Last updated:2015.11.12.

Controlled vocabulary for /rpt_type qualifier

The original site; Controlled vocabulary for /rpt_type qualifier 2015.11.11 version.

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

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.

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