0  structures 19  species 21  sequences

Family: mir-612 (RF00959)

Description: mir-612 microRNA precursor family

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
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) ENA graphic
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) ENA graphic
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) ENA graphic
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) ENA graphic
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) ENA graphic
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 ENA graphic
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) ENA graphic
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) ENA graphic
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) ENA graphic
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) ENA graphic
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) ENA graphic
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 ENA graphic
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) ENA graphic
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) ENA graphic
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) ENA graphic
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) ENA graphic
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) ENA graphic

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.

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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:
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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

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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...

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

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Trees

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

This tree was built using the fasttree method.

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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
7 RM00008 GNRA tetraloop 3 0.500 26.4 Match Image
7 RM00029 UNCG tetraloop 3 0.500 27.7 Match Image

References

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

Literature references

  1. 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

  2. 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

  3. Kozomara A, Birgaoanu M, Griffiths-Jones S Nucleic Acids Res. 2019;47:D155. miRBase: from microRNA sequences to function. PUBMED:30423142

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.

Curation

Seed source Griffiths-Jones SR
Structure source Predicted; RNAalifold
Type Gene; miRNA;
Author Griffiths-Jones SRORCID logo, Griffiths-Jones SRORCID logo
Alignment details
Alignment Number of
sequences
full 17
seed 4

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 25.00 -Z 2958934 CM SEQDB
Gathering cutoff 100.0
Trusted cutoff 101.0
Noise cutoff 98.9
Covariance model Download
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