1.
Annotated protein coding genes:
Group of genes Name of genes
Subunits of ATP synthase atpA, atpB, atpE, atpF, atpH, atpI
Subunits of NADH-dehydrogenase ndhA, ndhB, ndhB_copy2, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK
Subunits of cytochrome b/f complex petA, petB, petD, petG, petL, petN
Subunits of photosystem I psaA, psaB, psaC, psaI, psaJ
Subunits of photosystem II psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ, ycf3
Large subunit of ribosome rpl14, rpl16, rpl2, rpl20, rpl22, rpl23, rpl23_copy2, rpl2_copy2, rpl32, rpl33, rpl36
Small subunit of ribosome rps11, rps12, rps12_copy2, rps14, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps7_copy2, rps8
DNA dependent RNA polymerase rpoA, rpoB, rpoC1, rpoC2
Subunit of rubisco rbcL
c-type cytochrom synthesis gene ccsA
Envelop membrane protein cemA
Maturase matK
Protease clpP
Subunit of Acetyl-CoA-carboxylase accD
Translational initiation factor infA
Conserved open reading frames ycf1, ycf15, ycf15_copy2, ycf2, ycf2_copy2, ycf4
Other genes None
Possible missing protein coding genes:
Group of genes Name of genes
Subunits of ATP synthase None
Subunits of NADH-dehydrogenase None
Subunits of cytochrome b/f complex None
Subunits of photosystem I None
Subunits of photosystem II None
Large subunit of ribosome None
Small subunit of ribosome None
DNA dependent RNA polymerase None
Subunit of rubisco None
c-type cytochrom synthesis gene None
Envelop membrane protein None
Maturase None
Protease None
Subunit of Acetyl-CoA-carboxylase None
Translational initiation factor None
Conserved open reading frames None
Other genes None
2.
Multicopy genes with different lengths:
Genes Length Location
None None None
3.
Common intron-contained genes:
Genes exons exon1 exon2 exon3
atpF (2/2) [12963:13109](-) [11561:11971](-)
clpP (3/3) [71547:71615](-) [70506:70796](-) [69621:69872](-)
ndhA (2/2) [116730:117281](+) [118361:118900](+)
ndhB (2/2) [96072:96848](-) [94617:95372](-)
ndhB_copy2 (2/2) [141069:141845](+) [142545:143300](+)
petB (2/2) [74543:74548](+) [75323:75964](+)
petD (2/2) [76159:76164](+) [76949:77470](+)
rpl16 (2/2) [82345:82353](-) [80948:81349](-)
rpl2 (2/2) [85323:85709](-) [84230:84661](-)
rpl2_copy2 (2/2) [152208:152594](+) [153256:153687](+)
rpoC1 (2/2) [23203:23637](-) [20848:22464](-)
rps12 (3/3) [69375:69488](-) [98265:98495](-) [97692:97718](-)
rps12_copy2 (3/3) [69375:69488](-) [139422:139652](+) [140199:140225](+)
rps16 (2/2) [5258:5296](-) [4885:4935](-)
ycf3 (3/3) [44751:44876](-) [43789:44016](-) [42881:43039](-)
### The exon column shows the number of (actual exons/expected exons). ###
4.
Genes with internal stop codon:
None
5.
Genes with nonstandard start codon:
Genes Start codon
matK GTG
psbN ATA
rps19 GTG
rpl2 ATA
ndhD ATT
rpl2_copy2 ATA
6.
Genes with nonstandard stop codon:
Genes Stop codon
None None
7. Conclusion
This genome has 125 genes (110 unique genes). Including:
87 protein-coding genes (80 are unique)
38 tRNA genes (30 are unique)
0 rRNA genes (0 are unique)
Details are as follows:
Nonstandard gene annotation ('/gene' tags possibly be missing in your GenBank file)
16S ribosomal RNA [135743:137234](-)
23S ribosomal RNA [130538:133341](-)
4.5S ribosomal RNA [130337:130440](-)
5S ribosomal RNA [129989:130110](-)
87 protein-coding genes (80 are unique)
Genes Length Location
accD 1500 [57459:58958](+)
atpA 1524 [9959:11482](-)
atpB 1503 [53014:54516](-)
atpE 405 [52613:53017](-)
atpF 558 [12963:13109](-) [11561:11971](-)
atpH 246 [13545:13790](-)
atpI 744 [14591:15334](-)
ccsA 978 [123313:124290](-)
cemA 690 [60998:61687](+)
clpP 612 [71547:71615](-) [70506:70796](-) [69621:69872](-)
infA 234 [79490:79723](-)
matK 1548 [1734:3281](-)
ndhA 1092 [116730:117281](+) [118361:118900](+)
ndhB 1533 [96072:96848](-) [94617:95372](-)
ndhB_copy2 1533 [141069:141845](+) [142545:143300](+)
ndhC 363 [50226:50588](-)
