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Annotation of putative function from unknown sequences is largely based upon sequence homology (similarity) to proteins of known characterised function and particularly the presence of specific sequence/structure motifs (such as the Rossmann fold or the P-loop motif).
Another group consists of proteins with domains of poorly characterised function, such as "unknown" or "general function"; fusion analysis can be used to predict the function of an unknown protein if it is fusion-linked to a partner of known function.
The best characterised function of E-cadherin is homotypic, calcium-dependent cell cell adhesion; however, the observation that E-cadherin is also capable of interacting with the αEβ7 integrin to mediate leukocyte cell cell adhesion [Nature 372 (1994) 190] suggests that it also participates in heterotypic interactions.
TaEP1 is highly conserved in plant genomes (even in Arabidopsis) but does not show any distinct characterised function in sequenced genomes such as S. bicolor and rice.
The best characterised function of VHL is its role as a negative regulator of hypoxia-inducible factor (HIF), through oxygen-dependent degradation of the HIF- α subunit, of which there are two isoforms HIF-1 α and HIF-2 α (Maxwell et al, 1999).
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For all genes, and the most similar genes in Arabidopsis, we searched for published data relative to their characterised functions.
SVAs contain sequences with G4 potential, specifically in their CCCTCT hexamer and central VNTR, therefore could show similar properties to already characterised functions of G4 DNA mentioned previously.
Whole-microRNAome and genome analysis of SOX2-silenced hECCs revealed many miRNAs regulated by SOX2, including several with highly characterised functions in both cancer and embryonic stem cell (ESC) biology.
Genes with increased expression and well characterised functions include the platelet-derived growth factor family, represented by the PDGFA and PDGFB genes (1.70 and 1.61 fold, respectively) and ECGF1 (1.77 fold).
They share a well-conserved hydroxylase domain in their C-terminal halves, whereas the N-terminal halves are more variable and have poorly characterised functions among these three isoforms [ 20].
The remaining proteins have no characterised ciliary function.
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