The Wikipedia text that you see displayed on our web site was retrieved from Wikipedia. This means that the information we display is a copy of the information from the Wikipedia database. The button above ("Edit wikipedia entry") takes you to the edit page for the article directly within Wikipedia.

Before you edit for the first time

Wikipedia is a free, online encyclopedia. Although anyone can edit or contribute to an article, Wikipedia has some strong editing guidelines and policies, which promote the Wikipedia standard of style and etiquette. Your edits and contributions are more likely to be accepted (and remain) if they are in accordance with this policy.

You should take a few minutes to view the following pages:

• Five pillars
• Policies and quidelines
• Wikipedia help contents
• Wikipedia Tips
• Editing help

Things you should know

How your contribution will be recorded

Anyone can edit a Wikipedia entry. You can do this either as a new user or you can register with Wikipedia and log on. When you click on the "Edit Wikipedia entry" button, your browser will direct you to the edit page for this entry in Wikipedia. If you are a registered user and currently logged in, your changes will be recorded under your Wikipedia user name. However, if you are not a registered user or are not logged on, your changes will be logged under your computer’s IP address. This has two main implications. Firstly, as a registered Wikipedia user your edits are more likely seen as valuable contribution (although all edits are open to community scrutiny regardless). Secondly, if you edit under an IP address you may be sharing this IP address with other users. If your IP address has previously been blocked (due to being flagged as a source of 'vandalism') your edits will also be blocked. You can find more information on this and creating a user account at Wikipedia.

If you have problems editing a particular page, contact us at rfam-help@ebi.ac.uk and we will try to help.

Information we would like to see added

We would value contributions that are referenced directly to the primary literature. Information on structure and function will be especially valuable.

Adding references is explained by this Wikipedia how-to article.

For a good example of what is possible in wikipedia, look at the Hammerhead Ribozyme entry.

Does Rfam agree with the content of the Wikipedia entry ?

Rfam has chosen to create Wikipedia entries for all of our RNA families and to open them up to community annotation. While the original Wikipedia article that we import was (in most cases) generated from Rfam annotations, the Wikipedia article you see now may bear little resemblance to that original text. The Wikipedia community does monitor edits to try to ensure that (a) the quality of article annotation increases, and (b) vandalism is very quickly dealt with. However, we would like to emphasise that Rfam does not curate the Wikipedia entries and we cannot guarantee the accuracy of the information on the Wikipedia page.

Contact us

If you have problems editing or experience problems with these pages please contact us.

If you are interested in contributing to a wide range of articles relating to RNA, see the Wikiproject RNA page.

Quick actions

Download all sequences Download table

Browse in Rfam Browse in RNAcentral

Table view (91 sequence regions)

