Quallity assession of Taeniopygia guttata (zebra finch)genome assembly
The zebra finch (Taeniopygia guttata) is a small songbird that inhabits arid regions of Australia and is easily bred in captivity. The zebra finch serves as an ideal model organism for studies of neural structure and function, the effect of steroid hormones on the development of neural networks, and the impact of the products of sex-chromosome-specific genes on brain development. The amount of genome assembly - 1.
| Total sequence length | 1,232,135,591 |
| Number of scaffolds | 37,422 |
| Number of contigs | 124,806 |
| Contig N50 | 38,639 |
| Contig L50 | 8,016 |
| BioProject | PRJNA17289 |
| Table of contings | Click |
| Contig sequence | Click |
| Pubmed | Click |
7 keys used in feature tables
| Key | Definition | Example |
| misc_feature | region of biological interest which cannot be described by any other feature key; a new or rare feature | misc_feature 67023..67201 /note="similar to Mus musculus EST BE290208 (NID:g9171084)" |
| polyA_site | site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation | 863
|
| tmRNA | transfer messenger RNA; tmRNA acts as a tRNA first, and then as an mRNA that encodes a peptide tag; the ribosome translates this mRNA region of tmRNA and attaches the encoded peptide tag to the C-terminus of the unfinished protein; this attached tag targets the protein for destruction or proteolysis; | 2755593..2755955
/gene="ssrA" /locus_tag="b2621" /gene_synonym="ECK2617; JWR0055; sipB" /product="tmRNA, 10Sa RNA" /note="acts as tRNA-Ala and mRNA template for tagging proteins resulting from premature transcription termination for degradation, a process known as trans-translation" |
| ncRNA | a non-protein-coding gene, other than ribosomal RNA and transfer RNA, the functional molecule of which is the RNA transcript; | 2167114..2167200
|
| misc_structure | any secondary or tertiary nucleotide structure or conformation that cannot be described by other Structure keys (stem_loop and D-loop) | 24
/note="n is modified as (NNK)9-12, in which N can be A, T, G, or C and K can be Tor G." |
| D-loop | displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein | 15654..16529
|
| exon | region of genome that codes for portion of spliced mRNA, rRNA and tRNA; may contain 5'UTR, all CDSs and 3' UTR; | 101..1279
/gene="ARL4AP1" /gene_synonym="ARL4B; ARL4P" /inference="alignment:Splign::RefSeq|NM_212460.3" /pseudo |
Genome projects
NIH Human Microbiome Project (HMP) Roadmap Project. The human microbiome refers to the community of microorganism that live in or on the human body. The Human Microbiome Project (HMP) is an United States National Institutes of Health (NIH) Roadmap project that was initiated to generate resources to enable comprehensive characterization of the human microbiota and analysis of its role in human health and disease. The HMP centers will sequence the genomes of a set of microoganisms that have been previously isolated from the human body. In addition, samples from the digestive tract, mouth, skin, nose, and female urogenital tract of human volunteers will be sequenced for 16S ribosomal RNA analysis and considered for metagenomic analysis.
This project, which ended in 2013, was the first part of a two-phase effort focused on the microbial communities that call humans home. The second phase, known as the Integrative Human Microbiome Project (iHMP) launched in 2014 with the aim of generating resources to characterize the microbiome and elucidating the roles of microbes in health and disease states.
According to NCBI, the project include about 676496 DNA sequences. Pubmed: Click
Mitochondrial genomes
Systematic group: Porifera. ENA (EMBL) on the EBI website was selected for search purpose. Search query:
tax_tree(6040) AND mol_type="genomic DNA" AND topology="CIRCULAR" AND organelle="mitochondrion"
AC: AM420314
Name: Negombata magnifica or Latrunculia magnifica, commonly known as toxic finger-sponge.
