2137  structures 9951  species 1430083  sequences

Family: tRNA (RF00005)

Description: tRNA



This family is a member of clan (CL00001), which contains the following 7 members:

alpha_tmRNA beta_tmRNA cyano_tmRNA mt-tmRNA tmRNA tRNA tRNA-Sec

Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry Transfer RNA. More...

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.



There are various ways to view or download the seed alignments that we store. You can use a sequence viewer to look at them, or you can look at a plain text version of the sequence in a variety of different formats. More...

View options

You can view Rfam seed alignments in your browser in various ways. Choose the viewer that you want to use and click the "View" button to show the alignment in a pop-up window.


Formatting options

You can view or download Rfam seed alignments in several formats. Check either the "download" button, to save the formatted alignment, or "view", to see it in your browser window, and click "Generate".

Alignment format:


Download a gzip-compressed, Stockholm-format file containing the seed alignment for this family. You may find RALEE useful when viewing sequence alignments.

Submit a new alignment

We're happy receive updated seed alignments for new or existing families. Submit your new alignment and we'll take a look.

Secondary structure

This section shows a variety of different secondary structure representations for this family. More...

You can view the secondary structure of the family using the VARNA applet. You can see more information about VARNA iself here.

Species distribution

We are unable to display the sunburst tree for this family.

  • There are too many sequences in this alignment

Tree controls


The tree shows the occurrence of this RNA across different species. More...


Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.


This page displays the predicted phylogenetic tree for the alignment. More...

This tree was built using the fasttree method.

Label the trees using or

Note: You can also download the data file for the seed tree.


For those sequences which have a structure in the Protein DataBank, we generate a mapping between EMBL, PDB and Rfam coordinate systems. The table below shows the structures on which the tRNA family has been found.

Loading structure mapping...

Motif matches

There are 1 motifs which match this family.

This section shows the Rfam motifs that match sequences within the seed alignment of this family. Users should be aware that the motifs are structural constructs and do not necessarily conform to taxonomic boundaries in the way that Rfam families do. More...

Original order Motif Accession Motif Description Number of Hits Fraction of Hits Sum of Bits Image
7 RM00024 T-loop 567 0.594 8155.1 Match Image


This section shows the database cross-references that we have for this Rfam family.

Literature references

  1. Hou YM Trends Biochem Sci 1993;18:362-364. The tertiary structure of tRNA and the development of the genetic code. PUBMED:8256282

  2. Lowe TM, Eddy SR Nucleic Acids Res 1997;25:955-964. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. PUBMED:9023104

External database links

Curation and family details

This section shows the detailed information about the Rfam family. We're happy to receive updated or improved alignments for new or existing families. Submit your new alignment and we'll take a look.


Seed source Eddy SR
Structure source Published; PMID:8256282
Type Gene; tRNA;
Author Eddy SRORCID logo, Griffiths-Jones SRORCID logo, Mifsud WORCID logo
Alignment details
Alignment Number of
full 1,429,129
seed 954

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 22.00 -Z 549862.597050 CM SEQDB
Gathering cutoff 29.0
Trusted cutoff 29.0
Noise cutoff 28.9
Covariance model Download