endoribonuclease Dicer [Nematostella vectensis]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||
| RIBOc | cd00593 | RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ... |
1637-1809 | 4.00e-37 | ||||
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing. : Pssm-ID: 238333 Cd Length: 133 Bit Score: 136.59 E-value: 4.00e-37
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| RIBOc | cd00593 | RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ... |
1269-1453 | 6.06e-23 | ||||
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing. : Pssm-ID: 238333 Cd Length: 133 Bit Score: 96.14 E-value: 6.06e-23
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| PAZ super family | cl00301 | PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two ... |
988-1071 | 6.36e-15 | ||||
PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. This parent model also contains structures of an archaeal PAZ domain. The actual alignment was detected with superfamily member cd02843: Pssm-ID: 469713 Cd Length: 122 Bit Score: 72.86 E-value: 6.36e-15
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| Dicer_dimer | pfam03368 | Dicer dimerization domain; This domain is found in members of the Dicer protein family which ... |
565-668 | 4.46e-12 | ||||
Dicer dimerization domain; This domain is found in members of the Dicer protein family which function in RNA interference, an evolutionarily conserved mechanism for gene silencing using double-stranded RNA (dsRNA) molecules. It is essential for the activity of Dicer. It is a divergent double stranded RNA-binding domain. The N-terminal alpha helix of this domain is in a different orientation to that found in canonical dsRNA-binding domains. This results in a change of charge distribution at the potential dsRNA-binding surface and in the N- and C-termini of the domain being in close proximity. This domain has weak dsRNA-binding activity. It mediates heterodimerization of Dicer proteins with their respective protein partners. : Pssm-ID: 460900 Cd Length: 89 Bit Score: 63.67 E-value: 4.46e-12
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| DSRM_SF super family | cl00054 | double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ... |
1814-1876 | 1.09e-09 | ||||
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 amino acid domain that adopts an alpha-beta-beta-beta-alpha fold. It is not sequence specific, but highly specific for double-stranded RNAs (dsRNAs) of various origin and structure. The DSRM domains are found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila Staufen protein, E. coli RNase III, RNase H1, and dsRNA dependent adenosine deaminases. They are involved in numerous cellular mechanisms ranging from localization and transport of messenger RNAs, through maturation and degradation of RNAs, to viral response and signal transduction. Some members harbor tandem DSRMs that act in small RNA biogenesis. The actual alignment was detected with superfamily member cd10843: Pssm-ID: 444671 Cd Length: 63 Bit Score: 55.89 E-value: 1.09e-09
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| P-loop_NTPase super family | cl38936 | P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ... |
453-505 | 1.68e-04 | ||||
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families. The actual alignment was detected with superfamily member cd18802: Pssm-ID: 476819 [Multi-domain] Cd Length: 142 Bit Score: 43.73 E-value: 1.68e-04
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| Name | Accession | Description | Interval | E-value | |||||
| RIBOc | cd00593 | RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ... |
1637-1809 | 4.00e-37 | |||||
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing. Pssm-ID: 238333 Cd Length: 133 Bit Score: 136.59 E-value: 4.00e-37
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| Rnc | COG0571 | dsRNA-specific ribonuclease [Transcription]; |
1621-1879 | 2.25e-34 | |||||
dsRNA-specific ribonuclease [Transcription]; Pssm-ID: 440336 [Multi-domain] Cd Length: 229 Bit Score: 132.53 E-value: 2.25e-34
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| RNaseIII | TIGR02191 | ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ... |
1626-1875 | 2.69e-33 | |||||
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing] Pssm-ID: 274024 [Multi-domain] Cd Length: 220 Bit Score: 128.86 E-value: 2.69e-33
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| RIBOc | smart00535 | Ribonuclease III family; |
1639-1806 | 2.35e-30 | |||||
Ribonuclease III family; Pssm-ID: 197778 Cd Length: 129 Bit Score: 117.32 E-value: 2.35e-30
