|Blood Group Antigen Gene Mutation Database|
|Home | Systems | Resources | Administration | About||16-Sep-2014|
The information on the various blood group systems is divided into two sections. One provides general information about the system, such as about the genes, relevant literature, etc. It also provides links to relevants system-related pages as well as to the allele listings. E.g., links to pages on Rh orthologs and non-erythroid homologs is provided at the bottom of such about section for the Rh system. These sections are the ones that are accessed first when clicking on the system links on the systems front page.
Allele listings are in the second section. More details than what is displayed for an allele can be obtained by clicking on the details link. A number of options are available on the listings page for searching the alleles and sorting the listings. Pull-down menus provide options such as parameters for searching, boolean searches and sequential sorting. One can also download the listings in Microsoft Excel or Comma-separated Values (CSV) format using the export options.
Most commonly used names are used for naming the blood group systems in this database. Other names and abbreviations are used as aliases. E.g., the Scianna system, which is also referred to as the Sc or the ERMAP system.
The naming of alleles has presented a problem compounded by names given to serological phenotypes of antigens they encode. At this time efforts by the transfusion medicine community are in progress to standardize and simplify this nomenclature (Storry, et al., Vox Sanguinis, 2011, 101:77-82). In the database, to more generally identify each allele, in most cases, 'name' includes the gene name followed by the DNA change particular to the allele. To facilitate the recognition of the phenotype//genotype connection, the allele designation, often based on serological phenotype, given by the original authors is provided under 'alias' if this information is available. In some cases, such as for the Rh system, because of traditional reasons, this arrangement is reversed. In others, such as ABO, only the phenotype designation marked by consecutive numbers is given. This is because the large number of sites of DNA changes in many alleles makes their listing under 'name' unwieldy.
Names make it easier to refer to alleles and can hint the associated phenotype and/or nucleotide or amino acid variation. Names given by the discoverers of the alleles are used. In case of more than one name (arising, e.g., when an allele was identified by two independent groups), the others are listed as aliases. We recommend that newly identified alleles be named with these points in mind:
- Names should be short and contain no more than two or three words.
- Arabic numerals (1,2...) instead of Roman ones (I, II,...) should be used if needed.
- Name of the gene should not be included in the name (redundancy).
- Styling such as superscripting or italicizing should not be done.
- A name should ideally hint the associated phenotype and/or nucleotide or amino acid variation (without getting too long).
- If possible, widely used system-specific systematic terminology should be followed if it exists.
The variation(s) should be typed in one line (without carriage or line returns); semi-colons (;) should be used to separate the different parts (e.g., T205A; 355fs).
IUPAC one-letter symbols for amino-acids and 'X' to indicate a stop codon should be used. They and nucleotides should be in capitals (upper case). Amino-acid change can be indicated as in this example: T205A (T at position 205 is replaced with an A), and nucleotide changes as in these examples: 1394G>T (G position 1394 is replaced with a T) and 1501Cdel (C at position 1501 is deleted).
These abbreviations are allowed: aa - amino-acids; cDNA - complementary DNA; gDNA - genomic DNA; del - deletion; ins - insertion; fs - frameshift; nt - nucleotide; orf - open reading frame; utr - untranslated region (3' or 5'). Use full words for 'intron,' 'exon,' 'truncation,' 'splice,' 'acceptor,' 'donor,' 'promoter,' 'alternate,' 'splicing,' 'gross,' 'rearrangement,' 'homologous,' non-homologous,' 'intergenic,' 'region,' 'recombination' and 'chromosomal.'
Use proper punctuation. E.g., use a single space after a period (.), comma (,), semi-colon (;), colon (:), or closing bracket ()) but none before. Flank plus (+) and hyphen (-) symbols with spaces.
Use Arabic and not Roman numerals (e.g., Exons 1 - 7 instead of Exons I - VII).
Use intron instead of intervening sequence or ivs and promoter instead of enhancer.