Original order	Download FASTA	Accession	Bit score	Type	Start	End	Description	Species	View context
0		Z71564.1	N/A	seed	474	570	S.cerevisiae chromosome XIV reading frame ORF YNL288w	Saccharomyces cerevisiae (baker's yeast)
1		AACG02000180.1	N/A	seed	13,913	13,817	Saccharomyces bayanus 623-6C YM4911-Contig02.510, whole genome shotgun sequence.	Saccharomyces bayanus 623-6C
2		AAZN01000021.1	N/A	seed	10,523	10,428	Vanderwaltozyma polyspora DSM 70294 KpolContig1020b, whole genome shotgun sequence.	Vanderwaltozyma polyspora DSM 70294
3		AACF01000363.1	N/A	seed	646	549	Naumovozyma castellii NRRL Y-12630 YM476-Contig360, whole genome shotgun sequence.	Naumovozyma castellii NRRL Y-12630
4		CR382125.1	N/A	seed	1,171,339	1,171,430	Kluyveromyces lactis strain NRRL Y-1140 chromosome E complete sequence.	Kluyveromyces lactis
5		AADM01000021.1	N/A	seed	38,814	38,722	Kluyveromyces waltii NCYC 2644 cont20, whole genome shotgun sequence.	Lachancea waltii NCYC 2644
6		AABZ01000174.1	N/A	seed	12,255	12,350	Saccharomyces mikatae IFO 1815 contig_1148, whole genome shotgun sequence.	Saccharomyces mikatae IFO 1815
7		CP000497.1	N/A	seed	358,606	358,529	Scheffersomyces stipitis CBS 6054 chromosome 3, complete sequence.	Scheffersomyces stipitis CBS 6054
8		DQ115396.1	N/A	seed	8,340	8,429	Pichia pastoris Sec16 (SEC16) gene, complete cds.	Komagataella pastoris
9		AAFM01000054.1	N/A	seed	140,217	140,293	Pichia guilliermondii ATCC 6260 cont1.40, whole genome shotgun sequence.	Meyerozyma guilliermondii ATCC 6260
10		AAFT01000015.1	N/A	seed	83,616	83,540	Clavispora lusitaniae ATCC 42720 cont1.15, whole genome shotgun sequence.	Clavispora lusitaniae ATCC 42720
11		AACQ01000170.1	N/A	seed	2,388	2,308	Candida albicans SC5314 chromosome 5 Ctg19-20155, whole genome shotgun sequence.	Candida albicans SC5314
12		AAPO01000074.1	N/A	seed	76,364	76,438	Lodderomyces elongisporus NRRL YB-4239 cont1.74, whole genome shotgun sequence.	Lodderomyces elongisporus NRRL YB-4239
13		AACE03000005.3	N/A	seed	1,082,925	1,082,831	Lachancea kluyveri NRRL Y-12651 chromosome C SKLU-Cont10104, whole genome shotgun sequence.	Lachancea kluyveri NRRL Y-12651
14		CR382137.2	N/A	seed	1,045,753	1,045,676	Debaryomyces hansenii strain CBS767 chromosome E complete sequence.	Debaryomyces hansenii
15		CR380959.2	N/A	seed	403,349	403,256	Candida glabrata strain CBS138 chromosome M complete sequence.	Candida glabrata
16		AE016818.2	N/A	seed	266,474	266,566	Ashbya gossypii ATCC 10895 chromosome V, complete sequence.	Ashbya gossypii ATCC 10895
17		U26015.1	N/A	seed	1	97	Saccharomyces cerevisiae small nuclear RNA snR40.	Saccharomyces cerevisiae (baker's yeast)
0		BK006947.3	100.40	full	89,210	89,306	TPA: Saccharomyces cerevisiae S288C chromosome XIV, complete sequence.	Saccharomyces cerevisiae S288c
1		CM001576.1	98.00	full	72,952	73,045	Saccharomyces arboricola H-6 chromosome XIV, whole genome shotgun sequence.	Saccharomyces arboricola H-6
2		CP059271.1	96.30	full	384,474	384,381	CP059271.1 Torulaspora sp. CBS 2947 strain CBS2947 chromosome 5	Torulaspora sp. CBS 2947
3		DS480414.1	93.10	full	32,762	32,667	Vanderwaltozyma polyspora DSM 70294 KpolScaffold1020 genomic scaffold, whole genome shotgun sequence.	Vanderwaltozyma polyspora DSM 70294
4		HE650821.1	92.60	full	1,660,798	1,660,704	Kazachstania africana CBS 2517 chromosome 1, complete genome	Kazachstania africana CBS 2517
5		HE612856.1	91.80	full	103,356	103,448	Tetrapisispora phaffii CBS 4417 chromosome 1, complete genome	Tetrapisispora phaffii CBS 4417