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| RIBOc | cd00593 | RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ... |
1269-1453 | 6.06e-23 | |||||
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing. Pssm-ID: 238333 Cd Length: 133 Bit Score: 96.14 E-value: 6.06e-23
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| Ribonuclease_3 | pfam00636 | Ribonuclease III domain; |
1660-1787 | 2.34e-22 | |||||
Ribonuclease III domain; Pssm-ID: 459883 Cd Length: 101 Bit Score: 93.49 E-value: 2.34e-22
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| RIBOc | smart00535 | Ribonuclease III family; |
1270-1460 | 1.73e-19 | |||||
Ribonuclease III family; Pssm-ID: 197778 Cd Length: 129 Bit Score: 86.12 E-value: 1.73e-19
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| PAZ_dicer_like | cd02843 | PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA ... |
988-1071 | 6.36e-15 | |||||
PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA interference pathway. It generates dsRNAs which are approximately 20 bp long (siRNAs), which in turn target hydrolysis of homologous RNAs. PAZ domains are named after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. Pssm-ID: 239209 Cd Length: 122 Bit Score: 72.86 E-value: 6.36e-15
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| PAZ | smart00949 | This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in ... |
990-1120 | 6.85e-13 | |||||
This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerisation. The three-dimensional structure of this domain has been solved. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteristic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway. Pssm-ID: 198017 Cd Length: 138 Bit Score: 67.70 E-value: 6.85e-13
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| Ribonuclease_3 | pfam00636 | Ribonuclease III domain; |
1287-1442 | 7.18e-13 | |||||
Ribonuclease III domain; Pssm-ID: 459883 Cd Length: 101 Bit Score: 66.14 E-value: 7.18e-13
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| Dicer_dimer | pfam03368 | Dicer dimerization domain; This domain is found in members of the Dicer protein family which ... |
565-668 | 4.46e-12 | |||||
Dicer dimerization domain; This domain is found in members of the Dicer protein family which function in RNA interference, an evolutionarily conserved mechanism for gene silencing using double-stranded RNA (dsRNA) molecules. It is essential for the activity of Dicer. It is a divergent double stranded RNA-binding domain. The N-terminal alpha helix of this domain is in a different orientation to that found in canonical dsRNA-binding domains. This results in a change of charge distribution at the potential dsRNA-binding surface and in the N- and C-termini of the domain being in close proximity. This domain has weak dsRNA-binding activity. It mediates heterodimerization of Dicer proteins with their respective protein partners. Pssm-ID: 460900 Cd Length: 89 Bit Score: 63.67 E-value: 4.46e-12
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| DSRM_DICER | cd10843 | double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins; Dicer (also ... |
1814-1876 | 1.09e-09 | |||||
double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins; Dicer (also known as helicase with RNase motif (HERNA), or helicase MOI) is a double-stranded RNA (dsRNA) endoribonuclease playing a central role in short dsRNA-mediated post-transcriptional gene silencing. It cleaves naturally occurring long dsRNAs and short hairpin pre-microRNAs (miRNA) into fragments of twenty-one to twenty-three nucleotides with 3' overhang of two nucleotides, producing respectively short interfering RNAs (siRNA) and mature microRNAs. Dicer contains a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. Pssm-ID: 380680 Cd Length: 63 Bit Score: 55.89 E-value: 1.09e-09
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| RNaseIII | TIGR02191 | ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ... |
1270-1344 | 6.57e-09 | |||||
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing] Pssm-ID: 274024 [Multi-domain] Cd Length: 220 Bit Score: 57.98 E-value: 6.57e-09
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| Rnc | COG0571 | dsRNA-specific ribonuclease [Transcription]; |
1270-1344 | 2.12e-08 | |||||
dsRNA-specific ribonuclease [Transcription]; Pssm-ID: 440336 [Multi-domain] Cd Length: 229 Bit Score: 56.65 E-value: 2.12e-08
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| PAZ | pfam02170 | PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain ... |
990-1119 | 5.95e-08 | |||||
PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerization. The three-dimensional structure of this domain has been solved. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteriztic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway. Pssm-ID: 460472 Cd Length: 123 Bit Score: 52.97 E-value: 5.95e-08
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| SF2_C_dicer | cd18802 | C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
453-505 | 1.68e-04 | |||||
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350189 [Multi-domain] Cd Length: 142 Bit Score: 43.73 E-value: 1.68e-04
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| Name | Accession | Description | Interval | E-value | |||||
| RIBOc | cd00593 | RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ... |
1637-1809 | 4.00e-37 | |||||
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing. Pssm-ID: 238333 Cd Length: 133 Bit Score: 136.59 E-value: 4.00e-37
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| Rnc | COG0571 | dsRNA-specific ribonuclease [Transcription]; |
1621-1879 | 2.25e-34 | |||||
dsRNA-specific ribonuclease [Transcription]; Pssm-ID: 440336 [Multi-domain] Cd Length: 229 Bit Score: 132.53 E-value: 2.25e-34
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| RNaseIII | TIGR02191 | ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ... |
1626-1875 | 2.69e-33 | |||||
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing] Pssm-ID: 274024 [Multi-domain] Cd Length: 220 Bit Score: 128.86 E-value: 2.69e-33
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| RIBOc | smart00535 | Ribonuclease III family; |
1639-1806 | 2.35e-30 | |||||
Ribonuclease III family; Pssm-ID: 197778 Cd Length: 129 Bit Score: 117.32 E-value: 2.35e-30
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| RIBOc | cd00593 | RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ... |
1269-1453 | 6.06e-23 | |||||
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing. Pssm-ID: 238333 Cd Length: 133 Bit Score: 96.14 E-value: 6.06e-23
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| Ribonuclease_3 | pfam00636 | Ribonuclease III domain; |
1660-1787 | 2.34e-22 | |||||
Ribonuclease III domain; Pssm-ID: 459883 Cd Length: 101 Bit Score: 93.49 E-value: 2.34e-22
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| RIBOc | smart00535 | Ribonuclease III family; |
1270-1460 | 1.73e-19 | |||||
Ribonuclease III family; Pssm-ID: 197778 Cd Length: 129 Bit Score: 86.12 E-value: 1.73e-19
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| Ribonucleas_3_3 | pfam14622 | Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ... |
1637-1790 | 5.87e-16 | |||||
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA processing. They probably also cleave a stem-loop structure at the 3' end of U2 snRNA to ensure formation of the correct U2 3' end; they are involved in polyadenylation-independent transcription termination. Some members may be mitochondrial ribosomal protein subunit L15, others may be 60S ribosomal protein L3. Pssm-ID: 434075 Cd Length: 127 Bit Score: 76.06 E-value: 5.87e-16
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| PAZ_dicer_like | cd02843 | PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA ... |
988-1071 | 6.36e-15 | |||||
PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA interference pathway. It generates dsRNAs which are approximately 20 bp long (siRNAs), which in turn target hydrolysis of homologous RNAs. PAZ domains are named after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. Pssm-ID: 239209 Cd Length: 122 Bit Score: 72.86 E-value: 6.36e-15
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| PAZ | smart00949 | This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in ... |
990-1120 | 6.85e-13 | |||||
This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerisation. The three-dimensional structure of this domain has been solved. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteristic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway. Pssm-ID: 198017 Cd Length: 138 Bit Score: 67.70 E-value: 6.85e-13
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| Ribonuclease_3 | pfam00636 | Ribonuclease III domain; |
1287-1442 | 7.18e-13 | |||||
Ribonuclease III domain; Pssm-ID: 459883 Cd Length: 101 Bit Score: 66.14 E-value: 7.18e-13
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| Dicer_dimer | pfam03368 | Dicer dimerization domain; This domain is found in members of the Dicer protein family which ... |
565-668 | 4.46e-12 | |||||
