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1007  structures 7614  species 22  interactions 190937  sequences 2352  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 46 families and the total number of domains in the clan is 190937. 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 46 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 DUF458 Maelstrom MULE NurA Piwi Plant_tran Pox_A22 RNase_H RNase_H_2 RNase_HII RNase_T 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) 47519 (24.9%) View
RNase_T (PF00929) 17634 (9.2%) View
RNase_H (PF00075) 16967 (8.9%) View
DDE_Tnp_1 (PF01609) 12598 (6.6%) View
DDE_Tnp_ISL3 (PF01610) 7865 (4.1%) View
DDE_3 (PF13358) 7080 (3.7%) View
DNA_pol_A_exo1 (PF01612) 6914 (3.6%) View
Transposase_mut (PF00872) 6867 (3.6%) View
RNase_HII (PF01351) 6064 (3.2%) View
DDE_Tnp_IS66 (PF03050) 5890 (3.1%) View
rve_3 (PF13683) 4386 (2.3%) View
RVT_3 (PF13456) 3907 (2.0%) View
DDE_Tnp_4 (PF13359) 3886 (2.0%) View
DNA_pol_B_exo1 (PF03104) 3652 (1.9%) View
DDE_Tnp_IS1 (PF03400) 3369 (1.8%) View
RuvC (PF02075) 3205 (1.7%) View
DDE_Tnp_IS240 (PF13610) 3068 (1.6%) View
DDE_1 (PF03184) 3031 (1.6%) View
DDE_Tnp_1_6 (PF13751) 2925 (1.5%) View
DDE_Tnp_1_2 (PF13586) 2848 (1.5%) View
MULE (PF10551) 2654 (1.4%) View
rve_2 (PF13333) 2406 (1.3%) View
Piwi (PF02171) 2067 (1.1%) View
DDE_Tnp_1_4 (PF13701) 2054 (1.1%) View
Pfam family Num. domains Alignment
DDE_Tnp_IS1595 (PF12762) 1888 (1.0%) View
DDE_5 (PF13546) 1337 (0.7%) View
CAF1 (PF04857) 1134 (0.6%) View
DDE_Tnp_1_3 (PF13612) 1053 (0.6%) View
RNase_H_2 (PF13482) 1043 (0.5%) View
DDE_Tnp_1_7 (PF13843) 1008 (0.5%) View
DDE_Tnp_1_5 (PF13737) 810 (0.4%) View
DNA_pol_B_exo2 (PF10108) 607 (0.3%) View
UPF0236 (PF06782) 519 (0.3%) View
Transposase_1 (PF01359) 449 (0.2%) View
NurA (PF09376) 438 (0.2%) View
DDE_Tnp_ISAZ013 (PF07592) 318 (0.2%) View
Plant_tran (PF04827) 275 (0.1%) View
DUF458 (PF04308) 224 (0.1%) View
DUF2779 (PF11074) 211 (0.1%) View
DDE_Tnp_2 (PF04693) 202 (0.1%) View
DDE_2 (PF02914) 134 (0.1%) View
Maelstrom (PF13017) 133 (0.1%) View
Ydc2-catalyt (PF09159) 128 (0.1%) View
Pox_A22 (PF04848) 94 (0.0%) View
DUF3882 (PF07066) 63 (0.0%) View
DUF4152 (PF13680) 13 (0.0%) View
Total: 46 Total: 190937 Clan alignment

Please note: Clan alignments can be very large and can cause problems for some browsers. Read the note above before viewing.

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

Tree controls


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



There are 22 interactions for this clan. More...

Interacting families
RNase_H RNase_H
DNA_pol_A_exo1 DNA_pol_A
NurA NurA
DNA_pol_B_exo1 DNA_pol_B
rve IN_DBD_C
DDE_Tnp_1 Dimer_Tnp_Tn5
Ydc2-catalyt Ydc2-catalyt
RuvC RuvC
RNase_T RNase_T


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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