6		CP002499.1	91.80	full	1,017,052	1,017,148	Eremothecium cymbalariae DBVPG#7215 chromosome 3, complete sequence.	Eremothecium cymbalariae DBVPG#7215
7		LT598491.1	91.70	full	1,441,531	1,441,441	Lachancea fermentati genome assembly, chromosome: H	Lachancea fermentati
8		HE576752.1	90.70	full	1,970,364	1,970,267	Naumovozyma castellii CBS 4309 chromosome 1, complete genome	Naumovozyma castellii CBS 4309
9		HE580267.1	90.70	full	1,371,958	1,371,862	Naumovozyma dairenensis CBS 421 chromosome 1, complete genome	Naumovozyma dairenensis CBS 421
10		FXLY01000004.1	90.00	full	117,387	117,483	Kazachstania saulgeensis genome assembly, contig: scaffold_03	Kazachstania saulgeensis
11		CU928175.1	88.40	full	162,879	162,788	Zygosaccharomyces rouxii strain CBS732 chromosome C complete sequence.	Zygosaccharomyces rouxii CBS 732
12		KV454212.1	86.80	full	570,848	570,938	Wickerhamomyces anomalus NRRL Y-366-8 unplaced genomic scaffold WICANscaffold_5, whole genome shotgun sequence.	Wickerhamomyces anomalus NRRL Y-366-8
13		KV453931.1	85.40	full	228,395	228,486	Cyberlindnera jadinii NRRL Y-1542 unplaced genomic scaffold CYBJAscaffold_7, whole genome shotgun sequence.	Cyberlindnera jadinii NRRL Y-1542
14		LT598467.1	85.20	full	1,197,547	1,197,456	Lachancea mirantina genome assembly, chromosome: F	Lachancea mirantina
15		CP058609.1	84.90	full	467,633	467,735	CP058609.1 Zygotorulaspora mrakii strain NRRL Y-6702 chromosome 6	Zygosaccharomyces mrakii
16		MPUK01000011.1	84.90	full	68,920	69,010	Cyberlindnera fabianii strain 65 BON22_Sc11, whole genome shotgun sequence.	Cyberlindnera fabianii
17		HE616746.1	84.90	full	164,295	164,385	Torulaspora delbrueckii CBS 1146 chromosome 5, complete genome	Torulaspora delbrueckii CBS 1146
18		HE806317.1	84.40	full	2,022,692	2,022,602	Tetrapisispora blattae CBS 6284 chromosome 2, complete genome	Tetrapisispora blattae CBS 6284
19		CAIF01000168.1	84.30	full	25,918	25,828	Wickerhamomyces ciferrii, NRRL Y-1031 F-60-10, WGS project CAIF01000000 data, contig: 00168	Wickerhamomyces ciferrii NRRL Y-1031
20		HE978324.1	83.80	full	457,917	457,819	Kazachstania naganishii CBS 8797 chromosome 11, complete genome	Kazachstania naganishii CBS 8797
21		CU928165.1	82.20	full	142,564	142,656	Lachancea thermotolerans CBS 6340 chromosome A complete sequence.	Lachancea thermotolerans CBS 6340
22		JAEUBG010001417.1	82.10	full	129	234	JAEUBG010001417.1 Wickerhamomyces pijperi strain CBS2887 scaffold1029, whole genome shotgun sequence	Pichia pijperi
23		JAEUBG010005498.1	82.10	full	21,728	21,833	JAEUBG010005498.1 Wickerhamomyces pijperi strain CBS2887 scaffold63, whole genome shotgun sequence	Pichia pijperi
24		KV454443.1	81.60	full	119,233	119,143	Babjeviella inositovora NRRL Y-12698 unplaced genomic scaffold BABINscaffold_18, whole genome shotgun sequence.	Babjeviella inositovora NRRL Y-12698
25		CH408158.1	80.20	full	140,217	140,293	Pichia guilliermondii ATCC 6260 scaffold_4 genomic scaffold, whole genome shotgun sequence.	Meyerozyma guilliermondii ATCC 6260
26		NSDU01000024.1	80.20	full	1,042,383	1,042,307	NSDU01000024.1 Meyerozyma sp. JA9 scaffold_4, whole genome shotgun sequence	Meyerozyma sp. JA9
27		NSGQ01000006.1	79.80	full	272,319	272,236	NSGQ01000006.1 Spathaspora sp. JA1 scaffold_5, whole genome shotgun sequence	Spathaspora sp. JA1
28		GL996524.1	79.10	full	1,056,701	1,056,623	Candida tenuis ATCC 10573 unplaced genomic scaffold CANTEscaffold_00018, whole genome shotgun sequence.	Candida tenuis ATCC 10573
29		KV454011.1	78.70	full	1,357,055	1,356,965	Pachysolen tannophilus NRRL Y-2460 unplaced genomic scaffold PACTA_scaffold_1, whole genome shotgun sequence.	Pachysolen tannophilus NRRL Y-2460
