| GOID Link to GO |
Functional Category | Description | Protein Count link to protein list |
|---|---|---|---|
| GO:0043565 | sequence-specific DNA binding | 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. | 176 |
| GO:0003690 | double-stranded DNA binding | Interacting selectively and non-covalently with double-stranded DNA. | 95 |
| GO:0044212 | transcription regulatory region DNA binding | Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. | 87 |
| GO:0003697 | single-stranded DNA binding | Interacting selectively and non-covalently with single-stranded DNA. | 67 |
| GO:0000977 | RNA polymerase II regulatory region sequence-specific DNA binding | 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. | 60 |
| GO:0000978 | RNA polymerase II core promoter proximal region sequence-specific DNA binding | Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II. | 58 |
| GO:0000980 | RNA polymerase II distal enhancer sequence-specific DNA binding | Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter. | 51 |
| GO:0000979 | RNA polymerase II core promoter sequence-specific DNA binding | Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase II basal transcription machinery. | 43 |
| GO:0031490 | chromatin DNA binding | Interacting selectively and non-covalently with DNA that is assembled into chromatin. | 41 |
| GO:0003680 | AT DNA binding | Interacting selectively and non-covalently with oligo(A) and oligo(T) tracts of DNA (AT DNA). | 38 |
| GO:0003684 | damaged DNA binding | Interacting selectively and non-covalently with damaged DNA. | 28 |
| GO:0008301 | DNA binding, bending | The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence. | 27 |
| GO:0070888 | E-box binding | Interacting selectively and non-covalently with an E-box, a DNA motif with the consensus sequence CANNTG that is found in the promoters of a wide array of genes expressed in neurons, muscle and other tissues. | 24 |
| GO:0000976 | transcription regulatory region sequence-specific DNA binding | Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon. | 22 |
| GO:0043566 | structure-specific DNA binding | Interacting selectively and non-covalently with DNA of a specific structure or configuration e.g. triplex DNA binding or bent DNA binding. | 19 |
| GO:0000987 | core promoter proximal region sequence-specific DNA binding | Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon. | 16 |
| GO:0001047 | core promoter binding | Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. | 12 |
| GO:0001158 | enhancer sequence-specific DNA binding | 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. | 9 |
| GO:0003688 | DNA replication origin binding | Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally. | 9 |
| GO:0019237 | centromeric DNA binding | Interacting selectively and non-covalently with a centromere, a region of chromosome where the spindle fibers attach during mitosis and meiosis. | 8 |
| GO:0044323 | retinoic acid-responsive element binding | Interacting selectively and non-covalently with a retinoic acid-responsive element, a variable direct repeat of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind. | 8 |
| GO:0000217 | DNA secondary structure binding | Interacting selectively and non-covalently with DNA containing secondary structure elements such as four-way junctions, bubbles, loops, Y-form DNA, or double-strand/single-strand junctions. | 8 |
| GO:0000182 | rDNA binding | Interacting selectively and non-covalently with DNA sequences encoding ribosomal RNA. | 8 |
| GO:0000975 | regulatory region DNA binding | Interacting selectively and non-covalently with a DNA region that regulates a DNA-based process. Such processes include transcription, DNA replication, and DNA repair. | 8 |
| GO:0070644 | vitamin D response element binding | Interacting selectively and non-covalently with the vitamin D response element (VDRE), a short sequence with dyad symmetry found in the promoters of some of the cellular immediate-early genes, regulated by serum. | 6 |
| GO:0043047 | single-stranded telomeric DNA binding | Interacting selectively and non-covalently with single-stranded telomere-associated DNA. | 6 |
| GO:0031492 | nucleosomal DNA binding | Interacting selectively and non-covalently with the DNA portion of a nucleosome. | 6 |
| GO:0003689 | DNA clamp loader activity | Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the opening of the ring structure of the PCNA complex, or any of the related sliding clamp complexes, and their closing around the DNA duplex. | 5 |
| GO:0001016 | RNA polymerase III regulatory region DNA binding | Interacting selectively and non-covalently with a DNA region that controls the transcription of a gene by RNA polymerase III. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. | 5 |
| GO:0070594 | juvenile hormone response element binding | Interacting selectively and non-covalently with the juvenile hormone response element (JHRE), a conserved sequence found in the promoters of genes whose expression is regulated in response to juvenile hormone. | 5 |
| GO:0032135 | DNA insertion or deletion binding | Interacting selectively and non-covalently with double-stranded DNA containing insertions or deletions. | 4 |
