Genome Feature Type Definitions
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Many of the MGI classification terms come from the Sequence Ontology (SO) project. The SO project develops terms and relationships describing features and attributes of biological sequences. When the MGI term definition comes from the SO project, the corresponding SO ID for that term appears.

Feature TypeMGI DefinitionCorresponding
SO ID
geneA region (or regions) that include all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions, and/or other functional sequence regions. SO:0000704
protein coding geneA gene that produces at least one transcript that is translated into a protein.  
non-coding RNA geneA gene that produces an RNA transcript that functions as the gene product. 
rRNA geneA gene that encodes ribosomal RNA.SO:0001637
tRNA geneA gene that encodes Transfer RNA.  
snRNA geneA gene that encodes a Small Nuclear RNA. 
snoRNA geneA gene that encodes for Small Nucleolar RNA. 
miRNA geneA gene that encodes for microRNA.  
scRNA geneA gene that encodes for Small Cytoplasmic RNA. 
lincRNA geneA gene that encodes large intervening non-coding RNA. SO:0001641
SRP RNA geneA gene that encodes the signal recognition particle RNA. SO:0000590
RNase P RNA geneA gene that encodes RNase P RNA, the RNA component of Ribonuclease P (RNase P). 
RNase MRP RNA geneA gene that encodes RNase MRP RNA.SO:0001640
telomerase RNA geneA non-coding RNA gene, the RNA product of which is a component of telomerase. SO:0001643
Unclassified non-coding RNA geneA non-coding RNA gene not classified The RNA product of this non-coding is a component of telomerase. 
heritable phenotypic markerA biological region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus. SO:0001500
gene segmentA gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination. SO:3000000
unclassified geneA region of the genome associated with transcript and/or prediction evidence but where feature classification is imprecise. 
other feature typesMGI markers that are not classified as gene including pseudogenes, QTL, transgenes, gene clusters, cytogenetic markers, & unclassified genome features.  
QTLA quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci. SO:0000771
transgeneA gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another. SO:0000902
complex/cluster/regionA group of linked markers characterized by related sequence and/or function where the precise location or identity of the individual components is obscure.  
cytogenetic markerA structure within a chromosome or a chromosomal rearrangement that is visible by microscopic examination.  
chromosomal deletionAn incomplete chromosome.SO:1000029
insertionThe sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.SO:0000667
chromosomal inversionAn interchromosomal mutation where a region of the chromosome is inverted with respect to wild type.SO:1000030
Robertsonian fusionA non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere.SO:1000043
reciprocal chromosomal translocationA chromosomal translocation with two breaks; two chromosome segments have simply been exchanged.SO:1000048
chromosomal translocationAn interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations.SO:1000044
chromosomal duplicationAn extra chromosome.SO:1000037
chromosomal transpositionA chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type.SO:0000453
unclassified cytogenetic markerA cytogenetic marker not classifiable within current cytogenetic subcategories. 
BAC/YAC endA region of sequence from the end of a BAC or YAC clone used as a reagent in mapping and genome assembly.  
other genome featureA region of the genome associated with biological interest (includes regulatory regions, conserved regions and related sequences, repetitive sequences, and viral integrations).  
DNA segmentA region of the genome associated with experimental interest, often used as a reagent for genetic mapping. Includes RFLP and other hybridization probes, sequence-tagged sites (STS), and regions defined by PCR primer pairs such as microsatellite markers).
pseudogenic regionA non-functional descendant of a functional entity.SO:0000462
pseudogeneA sequence that closely resembles a known functional gene, at another locus within the genome, that is non-functional a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their normal paralog, in which case the pseudogene typically lacks introns and includes a poly(A) tail, or from recombination, in which case the pseudogene is typically a tandem duplication of its normal paralog. SO:0000336
pseudogenic gene segmentA recombinational unit of a gene which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product.SO:0001741
polymorphic pseudogenePseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated. 

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