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 RefSeq Organelles
The Reference Sequence (RefSeq) organelle pages aim to provide a comprehensive, non-redundant set of sequences for scientific analysis. The
complete list of organelles can be displayed by clicking on Organism List in the blue side
bar. This is an alphabetical list of organisms that is color coded to indicate mitochondrial, plastid, plasmid, or nucleomorph sequences.
The blue side bar links from the any Organelle Genome Resources page leads
to organism lists
for metazoa, fungi, plants, and other mitochondria, and plasmids and plastids. You can also link to additional information pages about the Organelle
RefSeqs.
Metazoa Mitochondrion
At this time only the Metazoan (animal) mitochondrial records are considered "reviewed". These genomes have been manually curated by NCBI staff and
additional information for analysis is available only for these genomes. Clicking on the Metazoa
link on the blue side bar displays a taxonomic tree for the metazoan
genomes. Clicking on the name links to the taxonomic lineage information page for this group. To the left of each name is a
number which represents the total number of genomes in this taxonomic division. To display the
list of organisms in a particular taxonomic group click on the number. The resulting page displays an alphabetical list of organism names. There are 7
columns
representing organism, accession, length, protein, RNA, date released to public and common name. Directly above the columns are the columns are the
taxonomic groups listed listed in this main group. The up arrow can be used to move one level of the taxonomy tree represented in the main metazoa page.
- Organism-clicking on the organism name will bring you to the taxonomy database information page about this organism.
- Accession-clicking on the accession number launches the Genome Reference Page. This page displays a circular graphical display of the genome,
including the relative
positions of all annotated CDSs and RNAs. If the accession number is clicked from this page a new window is generated that displays the
flatfile view of the genome. The genome reference page also provides information about publications, genome size, date completed, and taxonomic lineage.
- Length-total number of nucleotides in the genome.
- Protein- clicking on the protein number displays a list of protein product names annotated on the genome. From the resulting links page you can
access the flatfile view and save FASTA protein and nucleotide files. Clicking on the PID will result in a BLINK anaysis for this protein. Clicking on
the gene name displays a zoomed view of the genome gene features.
- RNA-clicking on the RNA number displays the list of ribosomal RNAs and tRNAs annotated on the genome.
- Date-date genome was released to the public.
- Common Name-common name for the organism.
Metazoan Protein, Gene, and RNA Nomenclature
As part of the curation of the Metazoan mitochondrial genome reference sequences, we have standardized protein, gene, and RNA names
annotated on the RefSeq flatfiles. The names are listed below.
| Protein | Gene | Acronym |
| NADH dehydrogenase subunit 1 | ND1 | N1 |
| NADH dehydrogenase subunit 2 | ND2 | N2 |
| NADH dehydrogenase subunit 3 | ND3 | N3 |
| NADH dehydrogenase subunit 4 | ND4 | N4 |
| NADH dehydrogenase subunit 4L | ND4L | 4L |
| NADH dehydrogenase subunit 5 | ND5 | N5 |
| NADH dehydrogenase subunit 6 | ND6 | N6 |
| cytochrome c oxidase subunit I | COX1 | C1 |
| cytochrome c oxidase subunit II | COX2 | C2 |
| cytochrome c oxidase subunit III | COX3 | C3 |
| ATP synthase F0 subunit 6 | ATP6 | A6 |
| ATP synthase F0 subunit 8 | ATP8 | A8 |
| cytochrome b | CYTB | CB |
| RNA | Acronym | | RNA | Acronym |
| l-rRNA | lr | | s-rRNA | sr |
| tRNA-Ala | A | | tRNA-Cys | C |
| tRNA-Asp | D | | tRNA-Glu | E |
| tRNA-Phe | F | | tRNA-Gly | G
|
| tRNA-His | H | | tRNA-Ile | I |
| tRNA-Lys | K | | tRNA-Leu (UUR) | L1 |
| tRNA-Leu (CUN) | L2 | | tRNA-Met | M |
| tRNA-Asn | N | | tRNA-Pro | P |
| tRNA-Gln | Q | | tRNA-Arg | R |
| tRNA-Ser (UCN) | S1 | | tRNA-Ser (AGY or AGN)
| S2 |
| tRNA-Thr | T | | tRNA-Val | V |
| tRNA-Trp | W | | tRNA-Tyr | Y |
Metazoan Analysis Tools
