-covalently with a methylated cytosine/guanine dinucleotide.
1 P70321 (/ISS)
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.
1 P31271 (/IMP)
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.
1 P70321 (/ISO)
Sequence-specific double-stranded DNA binding GO:1990837
Interacting selectively and non-covalently with double-stranded 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.
1 D4ACD0 (/IDA)

There are 39 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.
13 P79724 (/IDA) Q6W990 (/IDA) Q6W990 (/IDA) Q92826 (/IDA) Q92826 (/IDA) Q92826 (/IDA) Q92826 (/IDA) Q92826 (/IDA) Q92826 (/IDA) Q92826 (/IDA)
(3 more)
Angiogenesis GO:0001525
Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
10 Q92826 (/IEP) Q92826 (/IEP) Q92826 (/IEP) Q92826 (/IEP) Q92826 (/IEP) Q92826 (/IEP) Q92826 (/IEP) Q92826 (/IEP) Q92826 (/IEP) Q92826 (/IEP)
Epidermis development GO:0008544
The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species.
10 Q92826 (/TAS) Q92826 (/TAS) Q92826 (/TAS) Q92826 (/TAS) Q92826 (/TAS) Q92826 (/TAS) Q92826 (/TAS) Q92826 (/TAS) Q92826 (/TAS) Q92826 (/TAS)
Response to wounding GO:0009611
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.
10 Q92826 (/TAS) Q92826 (/TAS) Q92826 (/TAS) Q92826 (/TAS) Q92826 (/TAS) Q92826 (/TAS) Q92826 (/TAS) Q92826 (/TAS) Q92826 (/TAS) Q92826 (/TAS)
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.
4 G5EFY5 (/IMP) G5EGL1 (/IMP) P70217 (/IMP) P70217 (/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.
3 P24344 (/ISS) Q5EU41 (/ISS) Q9IA17 (/ISS)
Prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis GO:0060527
The branching morphogenesis process in which the prostate epithelial cords branch freely to create the structure of the prostate acini.
3 P70217 (/IGI) P70217 (/IGI) P70321 (/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).
2 P70217 (/IMP) P70217 (/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).
2 P31271 (/TAS) P35453 (/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.
2 P70217 (/IGI) P70217 (/IGI)
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.
2 P70217 (/IMP) P70217 (/IMP)
Embryonic pattern specification GO:0009880
The process that results in the patterns of cell differentiation that will arise in an embryo.
2 G5EFY5 (/IMP) G5EGL1 (/IMP)
Embryonic body morphogenesis GO:0010172
The process in which the anatomical structures of the embryonic soma are generated and organized.
2 G5EFY5 (/IMP) G5EGL1 (/IMP)
Gland morphogenesis GO:0022612
The process in which the anatomical structures of a gland are generated and organized.
2 P70217 (/IMP) P70217 (/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.
2 P70217 (/IMP) P70217 (/IMP)
Male genitalia development GO:0030539
The process whose specific outcome is the progression of the male genitalia over time, from its formation to the mature structure.
2 P70217 (/IMP) P70217 (/IMP)
Prostate gland development GO:0030850
The process whose specific outcome is the progression of the prostate gland over time, from its formation to the mature structure. The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid.
2 D3ZWL5 (/IEP) D4ACD0 (/IEP)
Response to testosterone GO:0033574
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a testosterone stimulus.
2 D3ZWL5 (/IEP) D4ACD0 (/IEP)
Limb morphogenesis GO:0035108
The process in which the anatomical structures of a limb are generated and organized. A limb is a paired appendage of a tetrapod used for locomotion or grasping.
2 P70217 (/IGI) P70217 (/IGI)
Limb morphogenesis GO:0035108
The process in which the anatomical structures of a limb are generated and organized. A limb is a paired appendage of a tetrapod used for locomotion or grasping.
2 P70217 (/IMP) P70217 (/IMP)
Regulation of cell population proliferation GO:0042127
Any process that modulates the frequency, rate or extent of cell proliferation.
2 P70217 (/IMP) P70217 (/IMP)
Embryonic digit morphogenesis GO:0042733
The process, occurring in the embryo, by which the anatomical structures of the digit are generated and organized. A digit is one of the terminal divisions of an appendage, such as a finger or toe.
2 P70217 (/IGI) P70217 (/IGI)
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.
2 G5EFY5 (/IMP) G5EGL1 (/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.
2 P70217 (/IDA) P70217 (/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 P70217 (/ISO) P70217 (/ISO)
Embryonic hindgut morphogenesis GO:0048619
The process in which the anatomical structures of the hindgut are generated and organized, during the embryonic phase.
2 P70217 (/ISO) P70217 (/ISO)
Morphogenesis of an epithelial fold GO:0060571
The morphogenetic process in which an epithelial sheet bends along a linear axis.
2 P70217 (/IMP) P70217 (/IMP)
Branch elongation of an epithelium GO:0060602
The growth process in which a branch increases in length from its base to its tip.
2 P70217 (/IMP) P70217 (/IMP)
Regulation of branching involved in prostate gland morphogenesis GO:0060687
Any process that modulates the rate, frequency, or extent of prostate gland branching, the process in which the branching structure of the prostate gland is generated and organized. A branch is a division or offshoot from a main stem.
2 P70217 (/IMP) P70217 (/IMP)
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.
1 P70321 (/ISO)
Morphogenesis of an epithelium GO:0002009
The process in which the anatomical structures of epithelia are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube.
1 P70321 (/IMP)
Regulation of transcription, DNA-templated GO:0006355
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
1 P35453 (/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).
1 P35453 (/TAS)
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 P35453 (/TAS)
Regulation of asymmetric cell division GO:0009786
Any process that modulates the frequency, rate or extent of asymmetric cell division.
1 G5EFY5 (/IMP)
Regulation of growth GO:0040008
Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development.
1 P70321 (/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 P35453 (/IMP)
Embryonic hindgut morphogenesis GO:0048619
The process in which the anatomical structures of the hindgut are generated and organized, during the embryonic phase.
1 D4ACD0 (/IMP)
Epithelial cell maturation involved in prostate gland development GO:0060743
The developmental process, independent of morphogenetic (shape) change, that is required for an epithelial cell of the prostate gland to attain its fully functional state. An epithelial cell is a cell usually found in a two-dimensional sheet with a free surface.
1 P70321 (/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
Nucleoplasm GO:0005654
That part of the nuclear content other than the chromosomes or the nucleolus.
10 Q92826 (/IDA) Q92826 (/IDA) Q92826 (/IDA) Q92826 (/IDA) Q92826 (/IDA) Q92826 (/IDA) Q92826 (/IDA) Q92826 (/IDA) Q92826 (/IDA) Q92826 (/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.
4 D4ACD0 (/IDA) P35453 (/IDA) P70217 (/IDA) P70217 (/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.
2 P70217 (/ISO) P70217 (/ISO)
Nucleoplasm GO:0005654
That part of the nuclear content other than the chromosomes or the nucleolus.
1 P70321 (/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 P70321 (/IDA)
CATH-Gene3D is a Global Biodata Core Resource Learn more...