Summary
Wikipedia annotation Edit Wikipedia article
The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry Mir-612 microRNA precursor family. More...
This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.
Sequences
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Table view (21 sequence regions)
Original order | Download FASTA | Accession | Bit score | Type | Start | End | Description | Species | View context |
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0 | URS00006E8395_9606 | N/A | seed | 7 | 92 | Homo sapiens (human) microRNA hsa-mir-612 precursor | Homo sapiens (human) | ||
1 | URS000075A3D4_9598 | N/A | seed | 6 | 91 | Pan troglodytes (chimpanzee) microRNA ptr-mir-612 precursor | Pan troglodytes (chimpanzee) | ||
2 | URS0000D4F236_9600 | N/A | seed | 4 | 88 | Pongo pygmaeus (Bornean orangutan) microRNA ppy-mir-612 precursor | Pongo pygmaeus (Bornean orangutan) | ||
3 | URS000072D785_9544 | N/A | seed | 7 | 92 | Macaca mulatta (Rhesus monkey) microRNA mml-mir-612 precursor | Macaca mulatta (Rhesus monkey) | ||
0 | CM000673.2 | 109.50 | full | 65,444,464 | 65,444,549 | Homo sapiens chromosome 11, GRCh38 reference primary assembly. | Homo sapiens (human) |
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1 | QGDE01002567.1 | 109.50 | full | 1,430 | 1,515 | QGDE01002567.1 Theropithecus gelada isolate Dixy HiC_scaffold_2189, whole genome shotgun sequence | Theropithecus gelada (gelada baboon) |
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2 | MCGX01000834.1 | 109.50 | full | 1,534,336 | 1,534,421 | MCGX01000834.1 Rhinopithecus bieti isolate Rb0 scaffold_1017, whole genome shotgun sequence | Rhinopithecus bieti (Black snub-nosed monkey) |
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3 | KQ012441.1 | 109.50 | full | 8,938,202 | 8,938,117 | KQ012441.1 Cercocebus atys isolate FAK unplaced genomic scaffold Scaffold5, whole genome shotgun sequence | Cercocebus atys (sooty mangabey) |
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4 | KQ007745.1 | 109.50 | full | 4,129,943 | 4,130,028 | KQ007745.1 Macaca nemestrina isolate M95218 unplaced genomic scaffold Scaffold40, whole genome shotgun sequence | Macaca nemestrina (pig-tailed macaque) |
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5 | KN980607.1 | 109.50 | full | 4,648,088 | 4,648,003 | KN980607.1 Colobus angolensis palliatus isolate OR3802 unplaced genomic scaffold Scaffold21, whole genome shotgun sequence | Colobus angolensis palliatus |
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6 | KN979072.1 | 109.50 | full | 55,737 | 55,822 | KN979072.1 Mandrillus leucophaeus isolate KB7577 unplaced genomic scaffold Scaffold718, whole genome shotgun sequence | Mandrillus leucophaeus (drill) |
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7 | KN295605.1 | 109.50 | full | 105,685 | 105,600 | KN295605.1 Rhinopithecus roxellana isolate Xiao Hai unplaced genomic scaffold ENSRROG016160, whole genome shotgun sequence | Rhinopithecus roxellana (golden snub-nosed monkey) |
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8 | CM021952.1 | 109.50 | full | 8,951,788 | 8,951,703 | CM021952.1 Macaca fascicularis isolate cy0333 breed Mauritian cynomolgus macaque chromosome 14, whole genome shotgun sequence | Macaca fascicularis (crab-eating macaque) |
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9 | CM019252.1 | 109.50 | full | 8,686,034 | 8,685,949 | CM019252.1 Piliocolobus tephrosceles isolate RC106 chromosome 13, whole genome shotgun sequence | Piliocolobus tephrosceles (Ugandan red Colobus) |
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10 | CM003394.1 | 109.50 | full | 64,145,059 | 64,145,144 | CM003394.1 Pan paniscus isolate Ulindi chromosome 11, whole genome shotgun sequence | Pan paniscus (pygmy chimpanzee) |
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11 | CM001941.2 | 109.50 | full | 8,788,953 | 8,788,868 | Chlorocebus sabaeus isolate 1994-021 chromosome 1, whole genome shotgun sequence. | Chlorocebus sabaeus |
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12 | CM000325.3 | 109.50 | full | 65,507,721 | 65,507,806 | Pan troglodytes isolate Yerkes chimp pedigree #C0471 (Clint) chromosome 11, whole genome shotgun sequence. | Pan troglodytes (chimpanzee) |
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13 | CM018191.2 | 106.40 | full | 114,875,666 | 114,875,751 | CM018191.2 Papio anubis isolate 15944 chromosome 12, whole genome shotgun sequence | Papio anubis (Olive baboon) |