30		JAHMUF010000015.1	78.40	full	162,247	162,168	JAHMUF010000015.1 Scheffersomyces spartinae strain ARV_011 scaffold_15, whole genome shotgun sequence	Scheffersomyces spartinae
31		FN392322.1	77.60	full	186,126	186,037	Pichia pastoris GS115 chromosome 4, complete sequence	Komagataella pastoris GS115
32		GL996502.1	77.30	full	415,535	415,458	Spathaspora passalidarum NRRL Y-27907 unplaced genomic scaffold SPAPAscaffold_4, whole genome shotgun sequence.	Spathaspora passalidarum NRRL Y-27907
33		PYFQ01000001.1	76.20	full	1,373,741	1,373,665	PYFQ01000001.1 [Candida] pseudohaemuli strain B12108 scaffold00001, whole genome shotgun sequence	Candida pseudohaemulonii
34		CAKXYY010000008.1	75.80	full	410,128	410,051	CAKXYY010000008.1 [Candida] railenensis strain CLIB 1423 genome assembly, contig: CLIB1423_08S, whole genome shotgun sequence	Candida railenensis
35		JAGSYN010000135.1	75.70	full	43,114	43,034	JAGSYN010000135.1 [Candida] subhashii strain CBS 10753 scaffold48, whole genome shotgun sequence	Candida subhashii
36		KV453913.1	75.60	full	1,273,149	1,273,225	Candida tanzawaensis NRRL Y-17324 unplaced genomic scaffold CANTAscaffold_5, whole genome shotgun sequence.	Candida tanzawaensis NRRL Y-17324
37		JABWAD010000069.1	75.40	full	69,956	70,036	JABWAD010000069.1 Candida albicans strain FDAARGOS_656 tig00000170_pilon, whole genome shotgun sequence	Candida albicans
38		CP017627.1	75.40	full	776,791	776,871	Candida albicans SC5314 chromosome 5 sequence.	Candida albicans SC5314
39		PKFO01000003.1	75.00	full	1,475,544	1,475,620	PKFO01000003.1 [Candida] haemuli strain B11899 C_2014730914, whole genome shotgun sequence	Candida haemulonis
40		LT598455.1	74.90	full	71,161	71,251	Lachancea dasiensis CBS 10888 genome assembly, chromosome: E	Lachancea dasiensis CBS 10888
41		LN736372.1	73.70	full	97,142	97,233	Lachancea lanzarotensis strain CBS 12615 genome assembly, scaffold: LALA0S13	Lachancea lanzarotensis
42		GG692397.1	73.70	full	1,470,173	1,470,253	Candida tropicalis MYA-3404 genomic scaffold supercont3.3, whole genome shotgun sequence.	Candida tropicalis MYA-3404
43		GG692397.1	73.70	full	1,496,030	1,495,950	Candida tropicalis MYA-3404 genomic scaffold supercont3.3, whole genome shotgun sequence.	Candida tropicalis MYA-3404
44		QLNQ01000019.1	73.50	full	380,246	380,326	QLNQ01000019.1 Candida viswanathii strain ATCC 20962 contig13, whole genome shotgun sequence	Candida viswanathii
45		QLNQ01000019.1	73.50	full	391,622	391,702	QLNQ01000019.1 Candida viswanathii strain ATCC 20962 contig13, whole genome shotgun sequence	Candida viswanathii
46		QLNQ01000019.1	73.50	full	410,083	410,003	QLNQ01000019.1 Candida viswanathii strain ATCC 20962 contig13, whole genome shotgun sequence	Candida viswanathii
47		QLNQ01000028.1	73.50	full	1,503,245	1,503,325	QLNQ01000028.1 Candida viswanathii strain ATCC 20962 contig4, whole genome shotgun sequence	Candida viswanathii
48		QLNQ01000028.1	73.50	full	1,514,667	1,514,747	QLNQ01000028.1 Candida viswanathii strain ATCC 20962 contig4, whole genome shotgun sequence	Candida viswanathii
49		QLNQ01000028.1	73.50	full	1,533,128	1,533,048	QLNQ01000028.1 Candida viswanathii strain ATCC 20962 contig4, whole genome shotgun sequence	Candida viswanathii
50		CH408077.1	71.90	full	108,454	108,378	Clavispora lusitaniae ATCC 42720 scaffold_2 genomic scaffold, whole genome shotgun sequence.	Clavispora lusitaniae ATCC 42720
51		ML004445.1	71.30	full	144,872	144,948	ML004445.1 Metschnikowia bicuspidata strain Baker2002 unplaced genomic scaffold METBISCscaffold_18, whole genome shotgun sequence	Metschnikowia bicuspidata
