Controlled vocabulary for /rpt_type qualifier

This page contains the current definition, format and controlled vocabularly for repeat type qualifier.

The page has been created on Ocober 9, 2013. Last updated October 2015.

 

Qualifier: /rpt_type=

Definition: organization of repeated sequence 

Value format: tandem, inverted, flanking, terminal, direct, dispersed, and other

Example:

/rpt_type=INVERTED 

Comment: the values are case-insensitive, i.e. both "INVERTED" and "inverted" are valid;

Definitions of the values:

tandem: a repeat that consists of two or more adjacent copies of a region whose length is greater than one in the same orientation;

inverted: a repeat pair occurring in reverse orientation to one another on the same molecule;

flanking: a repeat lying outside the sequence for which it has functional significance (eg. transposon insertion target sites);

terminal: a repeat at the ends of and within the sequence for which it has functional significance other than long terminal repeat;

direct: a repeat where the same sequence is repeated in the same direction;

dispersed: a repeat that is located at dispersed sites in the genome;

nested: a repeat that is disrupted by the insertion of another element;

long_terminal_repeat: a sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses (replaces LTR Feature Key);

non_ltr_retrotransposon_polymeric_tract: a polymeric tract, such as poly(dA), within a non LTR retrotransposon;

x_element_combinatorial_repeat: a repeat region located between the X element and the telomere or adjacent Y' element;

y_prime_element: a repeat region located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies;

telomeric_repeat: a repeat region found within the telomere;

centromeric_repeat: a repeat region found within the modular centromere;

other: a repeat exhibiting important attributes that cannot be described by other values.

Note: terms in italics are going to be supported from December 2015.