Computational protocol: Diversification of the insulin-like growth factor 1 gene in mammals

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Protocol publication

[…] Mammalian genomic databases were accessed using the Ensembl Genome Browser (www.ensemble.org) []. Searches were conducted using BlastN or BlastP under normal sensitivity, with rat Igf1 gene DNA segments (Rattus norvegicus, genome assembly Rnor_6.0), or protein sequences (from the National Center for Biotechnology Information Protein database) as initial queries, respectively. Additional searches were performed in Ensembl with other mammalian species DNA sequences as queries to follow-up and verify initial results. In addition, when relevant information could not be found in the Ensembl Genome Browser, both genomic DNA and gene expression data files were searched using the Sequence Read Archive of the National Center for Biotechnology Information (SRA NCBI; www.ncbi.nlm.nih.gov/sra/), and for human IGF1, RNA data from the Portal for the Genotype-Expression Project (GTEx V7, https://www.gtexportal.org/home/). The following genome assemblies were examined: armadillo (Dasypus novemcinctus, Dasnov3.0), cat (Felis catus, Felis_catus_6.2), chimpanzee (Pan troglodytes, CHIMP2.1.4), cow (Bos taurus, UMD3.1), dog (Canis lupus familiaris, CanFam3.1), dolphin (Tursiops truncates, turTru1), elephant (Loxodonta Africana, loxAfr3), gibbon (Nomascus leucogenys, Nleu1.0), guinea pig (Cavia porcellus, cavPor3), human (Homo sapiens, GRCh38), megabat (Pteropus vampyrus, pteVam1), microbat (Myotis lucifugus, Myoluc2.0), mouse (Mus musculus, GRCm38), opossum (Monodelphis domestica, BROADO5), orangutan (Pongo abelii, PPYG2), pig (Sus scrofa, Sscrofa10.2), platypus (Ornithorhynchus anatinus, OANA5), rabbit (Oryctolagus cuniculus, OryCun2.0), sheep (Ovis aries, Oar_v3.1), sloth (Choloepus hoffmanni, choHof1), squirrel (Ictidomys tridecemlineatus, spetri2), Tasmanian devil (Sarcophilus harrisii, DEVIL7.0), tree shrew (Tupaia belangeri, TREESHREW), and wallaby (Macropus eugenii, Meug_1.0). GENCODE/Ensemble databases were searched for protein sequences. In all outcomes, the highest scoring results mapped to the respective IGF1/Igf1 gene, locus, or protein. In text and Tables, results are reported as percent identity over the entire query region, unless otherwise specified. […]

Pipeline specifications

Software tools BLASTN, BLASTP
Application Genome data visualization
Organisms Homo sapiens, Rattus norvegicus
Chemicals Carbohydrates, Nucleotides