| GO:0000400 | four-way junction DNA binding | Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices. | 4 |
| GO:0001163 | RNA polymerase I regulatory region sequence-specific DNA binding | 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 I. | 4 |
| GO:0032422 | purine-rich negative regulatory element binding | Interacting selectively and non-covalently with a 30-bp purine-rich negative regulatory element; the best characterized such element is found in the first intronic region of the rat cardiac alpha-myosin heavy chain gene, and contains two palindromic high-affinity Ets-binding sites (CTTCCCTGGAAG). The presence of this element restricts expression of the gene containing it to cardiac myocytes. | 4 |
| GO:0001162 | RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding | Interacting selectively and non-covalently with an RNA polymerase II intronic DNA sequence that regulates the transcription of the transcript it is contained within. | 3 |
| GO:0001031 | RNA polymerase III type 2 promoter DNA binding | Interacting selectively and non-covalently with a region of DNA that is a part of a type 2 promoter that controls transcription by RNA polymerase III. Type 2 promoters consist of an A box and a B box downstream of the transcription start site within the sequence within the sequence of the mature RNA. Type 2 promoters are found in many tRNA genes as well as in other small RNAs. | 3 |
| GO:0035939 | microsatellite binding | Interacting selectively and non-covalently with a microsatellite, a repeat_region in DNA containing repeat units (2 to 4 base pairs) that is repeated multiple times in tandem. | 3 |
| GO:0000403 | Y-form DNA binding | Interacting selectively and non-covalently with segment of DNA shaped like a Y. This shape occurs when DNA contains a region of paired double-stranded DNA on one end and a region of unpaired DNA strands on the opposite end. | 3 |
| GO:0001032 | RNA polymerase III type 3 promoter DNA binding | Interacting selectively and non-covalently with a region of DNA that is a part of a type 3 promoter that controls transcription by RNA polymerase III. A type 3 Pol III promoter is composed of elements upstream of the transcription start site, including a TATA box. The human U6 snRNA gene has a type 3 promoter. Type 3 Pol III promoters have not been observed in S. cerevisiae. | 3 |
| GO:0032137 | guanine/thymine mispair binding | Interacting selectively and non-covalently with double-stranded DNA containing a G/T mispair. | 3 |
| GO:0001030 | RNA polymerase III type 1 promoter DNA binding | Interacting selectively and non-covalently with a region of DNA that is a part of a type 1 promoter that controls transcription by RNA polymerase III. Type 1 promoters are found in 5S rRNA genes, downstream of the transcription start site within the sequence of the mature RNA, and require TFIIIA for recognition. | 3 |
| GO:0042162 | telomeric DNA binding | Interacting selectively and non-covalently with a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end. | 3 |
| GO:0032139 | dinucleotide insertion or deletion binding | Interacting selectively and non-covalently with double-stranded DNA containing a dinucleotide insertion or deletion. | 3 |
| GO:0001046 | core promoter sequence-specific DNA binding | Interacting selectively and non-covalently with a sequence of DNA that is part of a core promoter region composed of the transcription start site and binding sites for the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon. | 3 |
| GO:0071820 | N-box binding | Interacting selectively and non-covalently with an N-box, a DNA motif with the consensus sequence CACNAG that is found in the promoters of genes expressed preferentially at synapses. | 2 |
| GO:0034056 | estrogen response element binding | Interacting selectively and non-covalently with the estrogen response element (ERE), a conserved sequence found in the promoters of genes whose expression is regulated in response to estrogen. | 2 |
| GO:0070364 | mitochondrial heavy strand promoter sense binding | Interacting selectively and non-covalently with the sense strand of the heavy strand promoter, a promoter located on the heavy, or guanine-rich, strand of mitochondrial DNA. | 2 |
| GO:0003696 | satellite DNA binding | Interacting selectively and non-covalently with satellite DNA, the many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA. | 2 |
| GO:0010736 | serum response element binding | Interacting selectively and non-covalently with the serum response element (SRE), a short sequence with dyad symmetry found in the promoters of some of the cellular immediate-early genes, regulated by serum. | 2 |
| GO:0000405 | bubble DNA binding | Interacting selectively and non-covalently with DNA that contains a bubble. A bubble occurs when DNA contains a region of unpaired, single-stranded DNA flanked on both sides by regions of paired, double-stranded DNA. | 2 |
| GO:0070363 | mitochondrial light strand promoter sense binding | Interacting selectively and non-covalently with the sense strand of the light strand promoter, a promoter located on the light, or cytosine-rich, strand of mitochondrial DNA. | 2 |
| GO:0003681 | bent DNA binding | Interacting selectively and non-covalently with DNA in a bent conformation. | 2 |
