CATH Superfamily 2.20.25.10
The name of this superfamily has been modified since the most recent official CATH+ release (v4_2_0). At the point of the last release, this superfamily was: waiting to be named.
FunFam 6786: Transcription initiation factor IIB
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 15 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 |
|---|---|---|
|
Transcription factor activity, RNA polymerase III transcription factor binding GO:0001007
Interacting selectively and non-covalently with an RNA polymerase III transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
|
7 | A4QNR3 (/ISS) A8KBY2 (/ISS) Q29S07 (/ISS) Q3UAW9 (/ISS) Q4R318 (/ISS) Q4V8D6 (/ISS) Q66IW8 (/ISS) |
|
RNA polymerase III type 3 promoter DNA binding GO:0001032
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.
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7 | A4QNR3 (/ISS) A8KBY2 (/ISS) Q29S07 (/ISS) Q3UAW9 (/ISS) Q4R318 (/ISS) Q4V8D6 (/ISS) Q66IW8 (/ISS) |
|
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).
|
2 | P29052 (/IPI) Q00403 (/IPI) |
|
Transcription factor binding GO:0008134
Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
|
2 | P29052 (/IPI) Q00403 (/IPI) |
|
Transcription factor activity, RNA polymerase III transcription factor binding GO:0001007
Interacting selectively and non-covalently with an RNA polymerase III transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
|
1 | Q9HAW0 (/IMP) |
|
Transcription factor activity, RNA polymerase III transcription factor binding GO:0001007
Interacting selectively and non-covalently with an RNA polymerase III transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
|
1 | Q3UAW9 (/ISO) |
|
RNA polymerase III type 3 promoter DNA binding GO:0001032
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.
|
1 | Q9HAW0 (/IDA) |
|
RNA polymerase III type 3 promoter DNA binding GO:0001032
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.
|
1 | Q3UAW9 (/ISO) |
|
Core promoter binding GO:0001047
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.
|
1 | P62915 (/IDA) |
|
DNA binding GO:0003677
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
|
1 | P62915 (/IDA) |
|
Transcription factor binding GO:0008134
Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
|
1 | P62915 (/ISO) |
|
TBP-class protein binding GO:0017025
Interacting selectively and non-covalently with a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs).
|
1 | Q00403 (/IPI) |
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TBP-class protein binding GO:0017025
Interacting selectively and non-covalently with a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs).
|
1 | P62915 (/ISO) |
|
Thyroid hormone receptor binding GO:0046966
Interacting selectively and non-covalently with a thyroid hormone receptor.
|
1 | Q00403 (/IPI) |
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Thyroid hormone receptor binding GO:0046966
Interacting selectively and non-covalently with a thyroid hormone receptor.
|
1 | P62915 (/ISO) |
There are 20 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 |
|---|---|---|
|
Regulation of transcription from RNA polymerase III promoter GO:0006359
Any process that modulates the frequency, rate or extent of transcription from an RNA ploymerase III promoter.
|
7 | A4QNR3 (/ISS) A8KBY2 (/ISS) Q29S07 (/ISS) Q3UAW9 (/ISS) Q4R318 (/ISS) Q4V8D6 (/ISS) Q66IW8 (/ISS) |
|
Cellular response to oxidative stress GO:0034599
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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
|
7 | A4QNR3 (/ISS) A8KBY2 (/ISS) Q29S07 (/ISS) Q3UAW9 (/ISS) Q4R318 (/ISS) Q4V8D6 (/ISS) Q66IW8 (/ISS) |
|
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.
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1 | P29052 (/IDA) |
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Regulation of transcription from RNA polymerase II promoter GO:0006357
Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
|
1 | P29052 (/IDA) |
|
Regulation of transcription from RNA polymerase III promoter GO:0006359
Any process that modulates the frequency, rate or extent of transcription from an RNA ploymerase III promoter.
|
1 | Q9HAW0 (/IMP) |
|
Regulation of transcription from RNA polymerase III promoter GO:0006359
Any process that modulates the frequency, rate or extent of transcription from an RNA ploymerase III promoter.
|
1 | Q3UAW9 (/ISO) |
|
Transcription from RNA polymerase II promoter GO:0006366
The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
|
1 | Q00403 (/TAS) |
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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.
