GeneID

[…] map detailing the protein architecture is shown in Supplementary Figure .An exon prediction analysis was made using five different tools: Augustus (Keller et al., ), FGenesh (Salamov and Solovyev, ), GeneID (Blanco et al., ), GeneMark (Besemer and Borodovsky, ) and GenScan (Burge and Karlin, ). Hnt CDS and mRNA coding regions were deduced and oligonucleotide primers for hnt amplification were desi […]

[…] els. Gene models generated from all the methods were integrated by EvidenceModeler (EVM). Weights for each type of evidence were set as follows: PASA-T-set > Homology-set > Cufflinks-set > Augustus > GeneID = SNAP = GlimmerHMM = GeneScan. The gene models were further updated by PASA2 to generate UTRs, alternative splicing variation information, which generated 26,872 gene models. Gene models only […]

[…] LASTN []. Then, we used Exonerate v2.2 [] to filter the genome sequences and the corresponding query proteins and search for accurately spliced alignments. For de novo annotation, Augustus v3.2.1 [], GeneID v1.4.4 [], and GlimmerHMM v3.0.3 [] were used to predict genes within the genome on the basis of a human training set. Next, we used EVidenceModeler v1.1.1 [] to integrate homologs and de novo […]

[…] sed as endogenous controls for constitutive expression: EF1-alfa (DDBJ/EMBL/GenBank Accession No. AB915828), beta-actin (No. AB915826), NADH-dh (No. AB936819) and three ribosomal protein genes (RS49: GeneID: KDR21989, RPS18: KDR22651 and RPL13a: KDR22610) [,]. The most appropriate gene was evaluated using GeNorm [] and NormFinder [], and EF1-alfa was selected in all real-time qPCR analyses perform […]

[…] ousekeeping genes like actin beta (ACTB, Gene ID: 60), cyclophilin A (PPIA, peptidylprolyl isomerase A, Gene ID: 5478) and RNA polymerase II subunit A (POLR2A, GeneID: 5430). […]

[…] (see Figure , data “Human gene hits”). The human protein hits of the last iteration were extracted from the files and redundancies removed. Each list of non-redundant proteins was annotated with its geneID by using the GCRh38 database.The human RNA-seq database at the Allen Brain Atlas contains normalized expression data on 22,318 genes. To see the normalization methods used go to documentation a […]