ArticleBMC genomics2010
Database of exact tandem repeats in the Zebrafish genome.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
1 citing paper in PubMed, 7 citations in OpenAlex.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author at 1 institution in 1 country.
Funding
Abstract
backgroundSequencing of the approximately 1.7 billion bases of the zebrafish genome is currently underway. To date, few high resolution genetic maps exist for the zebrafish genome, based mainly on single nucleotide polymorphisms (SNPs) and short microsatellite repeats. The desire to construct a higher resolution genetic map led to the construction of a database of tandemly repeating elements within the zebrafish Zv8 assembly. DESCRIPTION: Exact tandem repeats with a repeat length of at least three bases and a copy number of at least 10 were reported. Repeats with a total length of 250 or fewer bases and their flanking regions were masked for known vertebrate repeats. Optimal primer pairs were computationally designed in the regions flanking the detected repeats. This database of exact tandem repeats can then be used as a resource by molecular biologists with interests in experimentally testing VNTRs within a zebrafish population.
conclusionsA total of 116,915 repeats with a base length of at least three nucleotides were detected. The longest of these was a 54-base repeat with fourteen tandem copies. A significant number of repeats with a base length of 18, 24, 27 and 30 were detected, many with potentially novel proline-rich coding regions.Detection of exact tandem repeats in the zebrafish genome leads to a wealth of information regarding potential polymorphic sites for VNTRs. The association of many of these repeats with potentially novel yet similar coding regions yields an exciting potential for disease associated genes. A web interface for querying repeats is available at http://bioinformatics.louisville.edu/zebrafish/. This portal allows for users to search for a repeats of a selected base size from any valid specified region within the 25 linkage groups.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.