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: waiting to be named.

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 39: RNA polymerase II subunit A C-terminal domain phos...

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 10 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
RNA polymerase II CTD heptapeptide repeat phosphatase activity GO:0008420
Catalysis of the reaction: phospho-(DNA-directed RNA polymerase II) + H2O = (DNA-directed RNA polymerase II) + phosphate.
25 M9PHZ3 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA)
(15 more)
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).
23 P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI)
(13 more)
Protein serine/threonine phosphatase activity GO:0004722
Catalysis of the reaction: protein serine phosphate + H2O = protein serine + phosphate, and protein threonine phosphate + H2O = protein threonine + phosphate.
11 O42868 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP)
(1 more)
RNA polymerase II CTD heptapeptide repeat phosphatase activity GO:0008420
Catalysis of the reaction: phospho-(DNA-directed RNA polymerase II) + H2O = (DNA-directed RNA polymerase II) + phosphate.
11 Q17QI2 (/ISS) Q17QI2 (/ISS) Q4KLK9 (/ISS) Q4KLK9 (/ISS) Q4KLK9 (/ISS) Q4KLK9 (/ISS) Q4KLK9 (/ISS) Q4KLK9 (/ISS) Q4KLK9 (/ISS) Q4KLK9 (/ISS)
(1 more)
Phosphoprotein phosphatase activity GO:0004721
Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
10 P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI)
Protein serine/threonine phosphatase activity GO:0004722
Catalysis of the reaction: protein serine phosphate + H2O = protein serine + phosphate, and protein threonine phosphate + H2O = protein threonine + phosphate.
10 P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA)
Protein tyrosine phosphatase activity GO:0004725
Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
10 P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA)
RNA polymerase II CTD heptapeptide repeat phosphatase activity GO:0008420
Catalysis of the reaction: phospho-(DNA-directed RNA polymerase II) + H2O = (DNA-directed RNA polymerase II) + phosphate.
10 P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP)
Phosphatase activity GO:0016791
Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
2 M9PHZ3 (/IDA) Q9VWE4 (/IDA)
RNA polymerase II CTD heptapeptide repeat phosphatase activity GO:0008420
Catalysis of the reaction: phospho-(DNA-directed RNA polymerase II) + H2O = (DNA-directed RNA polymerase II) + phosphate.
1 Q9CY97 (/ISO)

