Table 2 SINE polymorphic loci in sequenced strains (AmoebaDB)
From: Genomic distribution of SINEs in Entamoeba histolytica strains: implication for genotyping
Strain | Scaffold ID in HM1:IMSS | Position of Sine in HM1 | Scaffold ID in strain | Comments |
|---|---|---|---|---|
SINE1 | ||||
Rahman | DS571157 (locus 13) ★ | 85456-86055 | EhRm_Scaffold01127 | |
DS571247 (locus 17) ● | 15166-14637 | EhRm_scaffold00561 | 90 bp of SINE present * | |
DS571226 (locus 19) ▲ | 27013-26485 | EhRm_scaffold00536 | ||
EhRm_contig21711 | ||||
DS571158 (locus 42) | 27165-27700 | EhRm_scaffold00892 | ||
DS571410 ⬌ | 9760-9214 | EhRm_scaffold01072 | ||
DS571210 | 20547-21121 | EhRm_scaffold00002 | ||
DS4 | DS571410 ⬌ | 9760-9214 | EHDS4_2898 | |
DS571358 ➞ | 20913-21457 | EHDS4_2995 | ||
KU27 | DS571358 ➞ | 20913-21457 | EHKU27_2995 | |
KU48 | DS571410 ⬌ | 9760-9214 | EHKU48_2898 | |
DS571979 | 698-1191 | EHKU48_3914 | ||
DS571226 ▲ | 27013-26485 | EHKU50_3346 | 40 bp of SINE present | |
KU50 | DS571145 ⧗ | 332477-331932 | EHKU50_3878 | |
DS571175 | 74276-74805 | EHKU50_4078 | ||
MS96 | DS571366 | 21421-20852 | EHMS96_3899 | 50 bp of SINE from 5’ end present |
DS571247 ● | 15166-14637 | EHMS96_2840 | Truncated from both side (397 bp present) * | |
DS571145 ⧗ | 332477-331932 | EHMS96_3878 | 150 bp upstream flank also missing | |
DS571358 ➞ | 20913-21457 | EHMS96_2995 | 60 bp downstream flank also missing | |
DS571157 ★ | 85453-86052 | EHMS96_4213 | Only 80 bp of SINE present* | |
HM1:CA | DS571426 | 1546-2044 | EHHM1_CA_4170 | 312 bp upstream and 275 bp downstream flank missing |
DS571487 | 12336-12883 | EHHM1_CA_3091 | 60 bp of SINE from 5’ end present and 500 bp downstream flank missing | |
SINE 2 | ||||
Rahman | DS571418 (locus 18) ↷ | 2292-1614 | EhRm_scaffold00754 | |
DS571150 (locus 50) ♦ | 145690-146349 | EhRm_scaffold00159 | ||
DS4 | DS571569 | 871-1494 | EHDS4_3206 | |
KU48 | DS571418 ↷ | 2292-1614 | EHKU48_4206 | |
KU50 | DS571418 ↷ | 2292-1614 | E EHKU50_4206 | |
DS571145 | 365212-365664 | EHKU50_3878 | ||
MS96 | DS571569 | 871-1494 | EHMS96_3206 | |
DS571150 ♦ | 145690-146349 | EHMS96_3252 | ||