52		BSXU01000355.1	70.70	full	8,149	8,237	BSXU01000355.1 Ambrosiozyma monospora NBRC 1965 DNA, scf7180000088212, whole genome shotgun sequence	Ambrosiozyma monospora
53		BSXU01010998.1	70.70	full	1,545	1,457	BSXU01010998.1 Ambrosiozyma monospora NBRC 1965 DNA, scf7180000101327, whole genome shotgun sequence	Ambrosiozyma monospora
54		FO082047.1	70.20	full	1,480,818	1,480,739	Pichia sorbitophila strain CBS 7064 chromosome M complete sequence.	Millerozyma farinosa CBS 7064 (Pichia farinosa CBS 7064)
55		FO082046.1	70.20	full	1,489,717	1,489,638	Pichia sorbitophila strain CBS 7064 chromosome N complete sequence.	Millerozyma farinosa CBS 7064 (Pichia farinosa CBS 7064)
56		KV454539.1	68.60	full	1,590,570	1,590,498	Hyphopichia burtonii NRRL Y-1933 unplaced genomic scaffold HYPBUscaffold_2, whole genome shotgun sequence.	Hyphopichia burtonii NRRL Y-1933
57		CABVLU010000002.1	67.40	full	4,347,439	4,347,538	CABVLU010000002.1 Saprochaete ingens strain CBS 517.90 genome assembly, contig: contig2, whole genome shotgun sequence	Saprochaete ingens
58		CM076438.1	67.40	full	1,677,129	1,677,206	CM076438.1 [Candida] auris strain B8441 chromosome 1, whole genome shotgun sequence	Candida auris
59		HE605207.1	65.90	full	365,012	365,094	Candida parapsilosis strain CDC317 annotated contig 006139	Candida parapsilosis CDC317
60		CANTUO010000005.1	64.60	full	812,007	811,926	CANTUO010000005.1 Candida verbasci genome assembly, contig: chrE, whole genome shotgun sequence	Candida verbasci
61		CH981528.1	64.10	full	389,645	389,719	Lodderomyces elongisporus NRRL YB-4239 supercont1.5 genomic scaffold, whole genome shotgun sequence.	Lodderomyces elongisporus NRRL YB-4239
62		LPNN01000010.1	58.50	full	153,835	153,762	LPNN01000010.1 Hanseniaspora uvarum strain AWRI3580 Hanseniaspora_uvarum_AWRI3580_scaffold10, whole genome shotgun sequence	Hanseniaspora uvarum
63		QQZK01000023.1	57.80	full	61,356	61,448	QQZK01000023.1 Geotrichum candidum strain LMA-70 Scaffold23, whole genome shotgun sequence	Geotrichum candidum (oospora lactis)
64		KV454300.1	56.80	full	256,563	256,470	Lipomyces starkeyi NRRL Y-11557 unplaced genomic scaffold LIPSTscaffold_12, whole genome shotgun sequence.	Lipomyces starkeyi NRRL Y-11557
65		LPNM01000010.1	56.30	full	699,243	699,349	Hanseniaspora osmophila strain AWRI3579 Hanseniaspora_osmophila_AWRI3579_scaffold10, whole genome shotgun sequence.	Hanseniaspora osmophila
66		SWFT01000050.1	55.80	full	339,027	339,105	SWFT01000050.1 Diutina rugosa strain CBS 613 scaffold4_size502443, whole genome shotgun sequence	Candida rugosa
67		LXPE01000004.1	55.40	full	579,662	579,590	Hanseniaspora valbyensis NRRL Y-1626 HANVAscaffold_4, whole genome shotgun sequence.	Hanseniaspora valbyensis NRRL Y-1626
68		LT635759.1	53.60	full	76,668	76,598	[Candida] intermedia strain CBS 141442 genome assembly, chromosome: IV	Candida intermedia
69		SWFS01000415.1	53.30	full	53,222	53,126	SWFS01000415.1 Trichomonascus ciferrii strain CBS 4856 scaffold57_size92944, whole genome shotgun sequence	Trichomonascus ciferrii
70		BIMT01000024.1	52.90	full	77,024	77,098	BIMT01000024.1 Metschnikowia sp. JCM 33374 DNA, tig00000069, whole genome shotgun sequence	Metschnikowia sp. JCM 33374
71		CP014501.1	51.80	full	3,040,209	3,040,093	Sugiyamaella lignohabitans strain CBS 10342 chromosome A, complete sequence.	Candida lignohabitans
72		LXTC01000001.1	50.60	full	538,246	538,320	Metschnikowia bicuspidata var. bicuspidata NRRL YB-4993 METBIscaffold_1, whole genome shotgun sequence.	Metschnikowia bicuspidata var. bicuspidata NRRL YB-4993

