Rfam Release 14.9

We are happy to announce the release of Rfam 14.9. This release features 14 new miRNA families, 23 updated miRNA families, 10 families improved with their first 3D structure, 10 families updated with additional 3D structures, and comprehensive improvements using R-scape. Read on for more details.

Updated and new miRNA families

In this release, we have updated 23 miRNA families in Rfam and created 14 new families based on miRBase miRNA alignments. We estimate that this project is 80 percent finished. The remaining families are undergoing extensive curation.

New miRNA Families:

Rfam ID	Family
RF04223	MIR2619
RF04224	mir-9229
RF04225	MIR7502
RF04226	mir-9186
RF04227	mir-9215
RF04228	MIR6140
RF04229	mir-9279
RF04230	mir-9261
RF04231	mir-9191
RF04232	mir-9318
RF04233	mir-680
RF04234	mir-1421
RF04235	mir-242_2
RF04236	mir-1285

Updated miRNA Families:

Rfam ID	Family
RF00241	mir-8/mir-141/mir-200
RF00456	mir-34
RF00661	mir-31
RF00672	mir-190
RF00700	mir-375
RF00702	mir-182
RF00706	mir-263
RF00713	mir-239
RF00716	mir-3
RF00717	mir-315
RF00726	mir-87
RF00727	microRNA bantam
RF00728	mir-81
RF00762	mir-412
RF00837	mir-251
RF00844	mir-67
RF00848	mir-61
RF00948	mir-996
RF01045	mir-544
RF01413	miR-430
RF01924	mir-2774
RF04088	MIR812
RF04195	MIR6217

3D families

We continue to review and update Rfam families with available 3D information, and in release 14.9 we include 10 new families updated with 3D information and we added additional 3D structures to 10 families. We have added 9 pseudoknots to the 10 families with new 3D structures.

Families with new 3D structures added:

Rfam ID	Family	New
RF00037	Iron response element I	3SNP_C, 3SNP_D
RF00522	PreQ1 riboswitch	2L1V_A
RF01073	Gag/pol translational readthrough site	2LC8_A
RF01727	SAM/SAH riboswitch	6HAG_A
RF02253	Iron response element II	3SN2_B
RF02519	ToxI antitoxin	4ATO_G
RF02553	Y RNA-like	6CU1_A
RF02796	Pab160 RNA	3HJW_D, 3LWO_D, 3LWP_D, 3LWQ_D, 3LWR_D, 3LWV_D
RF03054	Xanthine riboswitch/NMT1 RNA	7ELP_A, 7ELP_B, 7ELQ_A, 7ELQ_A, 7ELR_A, 7ELR_B, 7ELS_A, 7ELS_B
RF04222	Potato leafroll virus exoribonuclease-resistant RNA	7JJU_A, 7JJU_B

Families with additional 3D structures:

Rfam ID	Family	Update
RF00015	U4 spliceosomal RNA	5GAP_V
RF00025	Ciliate telomerase RNA	7LMA_B, 7LMB_B
RF00050	FMN riboswitch (RFN element)	6WJR_X, 6WJS_X
RF00059	TPP riboswitch (THI element)	7TD7_A, 7TDA_A, 7TDB_A, 7TDC_A, 7TZR_X, 7TZR_Y, 7TZS_X, 7TZS_Y, 7TZT_A, 7TZU_A
RF00162	SAM riboswitch (S box leader)	7EAF_A
RF00174	Cobalamin riboswitch	6VMY_A
RF00442	Guanidine-I riboswitch	5U3G_B, 7MLW_F
RF01763	ykkC-III Guanidine-III riboswitch	5NWQ_B, 5NY8_A, 5NY8_B, 5NZ3_A, 5NZ3_B, 5NZD_A, 5NZD_B, 5O62_A, 5O62_B, 5O69_A, 5O69_B
RF01831	THF riboswitch	6Q57_A, 7KD1_A
RF02680	PreQ1-III riboswitch	6XKN_A, 6XKO_A

We have also created rfam.org/3d which contains a table of all families with 3D structures and a link to download the seed alignments for those families. Additionally, there is a new file on our FTP site Rfam.3d.seed.gz which contains all seed alignments for these families. The page and file will be updated each release. Please reach out if you have any suggestions for improvements!

Families updated with R-scape model

We worked with Elena Rivas to analyse all Rfam families with R-scape. We then updated models where R-scape was able to suggest a better alignment. This led to 26 families with improvements, listed below by number of additional covarying base pairs.

Additional Covaring basepairs	Rfam ID	Family	Additional Covaring basepairs	Rfam ID	Family
24	RF02033	HEARO	2	RF01731	TwoAYGGAY
14	RF03065	IS605-orfB-I	2	RF01794	sok
8	RF03068	RT-3	2	RF02221	sRNA-Xcc1
5	RF03072	raiA	2	RF02947	cow-rumen-2
4	RF02969	DUF3800-I	2	RF03000	LOOT
3	RF01688	Actino-pnp	2	RF03158	L31-Actinobacteria
3	RF02004	group-II-D1D4-5	1	RF01864	plasmodium_snoR21
3	RF02005	group-II-D1D4-6	1	RF01867	CC2171
3	RF02913	pemK	1	RF02944	c4-2
3	RF03077	RT-2	1	RF02968	DUF3800-IX
3	RF03135	L4-Archaeoglobi	1	RF02987	GA-cis
3	RF03144	eL15-Euryarchaeota	1	RF03019	RT-16
2	RF00062	HgcC	1	RF03046	Pseudomonadales-1

Other updates

We have also updated 3 other families. We updated  Sarbecovirus 5’ UTR (RF03120) secondary structure to reflect the pairing from Correlated sequence signatures are present within the genomic 5′UTR RNA and NSP1 protein in coronaviruses. We modified the consensus secondary structure  of the stem loop 1 of the 5’ untranslated region of the family to reflect the secondary structure in that paper. Additionally we renamed RF03054 and RF03071 families, which were first reported by Zasha Weinberg in a comparative analysis of intergenic regions in bacteria.

The Xanthine riboswitch (RF03054) was first reported in Proteobacteria as NMT1 non-coding RNA (ncRNA). Later it was reported as a ncRNA that recognised Xanthine and the structure was reported in 7ELP, 7ELQ, 7ELR and 7ELS PDBs which have been added as part of the seed alignment.

The Na+ riboswitch (RF03071) was first reported by Zasha Weinberg and called DUF1646 RNA. More recently, Neil White from the Breaker group identified it as a riboswitch that selectively senses Na+ and  regulates the expression of genes related to the sodium biology.

Migrating Rfam’s public SVN repository

Rfam and Pfam used to provide a public copy of their SVN repositories on xfamsvn.ac.uk. With the recent depreciation of Pfam’s website and inclusion as part of InterPro, we have decided to move the Rfam svn repository to http://svn.rfam.org. Users interested in a nightly updated version of Rfam can browse the repository at this new location.