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 8: DNA-directed RNA polymerase II subunit RPB9

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 1 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
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).
8 P27999 (/IPI) P27999 (/IPI) P27999 (/IPI) P27999 (/IPI) P27999 (/IPI) P27999 (/IPI) P27999 (/IPI) P27999 (/IPI)

There are 9 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
Maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter GO:0001193
Suppression of the occurrence of transcriptional errors, such as substitutions and/or insertions of nucleotides that do not correctly match the template base, during the process of transcription elongation from an RNA polymerase II promoter.
8 P27999 (/IGI) P27999 (/IGI) P27999 (/IGI) P27999 (/IGI) P27999 (/IGI) P27999 (/IGI) P27999 (/IGI) P27999 (/IGI)
Maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter GO:0001193
Suppression of the occurrence of transcriptional errors, such as substitutions and/or insertions of nucleotides that do not correctly match the template base, during the process of transcription elongation from an RNA polymerase II promoter.
8 P27999 (/IMP) P27999 (/IMP) P27999 (/IMP) P27999 (/IMP) P27999 (/IMP) P27999 (/IMP) P27999 (/IMP) P27999 (/IMP)
Transcription-coupled nucleotide-excision repair GO:0006283
The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway.
8 P27999 (/IGI) P27999 (/IGI) P27999 (/IGI) P27999 (/IGI) P27999 (/IGI) P27999 (/IGI) P27999 (/IGI) P27999 (/IGI)
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).
8 P27999 (/IMP) P27999 (/IMP) P27999 (/IMP) P27999 (/IMP) P27999 (/IMP) P27999 (/IMP) P27999 (/IMP) P27999 (/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.
8 P27999 (/IMP) P27999 (/IMP) P27999 (/IMP) P27999 (/IMP) P27999 (/IMP) P27999 (/IMP) P27999 (/IMP) P27999 (/IMP)
Cellular response to DNA damage stimulus GO:0006974
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
8 P27999 (/HMP) P27999 (/HMP) P27999 (/HMP) P27999 (/HMP) P27999 (/HMP) P27999 (/HMP) P27999 (/HMP) P27999 (/HMP)
RNA-directed DNA methylation GO:0080188
An epigenetic RNA-based gene silencing process first elucidated in plants whereby 24-nt small interfering RNAs (siRNAs) guide DNA methyltransferases to the siRNA-generating genomic loci and other loci that are homologous to the siRNAs for de novo DNA methylation. In general this process consists of three phases: biogenesis of siRNAs, scaffold RNA production, and the formation of the guiding complex that recruits de novo DNA methyltransferases to the target loci.
6 Q8L5V0 (/IMP) Q8L5V0 (/IMP) Q8L5V0 (/IMP) Q8L5V0 (/IMP) Q8L5V0 (/IMP) Q8L5V0 (/IMP)
Transcription-coupled nucleotide-excision repair GO:0006283
The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway.
1 O74635 (/ISO)
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 O74635 (/IC)

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
RNA polymerase II, core complex GO:0005665
RNA polymerase II, one of three nuclear DNA-directed RNA polymerases found in all eukaryotes, is a multisubunit complex; typically it produces mRNAs, snoRNAs, and some of the snRNAs. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The largest subunit of RNA polymerase II contains an essential carboxyl-terminal domain (CTD) composed of a variable number of heptapeptide repeats (YSPTSPS). The remainder of the complex is composed of smaller subunits (generally ten or more), some of which are also found in RNA polymerases I and III. Although the core is competent to mediate ribonucleic acid synthesis, it requires additional factors to select the appropriate template.
17 O74635 (/IDA) P27999 (/IDA) P27999 (/IDA) P27999 (/IDA) P27999 (/IDA) P27999 (/IDA) P27999 (/IDA) P27999 (/IDA) P27999 (/IDA) Q6NLH0 (/IDA)
(7 more)
RNA polymerase V complex GO:0000419
RNA polymerase V is a multisubunit RNA polymerase complex found in the nucleus of plants and involved in accumulation of siRNAs and in DNA methylation-dependent silencing of endogenous repeated sequences. Pol V is composed of subunits that are paralogous or identical to the 12 subunits of Pol II. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The second largest subunit is also found in RNA polymerase IVa, while the largest subunit is found only in the IVa complex and contains an extended C-terminal domain (CTD) that includes multiple repeats of a 16 amino-acid consensus sequence as well as other sequences. The remainder of the complex is composed of smaller subunits.
8 Q6NLH0 (/IDA) Q6NLH0 (/IDA) Q8L5V0 (/IDA) Q8L5V0 (/IDA) Q8L5V0 (/IDA) Q8L5V0 (/IDA) Q8L5V0 (/IDA) Q8L5V0 (/IDA)
RNA polymerase IV complex GO:0000418
RNA polymerase IV is a multisubunit RNA polymerase complex found in the nucleus of plants and involved in accumulation of siRNAs and in DNA methylation-dependent silencing of endogenous repeated sequences. Pol IV is composed of subunits that are paralogous or identical to the 12 subunits of Pol II. The largest and second-largest subunits of Pol IV are the catalytic subunits and share similarity with the corresponding subunits of other eukaryotic and bacterial multisubunit RNA polymerases. The second largest subunit is also found in RNA polymerase V, while the largest subunit is found only in RNAP IV complex.
6 Q8L5V0 (/IDA) Q8L5V0 (/IDA) Q8L5V0 (/IDA) Q8L5V0 (/IDA) Q8L5V0 (/IDA) Q8L5V0 (/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 O74635 (/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 O74635 (/HDA)