transcription elongation factor A N-terminal and central domain-containing protein [Danio rerio]
transcription factor S-II family protein( domain architecture ID 13520976)
transcription factor S-II (TFS II) family protein similar to Drosophila melanogaster transcription elongation factor S-II, which is necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites
List of domain hits
Name | Accession | Description | Interval | E-value | ||||||
TFIIS_M | pfam07500 | Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase ... |
214-324 | 4.29e-30 | ||||||
Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and pfam01096 are required for transcription activity. : Pssm-ID: 462184 Cd Length: 112 Bit Score: 111.91 E-value: 4.29e-30
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TFSII super family | cl36890 | transcription elongation factor S-II; This model represents eukaryotic transcription ... |
5-386 | 8.39e-30 | ||||||
transcription elongation factor S-II; This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end. The actual alignment was detected with superfamily member TIGR01385: Pssm-ID: 273592 [Multi-domain] Cd Length: 299 Bit Score: 116.48 E-value: 8.39e-30
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Name | Accession | Description | Interval | E-value | ||||||
TFIIS_M | pfam07500 | Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase ... |
214-324 | 4.29e-30 | ||||||
Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and pfam01096 are required for transcription activity. Pssm-ID: 462184 Cd Length: 112 Bit Score: 111.91 E-value: 4.29e-30
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TFSII | TIGR01385 | transcription elongation factor S-II; This model represents eukaryotic transcription ... |
5-386 | 8.39e-30 | ||||||
transcription elongation factor S-II; This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end. Pssm-ID: 273592 [Multi-domain] Cd Length: 299 Bit Score: 116.48 E-value: 8.39e-30
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TFS2M | smart00510 | Domain in the central regions of transcription elongation factor S-II (and elsewhere); |
214-315 | 5.52e-16 | ||||||
Domain in the central regions of transcription elongation factor S-II (and elsewhere); Pssm-ID: 128786 [Multi-domain] Cd Length: 102 Bit Score: 73.12 E-value: 5.52e-16
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Med26 | pfam08711 | TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is ... |
28-77 | 6.37e-10 | ||||||
TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species {1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. Notably, the 'small' and 'large' Mediator complexes differ in their subunit composition: the Med26 subunit preferentially associates with the small, active complex, whereas cdk8, cyclin C, Med12 and Med13 associate with the large Mediator complex. This family includesthe C terminal region of a number of eukaryotic hypothetical proteins which are homologous to the Saccharomyces cerevisiae protein IWS1. IWS1 is known to be an Pol II transcription elongation factor and interacts with Spt6 and Spt5. Pssm-ID: 462573 [Multi-domain] Cd Length: 52 Bit Score: 54.44 E-value: 6.37e-10
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Zn-ribbon_TFIIS | cd13749 | domain III/zinc ribbon domain of Transcription Factor IIS; TFIIS is a zinc-containing ... |
331-386 | 1.15e-04 | ||||||
domain III/zinc ribbon domain of Transcription Factor IIS; TFIIS is a zinc-containing transcription factor. It has been shown in vitro to have distinct biochemical activities, including binding to RNA polymerases, stimulation of transcript elongation, and activation of a nascent RNA cleavage activity in the RNA polymerase II (Pol II) elongation complex. TFIIS consists of three domains. Domain II and III are sufficient for all known TFIIS activities. Domain III is a zinc ribbon that separated from domain II by a long linker and is indispensable for TFIIS function. The TFIIS homologs, subunits A12.2, B9, and C11, of Pol I, II, and III respectively, are required for RNA cleavage by the polymerases. In a single organism, there are tissue-specific TFIIS related proteins. Pssm-ID: 259796 Cd Length: 47 Bit Score: 39.51 E-value: 1.15e-04
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Name | Accession | Description | Interval | E-value | ||||||
TFIIS_M | pfam07500 | Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase ... |
214-324 | 4.29e-30 | ||||||
Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and pfam01096 are required for transcription activity. Pssm-ID: 462184 Cd Length: 112 Bit Score: 111.91 E-value: 4.29e-30
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TFSII | TIGR01385 | transcription elongation factor S-II; This model represents eukaryotic transcription ... |
5-386 | 8.39e-30 | ||||||
transcription elongation factor S-II; This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end. Pssm-ID: 273592 [Multi-domain] Cd Length: 299 Bit Score: 116.48 E-value: 8.39e-30
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TFS2M | smart00510 | Domain in the central regions of transcription elongation factor S-II (and elsewhere); |
214-315 | 5.52e-16 | ||||||
Domain in the central regions of transcription elongation factor S-II (and elsewhere); Pssm-ID: 128786 [Multi-domain] Cd Length: 102 Bit Score: 73.12 E-value: 5.52e-16
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Med26 | pfam08711 | TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is ... |
28-77 | 6.37e-10 | ||||||
TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species {1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. Notably, the 'small' and 'large' Mediator complexes differ in their subunit composition: the Med26 subunit preferentially associates with the small, active complex, whereas cdk8, cyclin C, Med12 and Med13 associate with the large Mediator complex. This family includesthe C terminal region of a number of eukaryotic hypothetical proteins which are homologous to the Saccharomyces cerevisiae protein IWS1. IWS1 is known to be an Pol II transcription elongation factor and interacts with Spt6 and Spt5. Pssm-ID: 462573 [Multi-domain] Cd Length: 52 Bit Score: 54.44 E-value: 6.37e-10
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Zn-ribbon_TFIIS | cd13749 | domain III/zinc ribbon domain of Transcription Factor IIS; TFIIS is a zinc-containing ... |
331-386 | 1.15e-04 | ||||||
domain III/zinc ribbon domain of Transcription Factor IIS; TFIIS is a zinc-containing transcription factor. It has been shown in vitro to have distinct biochemical activities, including binding to RNA polymerases, stimulation of transcript elongation, and activation of a nascent RNA cleavage activity in the RNA polymerase II (Pol II) elongation complex. TFIIS consists of three domains. Domain II and III are sufficient for all known TFIIS activities. Domain III is a zinc ribbon that separated from domain II by a long linker and is indispensable for TFIIS function. The TFIIS homologs, subunits A12.2, B9, and C11, of Pol I, II, and III respectively, are required for RNA cleavage by the polymerases. In a single organism, there are tissue-specific TFIIS related proteins. Pssm-ID: 259796 Cd Length: 47 Bit Score: 39.51 E-value: 1.15e-04
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TFIIS_C | pfam01096 | Transcription factor S-II (TFIIS); |
338-386 | 2.27e-03 | ||||||
Transcription factor S-II (TFIIS); Pssm-ID: 426046 Cd Length: 39 Bit Score: 35.66 E-value: 2.27e-03
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Zn-ribbon | cd00656 | C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The ... |
334-386 | 3.67e-03 | ||||||
C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The homologous C-terminal zinc ribbon domains of subunits A12.2, Rpb9, and C11 in RNA Polymerases (Pol) I, II, and III, respectively are required for intrinsic transcript cleavage. TFS is a related archaeal protein that is involved in RNA cleavage by archaeal polymerase. These proteins have two zinc-binding beta-ribbon domains, N-terminal zinc ribbon (N-ribbon) and C-terminal zinc ribbon (C-ribbon). Transcription Factor IIS (TFIIS) domain III is homologous to the C-ribbon domain that stimulates the weak cleavage activity of Rpb9 for Pol II. Pssm-ID: 259791 Cd Length: 45 Bit Score: 34.98 E-value: 3.67e-03
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Blast search parameters | ||||
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