There are 29 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
Dephosphorylation of RNA polymerase II C-terminal domain GO:0070940
The process of removing a phosphate group from an amino acid residue in the C-terminal domain of RNA polymerase II. Some dephosphorylation occurs during transcription while some may occur after the enzyme is released from the template in order to prepare it for the beginning of the transcription cycle again. RNA polymerase II with little or no phosphorylation is referred to as the hypophosphorylated or II(A) form.
25 M9PHZ3 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA)
(15 more)
MRNA polyadenylation GO:0006378
The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript.
13 Q9NP77 (/IMP) Q9NP77 (/IMP) Q9NP77 (/IMP) Q9NP77 (/IMP) Q9NP77 (/IMP) Q9NP77 (/IMP) Q9NP77 (/IMP) Q9NP77 (/IMP) Q9NP77 (/IMP) Q9NP77 (/IMP)
(3 more)
MRNA polyadenylation GO:0006378
The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript.
11 Q17QI2 (/ISS) Q17QI2 (/ISS) Q4KLK9 (/ISS) Q4KLK9 (/ISS) Q4KLK9 (/ISS) Q4KLK9 (/ISS) Q4KLK9 (/ISS) Q4KLK9 (/ISS) Q4KLK9 (/ISS) Q4KLK9 (/ISS)
(1 more)
Dephosphorylation of RNA polymerase II C-terminal domain GO:0070940
The process of removing a phosphate group from an amino acid residue in the C-terminal domain of RNA polymerase II. Some dephosphorylation occurs during transcription while some may occur after the enzyme is released from the template in order to prepare it for the beginning of the transcription cycle again. RNA polymerase II with little or no phosphorylation is referred to as the hypophosphorylated or II(A) form.
11 Q17QI2 (/ISS) Q17QI2 (/ISS) Q4KLK9 (/ISS) Q4KLK9 (/ISS) Q4KLK9 (/ISS) Q4KLK9 (/ISS) Q4KLK9 (/ISS) Q4KLK9 (/ISS) Q4KLK9 (/ISS) Q4KLK9 (/ISS)
(1 more)
Transcriptional start site selection at RNA polymerase II promoter GO:0001174
Any process involved in the selection of the specific location within the template strand of an RNA polymerase II promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript.
10 P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI)
Transcriptional start site selection at RNA polymerase II promoter GO:0001174
Any process involved in the selection of the specific location within the template strand of an RNA polymerase II promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript.
10 P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP)
Transcription initiation from RNA polymerase II promoter GO:0006367
Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
10 P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI)
Transcription initiation from RNA polymerase II promoter GO:0006367
Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
10 P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI)
Transcription elongation from RNA polymerase II promoter GO:0006368
The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
10 P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI)
Transcription elongation from RNA polymerase II promoter GO:0006368
The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
10 P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP)
Termination of RNA polymerase II transcription GO:0006369
The process in which the synthesis of an RNA molecule by RNA polymerase II using a DNA template is completed.
10 P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP)
SnoRNA transcription GO:0009302
The synthesis of small nucleolar RNA (snoRNA) from a DNA template.
10 P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP)
Termination of RNA polymerase II transcription, poly(A)-coupled GO:0030846
The process in which transcription of polyadenylated RNA polymerase II transcripts is terminated; cleavage and polyadenylylation of the mRNA 3' end is coupled to transcription termination.
10 P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP)
Termination of RNA polymerase II transcription, poly(A)-coupled GO:0030846
The process in which transcription of polyadenylated RNA polymerase II transcripts is terminated; cleavage and polyadenylylation of the mRNA 3' end is coupled to transcription termination.
10 P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI)
Termination of RNA polymerase II transcription, exosome-dependent GO:0030847
The process in which transcription of nonpolyadenylated RNA polymerase II transcripts is terminated; coupled to the maturation of the RNA 3'-end.
10 P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP)
Termination of RNA polymerase II transcription, exosome-dependent GO:0030847
The process in which transcription of nonpolyadenylated RNA polymerase II transcripts is terminated; coupled to the maturation of the RNA 3'-end.
10 P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI)
MRNA 3'-end processing GO:0031124
Any process involved in forming the mature 3' end of an mRNA molecule.
10 P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP)
Transcription antitermination GO:0031564
Regulation of transcription by a mechanism that allows RNA polymerase to continue transcription beyond termination site(s).
10 P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP)
Dephosphorylation of RNA polymerase II C-terminal domain GO:0070940
The process of removing a phosphate group from an amino acid residue in the C-terminal domain of RNA polymerase II. Some dephosphorylation occurs during transcription while some may occur after the enzyme is released from the template in order to prepare it for the beginning of the transcription cycle again. RNA polymerase II with little or no phosphorylation is referred to as the hypophosphorylated or II(A) form.
10 P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP)
Pre-mRNA cleavage required for polyadenylation GO:0098789
The targeted, endonucleolytic cleavage of a pre-mRNA, required for polyadenylation of the 3' end. This cleavage is directed by binding sites near the 3' end of the mRNA and leaves a 3' hydoxyl end which then becomes a target for adenylation.
10 P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP) P53538 (/IMP)
Protein dephosphorylation GO:0006470
The process of removing one or more phosphoric residues from a protein.
2 M9PHZ3 (/IDA) Q9VWE4 (/IDA)
MRNA 3'-end processing GO:0031124
Any process involved in forming the mature 3' end of an mRNA molecule.
2 M9PHZ3 (/ISS) Q9VWE4 (/ISS)
DNA-templated transcription, initiation GO:0006352
Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
1 O42868 (/ISO)
Termination of RNA polymerase II transcription GO:0006369
The process in which the synthesis of an RNA molecule by RNA polymerase II using a DNA template is completed.
1 O42868 (/ISO)
MRNA polyadenylation GO:0006378
The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript.
1 Q9CY97 (/ISO)
Signaling GO:0023052
The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered.
1 O42868 (/NAS)
Negative regulation of telomere maintenance via telomerase GO:0032211
Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of telomeric repeats by telomerase.
1 O42868 (/IMP)
Positive regulation of telomere maintenance via semi-conservative replication GO:0032215
Any process that activates or increases the frequency, rate or extent of the semi-conservative replication of telomeric DNA.
1 O42868 (/IMP)
Dephosphorylation of RNA polymerase II C-terminal domain GO:0070940
The process of removing a phosphate group from an amino acid residue in the C-terminal domain of RNA polymerase II. Some dephosphorylation occurs during transcription while some may occur after the enzyme is released from the template in order to prepare it for the beginning of the transcription cycle again. RNA polymerase II with little or no phosphorylation is referred to as the hypophosphorylated or II(A) form.
1 Q9CY97 (/ISO)

There are 13 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.
13 Q9NP77 (/IDA) Q9NP77 (/IDA) Q9NP77 (/IDA) Q9NP77 (/IDA) Q9NP77 (/IDA) Q9NP77 (/IDA) Q9NP77 (/IDA) Q9NP77 (/IDA) Q9NP77 (/IDA) Q9NP77 (/IDA)
(3 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.
13 Q9NP77 (/IDA) Q9NP77 (/IDA) Q9NP77 (/IDA) Q9NP77 (/IDA) Q9NP77 (/IDA) Q9NP77 (/IDA) Q9NP77 (/IDA) Q9NP77 (/IDA) Q9NP77 (/IDA) Q9NP77 (/IDA)
(3 more)
MRNA cleavage and polyadenylation specificity factor complex GO:0005847
A multisubunit complex that binds to the canonical AAUAAA hexamer and to U-rich upstream sequence elements on the pre-mRNA, thereby stimulating the otherwise weakly active and nonspecific polymerase to elongate efficiently RNAs containing a poly(A) signal.
11 O42868 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA) P53538 (/IDA)
(1 more)
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.
10 P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI) P53538 (/IGI)
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.
10 P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI)
MRNA cleavage and polyadenylation specificity factor complex GO:0005847
A multisubunit complex that binds to the canonical AAUAAA hexamer and to U-rich upstream sequence elements on the pre-mRNA, thereby stimulating the otherwise weakly active and nonspecific polymerase to elongate efficiently RNAs containing a poly(A) signal.
10 P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI) P53538 (/IPI)
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 M9PHZ3 (/ISS) Q9VWE4 (/ISS)
Nuclear chromatin GO:0000790
The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
1 O42868 (/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 O42868 (/HDA)
Nucleoplasm GO:0005654
That part of the nuclear content other than the chromosomes or the nucleolus.
1 Q9CY97 (/ISO)
Cytosol GO:0005829
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
1 O42868 (/HDA)
Cytosol GO:0005829
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
1 Q9CY97 (/ISO)
Chloroplast GO:0009507
A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
1 Q9C9T0 (/IDA)