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14 | CM009273.2 | 102.00 | full | 8,848,626 | 8,848,542 | CM009273.2 Pongo abelii isolate Susie chromosome 11, whole genome shotgun sequence | Pongo abelii (Sumatran orangutan) |
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15 | CM001650.1 | 101.10 | full | 85,896,092 | 85,896,176 | Nomascus leucogenys chromosome 4, whole genome shotgun sequence. | Nomascus leucogenys (Northern white-cheeked gibbon) |
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16 | FR853082.2 | 101.00 | full | 64,645,499 | 64,645,584 | Gorilla gorilla gorilla genomic chromosome, chr11, whole genome shotgun sequence | Gorilla gorilla gorilla (western lowland gorilla) |
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Alignment
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.
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.
Current Rfam structure
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R-scape optimised structure
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- Colours
- Statistically significant basepair with covariation
- 97% conserved nucleotide
- 90% conserved nucleotide
- 75% conserved nucleotide
- 50% conserved nucleotide
- Nucleotides
- R: A or G
- Y: C or U
Tip: The diagrams are interactive:
you can pan and zoom to see more details
or hover over nucleotides and basepairs.
R-scape is a method for testing whether covariation analysis supports the presence of a conserved RNA secondary structure. This page shows R-scape analysis of the secondary structure from the Rfam seed alignment and a new structure with covariation support that is compatible with the same alignment.
To find out more about the method, see the R-scape paper by Rivas et al., 2016. The structures are visualised using R2R.
Species distribution
Sunburst controls
HideLineage
Move your mouse over the main tree to show the lineage of a particular node.
You can move this pane by dragging it.
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Change the size of the sunburst
Colour assignments
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Selections
Click on a node to select that node and its sub-tree.
Clear selection
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...
Tree controls
HideThe tree shows the occurrence of this RNA across different species. More...
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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.
Trees
This page displays the predicted phylogenetic tree for the alignment. More...
Note: You can also download the data file for the seed tree.
Motif matches
There are 2 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 |
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7 | RM00008 | GNRA tetraloop | 3 | 0.500 | 26.4 |
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7 | RM00029 | UNCG tetraloop | 3 | 0.500 | 27.7 |
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References
This section shows the database cross-references that we have for this Rfam family.
Literature references
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Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O, Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H, Kinzler KW, Vogelstein B, Velculescu VE; Proc Natl Acad Sci U S A. 2006;103:3687-3692. The colorectal microRNAome. PUBMED:16505370
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Baev V, Daskalova E, Minkov I Comput Biol Chem. 2009;33:62-70. Computational identification of novel microRNA homologs in the chimpanzee genome PUBMED:18760970
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Kozomara A, Birgaoanu M, Griffiths-Jones S Nucleic Acids Res. 2019;47:D155. miRBase: from microRNA sequences to function. PUBMED:30423142
External database links
Gene Ontology: | GO:0016442 (RISC complex); GO:0035195 (miRNA-mediated post-transcriptional gene silencing); |
Sequence Ontology: | SO:0001244 (pre_miRNA); |
MIPF: | MIPF0000464 |
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.
Curation
Seed source | Griffiths-Jones SR | ||||||
Structure source | Predicted; RNAalifold | ||||||
Type | Gene; miRNA; | ||||||
Author |
Griffiths-Jones SR |
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Alignment details |
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Model information
Build commands |
cmbuild -F CM SEED
cmcalibrate --mpi CM
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Search command |
cmsearch --cpu 4 --verbose --nohmmonly -T 25.00 -Z 2958934 CM SEQDB
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Gathering cutoff | 100.0 |
Trusted cutoff | 101.0 |
Noise cutoff | 98.9 |
Covariance model | Download |