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".

Download

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.

In this page you can view static images showing the secondary structure of this family using a variety of colouring schemes:

Conservation (cons): this plot colours each character by how well conserved it is. A site with 100% sequence conservation is coloured red, 0% is violet.

Covariation (cov): this plot colours each base-pair according to how much the corresponding nucleotides are co-varying. A base-pair position at which every pair of nucleotides is co-variant with respect to every other pair in the alignment gets a score of 2 and is coloured red. Conversely, a base-pair position at every pair is anti-co-variant with respect to every other pair (e.g. lots of mutations to non-canonical pairs) gets a score of -2 and is coloured violet. Further information on this metric can be found in this document.

Sequence entropy (ent): this plot colours each character by how under- or over-represented the residues at the site are. Sites where one or more nucleotides are over-represented while the other nucleotides are either non-existent or near the background frequencies, receive positive scores; sites where all the nucleotides are under-represented receive negative scores. Further information on this metric can be found in this document.

Fraction of canonical basepairs (fcbp): this plot colours each base-pair by the percentage of canonical basepairs (A:U, C:G, G:U) which are found in the corresponding position in the alignment. A pair of sites with 100% canonical pairs is coloured red, a site with 0% is violet.

Maximum parse of the covariance model (maxcm): this plot takes the covariance model for the family and generates the sequence with the maximum possible score for that model. Each character is coloured by how many bits it contributes to the total score.

Sequence: for most of the above cases, the representative sequence used for the backbone is the most informative sequence (MIS). Any residue that has a higher frequency than than the background frequency is projected into the IUPAC redundancy codes.

Normal: this plot simply colours each stem loop

R-chie (rchie): arc diagrams showing secondary structure, calculated using the R-chie package. The consensus secondary structure is visualized as arc diagrams on top of each diagram, where a basepair in an arc, connect two columns of the block of sequences below. The block of sequences below represent the multiple sequence alignment of the Rfam seed, where each sequence is a horizontal strip. Sequences in the alignments are ordered so sequences that best fit the structure are on top, and those that do not fit as well are towards the bottom. For seed alignments for over 500 sequences, 500 random sequences were chosen. Rfam entries without sturcture have a blank plot. Colour information can be found on the R-chie FAQ.

You can also view the secondary structure in the VARNA applet. The applet is shown in a separate pop-up window.

Acknowledgements

The bulk of the code for generating these graphics was kindly supplied by Andreas Gruber and Ivo Hofacker. The statistics were implemented by Rfam.

The VARNA applet is developed by Yann Ponty et al:

The R-chie arc diagrams were calculated using R-chie:

These trees were generated using either a maximum likelihood approach or neighbour-joining. If the number of sequences in the alignment was less than or equal to 64 then the maximum likelihood approach of Rivas and Eddy was used [1]. For families with more than 64 sequences in the alignment the neighbour-joining approach with F84 distances as implemented in phylip was used [2].

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

We do not have tree information for this family. This is most likely due to the size of the family and the number of species covered. For very large families it is too computationally expensive to calculate trees and the resulting tree images would be too large to display in a browser.