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:

"
Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
".

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 35: General transcription factor IIF subunit 2

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 4 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).
15 P13984 (/IPI) P13984 (/IPI) P13984 (/IPI) P13984 (/IPI) P13984 (/IPI) P13984 (/IPI) P41896 (/IPI) P41896 (/IPI) P41896 (/IPI) P41896 (/IPI)
(5 more)
RNA polymerase II complex binding GO:0000993
Interacting selectively and non-covalently with RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits.
9 P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41896 (/IDA)
TFIIF-class transcription factor complex binding GO:0001096
Interacting selectively and non-covalently with a general RNA polymerase II transcription factor belonging to the TFIIF complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II.
1 P41900 (/IPI)
RNA polymerase II general transcription initiation factor activity GO:0016251
An activity that contributes to transcription start site selection and transcription initiation of genes transcribed by RNA polymerase II. The general transcription factors for RNA polymerase II include TFIIB, TFIID, TFIIE, TFIIF, TFIIH and TATA-binding protein (TBP).
1 O94424 (/ISS)

There are 25 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
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 P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41900 (/IDA)
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 P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41900 (/IDA)
Promoter clearance from RNA polymerase II promoter GO:0001111
Any process involved in the transition from the initiation to the elongation phases of transcription by RNA polymerase II, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase and making contacts with elongation specific factors.
9 P41896 (/IC) P41896 (/IC) P41896 (/IC) P41896 (/IC) P41896 (/IC) P41896 (/IC) P41896 (/IC) P41896 (/IC) P41896 (/IC)
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.
9 P41896 (/IMP) P41896 (/IMP) P41896 (/IMP) P41896 (/IMP) P41896 (/IMP) P41896 (/IMP) P41896 (/IMP) P41896 (/IMP) P41896 (/IMP)
RNA polymerase II 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.
9 P41896 (/IC) P41896 (/IC) P41896 (/IC) P41896 (/IC) P41896 (/IC) P41896 (/IC) P41896 (/IC) P41896 (/IC) P41896 (/IC)
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.
8 Q03123 (/ISS) Q03123 (/ISS) Q2T9L9 (/ISS) Q2T9L9 (/ISS) Q2T9L9 (/ISS) Q54KT7 (/ISS) Q8R0A0 (/ISS) Q8R0A0 (/ISS)
MRNA splicing, via spliceosome GO:0000398
The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
6 P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/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).
6 P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS)
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.
6 P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS)
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.
6 P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS)
7-methylguanosine mRNA capping GO:0006370
Addition of the 7-methylguanosine cap to the 5' end of a nascent messenger RNA transcript.
6 P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS)
Fibroblast growth factor receptor signaling pathway GO:0008543
The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands.
6 P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS)
RNA metabolic process GO:0016070
The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
6 P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS)
SnRNA transcription by RNA polymerase II 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.
6 P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS)
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.
6 P13984 (/IMP) P13984 (/IMP) P13984 (/IMP) P13984 (/IMP) P13984 (/IMP) P13984 (/IMP)
Positive regulation of viral transcription GO:0050434
Any process that activates or increases the frequency, rate or extent of viral transcription.
6 P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS)
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.
3 O94424 (/ISS) P41900 (/ISS) Q54KT7 (/ISS)
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).
2 P41900 (/IDA) Q01750 (/IDA)
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).
2 Q8R0A0 (/ISO) Q8R0A0 (/ISO)
Positive regulation of transcription elongation from RNA polymerase II promoter GO:0032968
Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
2 Q8R0A0 (/ISO) Q8R0A0 (/ISO)
Positive regulation of RNA polymerase II transcriptional preinitiation complex assembly GO:0045899
Any process that activates or increases the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly.
2 Q8R0A0 (/ISO) Q8R0A0 (/ISO)
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 Q8R0A0 (/ISO) Q8R0A0 (/ISO)
Positive regulation of transcription elongation from RNA polymerase II promoter GO:0032968
Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
1 Q01750 (/IDA)
Positive regulation of RNA polymerase II transcriptional preinitiation complex assembly GO:0045899
Any process that activates or increases the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly.
1 Q01750 (/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.
1 Q01750 (/IDA)

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
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.
13 A0A024RDU9 (/IDA) A0A024RDU9 (/IDA) A0A024RDU9 (/IDA) A0A024RDU9 (/IDA) A0A024RDU9 (/IDA) A0A024RDU9 (/IDA) P13984 (/IDA) P13984 (/IDA) P13984 (/IDA) P13984 (/IDA)
(3 more)
Microtubule cytoskeleton GO:0015630
The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
12 A0A024RDU9 (/IDA) A0A024RDU9 (/IDA) A0A024RDU9 (/IDA) A0A024RDU9 (/IDA) A0A024RDU9 (/IDA) A0A024RDU9 (/IDA) P13984 (/IDA) P13984 (/IDA) P13984 (/IDA) P13984 (/IDA)
(2 more)
Transcription factor TFIIF complex GO:0005674
A general transcription initiation factor which in humans consists of a heterodimer of an alpha and a beta subunit. Helps recruit RNA polymerase II to the initiation complex and promotes translation elongation.
10 P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41896 (/IDA) P41900 (/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.
7 O94424 (/HDA) P13984 (/HDA) P13984 (/HDA) P13984 (/HDA) P13984 (/HDA) P13984 (/HDA) P13984 (/HDA)
Nucleoplasm GO:0005654
That part of the nuclear content other than the chromosomes or the nucleolus.
6 P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS) P13984 (/TAS)
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.
6 P13984 (/IDA) P13984 (/IDA) P13984 (/IDA) P13984 (/IDA) P13984 (/IDA) P13984 (/IDA)
Transcription factor TFIIF complex GO:0005674
A general transcription initiation factor which in humans consists of a heterodimer of an alpha and a beta subunit. Helps recruit RNA polymerase II to the initiation complex and promotes translation elongation.
3 O94424 (/ISS) P41900 (/ISS) Q54KT7 (/ISS)
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 Q8R0A0 (/ISO) Q8R0A0 (/ISO)
Transcription factor TFIIH holo complex GO:0005675
A complex that is capable of kinase activity directed towards the C-terminal Domain (CTD) of the largest subunit of RNA polymerase II and is essential for initiation at RNA polymerase II promoters in vitro. It is composed of the core TFIIH complex and the TFIIK complex.
2 Q8R0A0 (/ISO) Q8R0A0 (/ISO)
Mitochondrion GO:0005739
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
2 Q9LQZ4 (/IDA) Q9LQZ4 (/IDA)
Microtubule cytoskeleton GO:0015630
The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
2 Q8R0A0 (/ISO) Q8R0A0 (/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.
2 Q8R0A0 (/ISO) Q8R0A0 (/ISO)
Transcription factor TFIIH holo complex GO:0005675
A complex that is capable of kinase activity directed towards the C-terminal Domain (CTD) of the largest subunit of RNA polymerase II and is essential for initiation at RNA polymerase II promoters in vitro. It is composed of the core TFIIH complex and the TFIIK complex.
1 Q01750 (/IDA)
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