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1 | P29052 (/ISS) |
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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.
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1 | Q00403 (/TAS) |
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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.
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1 | Q00403 (/TAS) |
|
Cellular response to oxidative stress GO:0034599
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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
|
1 | Q9HAW0 (/IMP) |
|
Cellular response to oxidative stress GO:0034599
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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
|
1 | Q3UAW9 (/ISO) |
|
SnRNA transcription from RNA polymerase II promoter GO:0042795
The synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase II (Pol II), originating at a Pol II promoter.
|
1 | Q00403 (/TAS) |
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Positive regulation of viral transcription GO:0050434
Any process that activates or increases the frequency, rate or extent of viral transcription.
|
1 | Q00403 (/IMP) |
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Positive regulation of viral transcription GO:0050434
Any process that activates or increases the frequency, rate or extent of viral transcription.
|
1 | P62915 (/ISO) |
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Regulation of DNA binding GO:0051101
Any process that modulates the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
|
1 | P29052 (/IDA) |
|
RNA polymerase II transcriptional preinitiation complex assembly GO:0051123
The aggregation, arrangement and bonding together of proteins on an RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase.
|
1 | Q00403 (/IDA) |
|
RNA polymerase II transcriptional preinitiation complex assembly GO:0051123
The aggregation, arrangement and bonding together of proteins on an RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase.
|
1 | P62915 (/ISO) |
|
Positive regulation of core promoter binding GO:1904798
Any process that activates or increases the frequency, rate or extent of core promoter binding.
|
1 | Q00403 (/IDA) |
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Positive regulation of core promoter binding GO:1904798
Any process that activates or increases the frequency, rate or extent of core promoter binding.
|
1 | P62915 (/ISO) |
There are 10 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.
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5 | B1APE1 (/IDA) B1APE2 (/IDA) P29052 (/IDA) P62915 (/IDA) Q00403 (/IDA) |
|
Nuclear body GO:0016604
Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.
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3 | B1APE1 (/IDA) B1APE2 (/IDA) Q00403 (/IDA) |
|
Nucleoplasm GO:0005654
That part of the nuclear content other than the chromosomes or the nucleolus.
|
2 | Q00403 (/TAS) Q9HAW0 (/TAS) |
|
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 | P62915 (/ISO) |
|
Transcription factor TFIID complex GO:0005669
A complex composed of TATA binding protein (TBP) and TBP associated factors (TAFs); the total mass is typically about 800 kDa. Most of the TAFs are conserved across species. In TATA-containing promoters for RNA polymerase II (Pol II), TFIID is believed to recognize at least two distinct elements, the TATA element and a downstream promoter element. TFIID is also involved in recognition of TATA-less Pol II promoters. Binding of TFIID to DNA is necessary but not sufficient for transcription initiation from most RNA polymerase II promoters.
|
1 | Q00403 (/IDA) |
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Transcription factor TFIID complex GO:0005669
A complex composed of TATA binding protein (TBP) and TBP associated factors (TAFs); the total mass is typically about 800 kDa. Most of the TAFs are conserved across species. In TATA-containing promoters for RNA polymerase II (Pol II), TFIID is believed to recognize at least two distinct elements, the TATA element and a downstream promoter element. TFIID is also involved in recognition of TATA-less Pol II promoters. Binding of TFIID to DNA is necessary but not sufficient for transcription initiation from most RNA polymerase II promoters.
|
1 | P62915 (/ISO) |
|
Nuclear body GO:0016604
Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.
|
1 | P62915 (/ISO) |
|
Transcriptional preinitiation complex GO:0097550
A protein-DNA complex composed of proteins binding promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription.
|
1 | Q00403 (/IDA) |
|
Transcriptional preinitiation complex GO:0097550
A protein-DNA complex composed of proteins binding promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription.
|
1 | P62915 (/ISO) |
|
Transcriptional preinitiation complex GO:0097550
A protein-DNA complex composed of proteins binding promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription.
|
1 | P29052 (/ISS) |
