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1417  structures 23356  species 56  interactions 634844  sequences 3515  architectures

Clan: RNase_H (CL0219)


Ribonuclease H-like superfamily Add an annotation

This clan includes a diverse set of nucleases that share a similar structure to Ribonuclease H.

This clan contains 48 families and the total number of domains in the clan is 634844. The clan was built by A Bateman.

Literature references

  1. Rice P, Craigie R, Davies DR; , Curr Opin Struct Biol. 1996;6:76-83.: Retroviral integrases and their cousins. PUBMED:8696976 EPMC:8696976


This clan contains the following 48 member families:

CAF1 DDE_1 DDE_2 DDE_3 DDE_5 DDE_Tnp_1 DDE_Tnp_1_2 DDE_Tnp_1_3 DDE_Tnp_1_4 DDE_Tnp_1_5 DDE_Tnp_1_6 DDE_Tnp_1_7 DDE_Tnp_2 DDE_Tnp_4 DDE_Tnp_IS1 DDE_Tnp_IS1595 DDE_Tnp_IS240 DDE_Tnp_IS66 DDE_Tnp_ISAZ013 DDE_Tnp_ISL3 DNA_pol_A_exo1 DNA_pol_B_exo1 DNA_pol_B_exo2 DUF2779 DUF3882 DUF4152 DUF5051 Maelstrom MULE NurA OrfB_IS605 Piwi Plant_tran Pox_A22 RNase_H RNase_H_2 RNase_HII RNase_T RNaseH_like RuvC rve rve_2 rve_3 RVT_3 Transposase_1 Transposase_mut UPF0236 Ydc2-catalyt

External database links

Domain organisation

Below is a listing of the unique domain organisations or architectures from this clan. More...

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The table below shows the number of occurrences of each domain throughout the sequence database. More...

Pfam family Num. domains Alignment
rve (PF00665) 133725 (21.1%) View
RNase_T (PF00929) 71774 (11.3%) View
DDE_Tnp_1 (PF01609) 52565 (8.3%) View
Transposase_mut (PF00872) 31600 (5.0%) View
RNase_H (PF00075) 31511 (5.0%) View
DDE_Tnp_ISL3 (PF01610) 31273 (4.9%) View
DNA_pol_A_exo1 (PF01612) 27323 (4.3%) View
RNase_HII (PF01351) 26937 (4.2%) View
OrfB_IS605 (PF01385) 22328 (3.5%) View
DDE_Tnp_IS66 (PF03050) 21613 (3.4%) View
rve_3 (PF13683) 16380 (2.6%) View
DDE_Tnp_IS240 (PF13610) 16378 (2.6%) View
DDE_Tnp_IS1 (PF03400) 13305 (2.1%) View
DDE_3 (PF13358) 12779 (2.0%) View
RVT_3 (PF13456) 11917 (1.9%) View
RuvC (PF02075) 11917 (1.9%) View
DDE_Tnp_1_6 (PF13751) 11800 (1.9%) View
DNA_pol_B_exo1 (PF03104) 11544 (1.8%) View
DDE_Tnp_4 (PF13359) 8257 (1.3%) View
rve_2 (PF13333) 7407 (1.2%) View
DUF5051 (PF16473) 6540 (1.0%) View
DDE_Tnp_IS1595 (PF12762) 5686 (0.9%) View
DDE_Tnp_1_2 (PF13586) 5659 (0.9%) View
MULE (PF10551) 5345 (0.8%) View
DDE_Tnp_1_5 (PF13737) 5046 (0.8%) View
Pfam family Num. domains Alignment
DDE_1 (PF03184) 4305 (0.7%) View
Piwi (PF02171) 3833 (0.6%) View
RNase_H_2 (PF13482) 3752 (0.6%) View
DDE_Tnp_1_4 (PF13701) 3192 (0.5%) View
DDE_Tnp_1_3 (PF13612) 3148 (0.5%) View
CAF1 (PF04857) 2954 (0.5%) View
DDE_5 (PF13546) 2118 (0.3%) View
DNA_pol_B_exo2 (PF10108) 2104 (0.3%) View
DDE_Tnp_1_7 (PF13843) 2007 (0.3%) View
UPF0236 (PF06782) 1156 (0.2%) View
DDE_Tnp_ISAZ013 (PF07592) 1000 (0.2%) View
Transposase_1 (PF01359) 872 (0.1%) View
NurA (PF09376) 871 (0.1%) View
Plant_tran (PF04827) 635 (0.1%) View
DUF2779 (PF11074) 524 (0.1%) View
RNaseH_like (PF04308) 462 (0.1%) View
DDE_2 (PF02914) 270 (0.0%) View
DUF3882 (PF07066) 221 (0.0%) View
Maelstrom (PF13017) 219 (0.0%) View
Ydc2-catalyt (PF09159) 217 (0.0%) View
DDE_Tnp_2 (PF04693) 213 (0.0%) View
Pox_A22 (PF04848) 144 (0.0%) View
DUF4152 (PF13680) 18 (0.0%) View
Total: 48 Total: 634844 Clan alignment

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Family relationships

This diagram shows the relationships between members of this clan. More...

We could not retrieve a family relationship diagram for this clan.

Species distribution

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This tree shows the occurrence of the domains in this clan across different species. More...



For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.

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