On the blue side bar there are three analysis tools available: Protein List, Gene/RNA Order and Match Gene
- Protein List
The protein lists are separated into two sections. The top sections contains 3 parts: Align, FASTA and COGS. Clicking on any gene acronym for Align or
FASTA will bring you the alignment or FASTA output, respectively, for all the proteins in the taxonomic group for that gene. The COG link brings you to
the
COGnitor result for the that gene. The output includes a BLAST comparison between the mitochondrial and COG proteins. The second section lists the
organisms in alphabetical order. The number on the left is the genome gi and is a direct link to
the Genome Reference page. The genes are listed in the order they appear in the genome with the red vertical bar depicting the first protein on the
flatfile. Clicking on any one of the colored gene boxes will bring you to the COG for that gene. And clicking on the organism will bring you to its
taxonomy information page.
- Gene/RNA Order
This page lists all the genes, including tRNAs and rRNAs of the genome. The leftmost gene in the Gene/RNA order display is
N1 by default. The number on the left is the genome gi wich links to the Genome Reference page. The organism name links to the taxonomy information page.
- Match Gene
This tool allows protein sequence comparisons on the reviewed metazoan mitochondrial genomes. Paste the query protein sequence in the box, and choose
the set of proteins (e.g., ND1, ATP6) for the BLAST comparison. The taxonomic grouping of proteins can be changed by selecting the name from the pop-up
menu, or clicking on the name in the taxonomic tree. The master-slave output simultaneously aligns all hits to the query sequence; pairwise output
aligns each hit individually with the query.
Fungi, Plants, Other Mitochondrion, Plasmids and
Plastids
For the non-metazoan mitochondria and chloroplasts, which are not reviewed, two views are available. From the blue side bar clicking on any of these names
will link you to the current list
of organisms separated by taxonomic group. Clicking on a taxonomic group name will bring you to the taxonomy information page for this group. Clicking
on a specific
organism will result in the genome information page for this genome. From the genome information page you can directly link to the flatfile view of
the genome, the sequence from which the genome was derived at the bottom of the page, and view information about size, date published, and any publications.
This page also
includes a graphical view of the genome.
Clicking on Organism List on the blue side bar will bring you an alphabetical list of organisms from this group. This is separated into 6 columns.
- Organism- clicking the organism name will bring you to the taxonomy information page about this organism.
- Accession-clicking on the accession number launches the Genome Reference Page. This page displays a circular graphical display of the genome,
including the relative positions of
all annotated CDSs and RNAs. If the accession number is clicked on from this page a new window is generated tbat displays the flatfile view of
the genome. The
genome reference page also provides information about publications, genome size, date completed, and taxonomic lineage.
- Length-total number of nucleotides in the genome.
- Protein-clicking on the protein number displays a list of protein product names annotated on the genome. From the resulting links page you can
access the
flatfile view, and save FASTA protein and nucleotide files. Clicking on the PID will result in a BLINK anaysis for this protein. Clicking on
the gene name displays a zoomed view of the genome gene features.
- RNA-clicking on the RNA number displays the list of ribosomal RNAs and tRNAs annotated on the genome.
- Date-date genome was released to the public.
FTP Page
The NCBI FTP site contains the protein sequences, protein alignments, GenBank flatfiles, and ASN.1 records for the metazoan mitochondrial genomes.
The "Download" link off of the main organelle pages leads to the FTP site.
For more information about the FTP page see FTP README
Last modified: May 25, 2005
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