0  structures 9  species 20  sequences

Family: mir-2319 (RF03588)

Description: mir-2319 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 MicroRNA. More...

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Sequences

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Table view (20 sequence regions)

Original order Download FASTA Accession Bit score Type Start End Description Species View context
0
URS000075B00E_9913 N/A seed 3 73 Bos taurus (cattle) microRNA bta-mir-2319a precursor Bos taurus (cattle)  
1
URS000075E1D6_9913 N/A seed 1 71 Bos taurus (cattle) microRNA bta-mir-2319b precursor Bos taurus (cattle)  
0
CM011788.1 99.70 full 76,774,984 76,775,054 CM011788.1 Bos indicus x Bos taurus breed Angus x Brahman F1 hybrid chromosome 15, whole genome shotgun sequence Bos indicus x Bos taurus (hybrid cattle) ENA graphic
1
NC_032664.1 99.70 full 77,285,785 77,285,855 NC_032664.1 Bos indicus isolate QUIL7308 breed Nelore chromosome 15, Bos_indicus_1.0, whole genome shotgun sequence Bos indicus ENA graphic
2
CM008182.2 99.70 full 76,769,277 76,769,347 CM008182.2 Bos taurus isolate L1 Dominette 01449 registration number 42190680 breed Hereford chromosome 15, whole genome shotgun sequence Bos taurus (cattle) ENA graphic
3
CM008182.2 98.90 full 76,769,347 76,769,277 CM008182.2 Bos taurus isolate L1 Dominette 01449 registration number 42190680 breed Hereford chromosome 15, whole genome shotgun sequence Bos taurus (cattle) ENA graphic
4
CM011788.1 98.90 full 76,775,054 76,774,984 CM011788.1 Bos indicus x Bos taurus breed Angus x Brahman F1 hybrid chromosome 15, whole genome shotgun sequence Bos indicus x Bos taurus (hybrid cattle) ENA graphic
5
NC_032664.1 98.90 full 77,285,855 77,285,785 NC_032664.1 Bos indicus isolate QUIL7308 breed Nelore chromosome 15, Bos_indicus_1.0, whole genome shotgun sequence Bos indicus ENA graphic
6
CM016702.1 96.70 full 29,715,236 29,715,306 CM016702.1 Bos grunniens isolate yakHY00 ecotype maiwa chromosome 13, whole genome shotgun sequence Bos grunniens (domestic yak) ENA graphic
7
JH881474.1 96.70 full 606,822 606,892 JH881474.1 Bos grunniens mutus unplaced genomic scaffold scaffold1123_1, whole genome shotgun sequence Bos grunniens mutus ENA graphic
8
NW_011494750.1 96.70 full 1,798,913 1,798,983 NW_011494750.1 Bison bison bison isolate TAMUID 2011002044 unplaced genomic scaffold, Bison_UMD1.0 scf7180017864178, whole genome shotgun sequence Bison bison bison (north american plains bison) ENA graphic
9
CM004576.1 96.60 full 6,217,831 6,217,761 CM004576.1 Capra hircus breed San Clemente chromosome 15, whole genome shotgun sequence Capra hircus (goat) ENA graphic
10
PVHU020000642.1 94.30 full 6,216,701 6,216,631 PVHU020000642.1 Moschus moschiferus isolate BS20 Scw3uUT_591;HRSCAF=70466_0, whole genome shotgun sequence Moschus moschiferus (Siberian musk deer) ENA graphic
11
CM004576.1 93.50 full 6,217,761 6,217,831 CM004576.1 Capra hircus breed San Clemente chromosome 15, whole genome shotgun sequence Capra hircus (goat) ENA graphic
12
CM016702.1 93.40 full 29,715,306 29,715,236 CM016702.1 Bos grunniens isolate yakHY00 ecotype maiwa chromosome 13, whole genome shotgun sequence Bos grunniens (domestic yak) ENA graphic
13
JH881474.1 93.40 full 606,892 606,822 JH881474.1 Bos grunniens mutus unplaced genomic scaffold scaffold1123_1, whole genome shotgun sequence Bos grunniens mutus ENA graphic
14
NW_011494750.1 93.40 full 1,798,983 1,798,913 NW_011494750.1 Bison bison bison isolate TAMUID 2011002044 unplaced genomic scaffold, Bison_UMD1.0 scf7180017864178, whole genome shotgun sequence Bison bison bison (north american plains bison) ENA graphic
15
PVHU020000642.1 91.00 full 6,216,631 6,216,701 PVHU020000642.1 Moschus moschiferus isolate BS20 Scw3uUT_591;HRSCAF=70466_0, whole genome shotgun sequence Moschus moschiferus (Siberian musk deer) ENA graphic
16
CM001596.2 90.30 full 74,887,563 74,887,633 Ovis aries breed Texel chromosome 15, whole genome shotgun sequence. Ovis aries (sheep) ENA graphic
17
CM001596.2 89.50 full 74,887,633 74,887,563 Ovis aries breed Texel chromosome 15, whole genome shotgun sequence. Ovis aries (sheep) 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 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 RM00023 Rho independent terminator 2 2 1.000 22.3 Match Image

References

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

Literature references

  1. 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
Alignment details
Alignment Number of
sequences
full 18
seed 2

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 89.0
Trusted cutoff 89.5
Noise cutoff 84.1
Covariance model Download
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