| GO:0000404 | loop DNA binding | Interacting selectively and non-covalently with DNA containing a loop. A loop occurs when DNA contains a large insertion or deletion that causes a region of unpaired single-stranded DNA to loop out, while the rest of the DNA is in a paired double-stranded configuration. | 2 |
| GO:0001012 | RNA polymerase II regulatory region DNA binding | Interacting selectively and non-covalently with a DNA region that controls the transcription of a region of DNA by RNA polymerase II. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. | 2 |
| GO:0003691 | double-stranded telomeric DNA binding | Interacting selectively and non-covalently with double-stranded telomere-associated DNA. | 2 |
| GO:0045322 | unmethylated CpG binding | Interacting selectively and non-covalently with unmethylated CpG motifs. Unmethylated CpG dinucleotides are often associated with gene promoters. | 2 |
| GO:0051880 | G-quadruplex DNA binding | Interacting selectively and non-covalently with G-quadruplex DNA structures, in which groups of four guanines adopt a flat, cyclic Hoogsteen hydrogen-bonding arrangement known as a guanine tetrad. The stacking of guanine tetrads results in G-quadruplex DNA structures. G-quadruplex DNA can form under physiological conditions from some G-rich sequences, such as those found in telomeres, immunoglobulin switch regions, gene promoters, fragile X repeats, and the dimerization domain in the human immunodeficiency virus (HIV) genome. | 2 |
| GO:0043035 | chromatin insulator sequence binding | Interacting selectively and non-covalently and stoichiometrically with a chromatin insulator sequence, a DNA sequence that prevents enhancer-mediated activation or repression of transcription. | 2 |
| GO:0032357 | oxidized purine DNA binding | Interacting selectively and non-covalently with oxidized purine residues in DNA. | 1 |
| GO:0000401 | open form four-way junction DNA binding | Interacting selectively and non-covalently with DNA containing the open form of a four-way junction, also known as a Holliday junction, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices. The open form of a four-way junction can be diagrammed without any of the strands crossing over. | 1 |
| GO:0070362 | mitochondrial heavy strand promoter anti-sense binding | Interacting selectively and non-covalently with the anti-sense strand of the heavy strand promoter, a promoter located on the heavy, or guanine-rich, strand of mitochondrial DNA. | 1 |
| GO:0032143 | single thymine insertion binding | Interacting selectively and non-covalently with double-stranded DNA containing a single thymine insertion or a deletion that results in an unpaired thymine. | 1 |
| GO:0035497 | cAMP response element binding | Interacting selectively and non-covalently with the cyclic AMP response element (CRE), a short palindrome-containing sequence found in the promoters of genes whose expression is regulated in response to cyclic AMP. | 1 |
| GO:0032181 | dinucleotide repeat insertion binding | Interacting selectively and non-covalently with double-stranded DNA containing a dinucleotide repeat insertion or a deletion resulting in unpaired dinucleotide repeats. | 1 |
| GO:0044729 | hemi-methylated DNA-binding | Interacting selectively and non-covalently with double-stranded hemi-methylated DNA at replication foci (one strand methylated, while the other strand is unmethylated). Cytosine methylation in DNA is an important mechanism for establishing stable heritable epigenetic marks. | 1 |
| GO:0008327 | methyl-CpG binding | Interacting selectively and non-covalently with a methylated cytosine/guanine dinucleotide. | 1 |
| GO:0001159 | core promoter proximal region DNA binding | Interacting selectively and non-covalently with a region of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon. | 1 |
| GO:0030983 | mismatched DNA binding | Interacting selectively and non-covalently with double-stranded DNA containing one or more mismatches. | 1 |
| GO:0000402 | crossed form four-way junction DNA binding | Interacting selectively and non-covalently with DNA containing the crossed form of a four-way junction, also known as a Holliday junction, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices. The crossed form of a four-way junction cannot be diagrammed without any of the strands crossing over, and instead contains a single crossover between two of the strands. | 1 |
| GO:0000406 | double-strand/single-strand DNA junction binding | Interacting selectively and non-covalently with a region of DNA that contains double-stranded DNA flanked by a region of single-stranded DNA. | 1 |
| GO:0070361 | mitochondrial light strand promoter anti-sense binding | Interacting selectively and non-covalently with the anti-sense strand of the light strand promoter, a promoter located on the light, or cytosine-rich, strand of mitochondrial DNA. | 1 |
| GO:0032142 | single guanine insertion binding | Interacting selectively and non-covalently with double-stranded DNA containing a single guanine insertion or a deletion that results in an unpaired guanine. | 1 |
| GO:0032138 | single base insertion or deletion binding | Interacting selectively and non-covalently with double-stranded DNA containing a single base insertion or deletion. | 1 |