Dicer dimerization domain; This domain is found in members of the Dicer protein family which function in RNA interference, an evolutionarily conserved mechanism for gene silencing using double-stranded RNA (dsRNA) molecules. It is essential for the activity of Dicer. It is a divergent double stranded RNA-binding domain. The N-terminal alpha helix of this domain is in a different orientation to that found in canonical dsRNA-binding domains. This results in a change of charge distribution at the potential dsRNA-binding surface and in the N- and C-termini of the domain being in close proximity. This domain has weak dsRNA-binding activity. It mediates heterodimerization of Dicer proteins with their respective protein partners. Pssm-ID: 460900 Cd Length: 89 Bit Score: 63.67 E-value: 4.46e-12
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| PAZ_CAF_like | cd02844 | PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has ... |
990-1103 | 5.35e-12 | |||||
PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has been implicated in flower morphogenesis and in early Arabidopsis development and might function through posttranscriptional regulation of specific mRNA molecules. PAZ domains are named after the proteins Piwi, Argonaut, and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the Piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. Pssm-ID: 239210 Cd Length: 135 Bit Score: 65.13 E-value: 5.35e-12
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| DSRM_DICER | cd10843 | double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins; Dicer (also ... |
1814-1876 | 1.09e-09 | |||||
double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins; Dicer (also known as helicase with RNase motif (HERNA), or helicase MOI) is a double-stranded RNA (dsRNA) endoribonuclease playing a central role in short dsRNA-mediated post-transcriptional gene silencing. It cleaves naturally occurring long dsRNAs and short hairpin pre-microRNAs (miRNA) into fragments of twenty-one to twenty-three nucleotides with 3' overhang of two nucleotides, producing respectively short interfering RNAs (siRNA) and mature microRNAs. Dicer contains a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. Pssm-ID: 380680 Cd Length: 63 Bit Score: 55.89 E-value: 1.09e-09
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| RNaseIII | TIGR02191 | ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ... |
1270-1344 | 6.57e-09 | |||||
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing] Pssm-ID: 274024 [Multi-domain] Cd Length: 220 Bit Score: 57.98 E-value: 6.57e-09
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| Rnc | COG0571 | dsRNA-specific ribonuclease [Transcription]; |
1270-1344 | 2.12e-08 | |||||
dsRNA-specific ribonuclease [Transcription]; Pssm-ID: 440336 [Multi-domain] Cd Length: 229 Bit Score: 56.65 E-value: 2.12e-08
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| PAZ | pfam02170 | PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain ... |
990-1119 | 5.95e-08 | |||||
PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerization. The three-dimensional structure of this domain has been solved. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteriztic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway. Pssm-ID: 460472 Cd Length: 123 Bit Score: 52.97 E-value: 5.95e-08
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| SF2_C_dicer | cd18802 | C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
453-505 | 1.68e-04 | |||||
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350189 [Multi-domain] Cd Length: 142 Bit Score: 43.73 E-value: 1.68e-04
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| Ribonucleas_3_3 | pfam14622 | Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ... |
1269-1344 | 5.05e-04 | |||||
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA processing. They probably also cleave a stem-loop structure at the 3' end of U2 snRNA to ensure formation of the correct U2 3' end; they are involved in polyadenylation-independent transcription termination. Some members may be mitochondrial ribosomal protein subunit L15, others may be 60S ribosomal protein L3. Pssm-ID: 434075 Cd Length: 127 Bit Score: 41.78 E-value: 5.05e-04
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| PAZ | cd02825 | PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two ... |
1031-1066 | 9.63e-03 | |||||
PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. This parent model also contains structures of an archaeal PAZ domain. Pssm-ID: 239207 Cd Length: 115 Bit Score: 37.83 E-value: 9.63e-03
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