ndhD 1506 [121580:123085](+)
ndhE 306 [120520:120825](+)
ndhF 2235 [126179:128413](+)
ndhG 531 [119830:120360](+)
ndhH 1182 [115547:116728](+)
ndhI 543 [118989:119531](+)
ndhJ 477 [48875:49351](-)
ndhK 678 [49492:50169](-)
petA 963 [61907:62869](+)
petB 648 [74543:74548](+) [75323:75964](+)
petD 528 [76159:76164](+) [76949:77470](+)
petG 114 [65874:65987](+)
petL 96 [65598:65693](+)
petN 90 [29134:29223](+)
psaA 2253 [40003:42255](-)
psaB 2205 [37774:39978](-)
psaC 246 [121215:121460](+)
psaI 111 [59297:59407](+)
psaJ 141 [66814:66954](+)
psbA 1062 [138:1199](-)
psbB 1527 [72054:73580](+)
psbC 1422 [34476:35897](+)
psbD 1062 [33467:34528](+)
psbE 252 [64302:64553](-)
psbF 120 [64172:64291](-)
psbH 222 [74211:74432](+)
psbI 111 [7544:7654](+)
psbJ 123 [63787:63909](-)
psbK 186 [6963:7148](+)
psbL 117 [64032:64148](-)
psbM 105 [29997:30101](-)
psbN 189 [73893:74081](-)
psbT 108 [73778:73885](+)
psbZ 189 [36484:36672](+)
rbcL 1434 [55238:56671](+)
rpl14 369 [80407:80775](-)
rpl16 411 [82345:82353](-) [80948:81349](-)
rpl2 819 [85323:85709](-) [84230:84661](-)
rpl20 372 [68272:68643](-)
rpl22 330 [83218:83547](-)
rpl23 282 [85734:86015](-)
rpl23_copy2 282 [151902:152183](+)
rpl2_copy2 819 [152208:152594](+) [153256:153687](+)
rpl32 174 [125254:125427](-)
rpl33 201 [67402:67602](+)
rpl36 114 [79263:79376](-)
rpoA 1014 [77632:78645](-)
rpoB 3213 [23664:26876](-)
rpoC1 2052 [23203:23637](-) [20848:22464](-)
rpoC2 4143 [16545:20687](-)
rps11 417 [78714:79130](-)
rps12 372 [69375:69488](-) [98265:98495](-) [97692:97718](-)
rps12_copy2 372 [69375:69488](-) [139422:139652](+) [140199:140225](+)
rps14 303 [37352:37654](-)
rps15 273 [115165:115437](+)
rps16 90 [5258:5296](-) [4885:4935](-)
rps18 306 [67771:68076](+)
rps19 279 [83693:83971](-)
rps2 711 [15595:16305](-)
rps3 657 [82509:83165](-)
rps4 606 [45534:46139](-)
rps7 468 [97166:97633](-)
rps7_copy2 468 [140284:140751](+)
rps8 399 [79844:80242](-)
ycf1 5556 [109219:114774](+)
ycf15 60 [93221:93280](+)
ycf15_copy2 60 [144637:144696](-)
ycf2 6783 [86323:93105](+)
ycf2_copy2 6783 [144812:151594](-)
ycf3 513 [44751:44876](-) [43789:44016](-) [42881:43039](-)
ycf4 555 [59702:60256](+)
38 tRNA genes (30 are unique)
Genes Location
trnK-UUU [4022:4058](-) [1436:1470](-)
trnQ-UUG [6559:6630](-)
trnS-GCU [7800:7887](-)
trnG-UCC [8772:8795](+) [9572:9619](+)
trnR-UCU [9765:9836](+)
trnC-GCA [28102:28167](+)
trnD-GUC [31014:31087](-)
trnY-GUA [31464:31547](-)
trnE-UUC [31594:31666](-)
trnT-GGU [32422:32493](+)
trnS-UGA [36032:36124](-)
trnG-GCC [36944:37014](+)
trnfM-CAU [37123:37196](-)
trnS-GGA [45150:45236](+)
trnT-UGU [46525:46597](-)
trnL-UAA [47457:47491](+) [48028:48077](+)
trnF-GAA [48232:48304](+)
trnV-UAC [52189:52227](-) [51566:51602](-)
trnM-CAU [52396:52467](+)
trnW-CCA [66107:66180](-)
trnP-UGG [66339:66412](-)
trnH-GUG [84112:84186](+)
trnI-CAU [86181:86254](-)
trnL-CAA [94003:94083](-)
trnV-GAC [100384:100455](+)
trnI-GAU [102470:102511](+) [103459:103493](+)
trnA-UGC [103558:103595](+) [104388:104422](+)
trnR-ACG [108181:108254](+)
trnN-GUU [108830:108901](-)
trnL-UAG [124375:124454](-)
trnN-GUU_copy2 [129016:129087](+)
trnR-ACG_copy2 [129663:129736](-)
trnA-UGC_copy2 [134322:134359](-) [133495:133529](-)
trnI-GAU_copy2 [135406:135447](-) [134424:134458](-)
trnV-GAC_copy2 [137462:137533](-)
trnL-CAA_copy2 [143834:143914](+)
trnI-CAU_copy2 [151663:151736](+)
trnH-GUG_copy2 [153731:153805](-)
0 rRNA genes (0 are unique)
Genes Location
This genome has 23 genes with intron(s).
Details are as follows:
19 gene(s) have 1 intron(s)
Genes Exons
rps16 [5258:5296](-) [4885:4935](-)
atpF [12963:13109](-) [11561:11971](-)
rpoC1 [23203:23637](-) [20848:22464](-)
petB [74543:74548](+) [75323:75964](+)
petD [76159:76164](+) [76949:77470](+)
rpl16 [82345:82353](-) [80948:81349](-)
rpl2 [85323:85709](-) [84230:84661](-)
ndhB [96072:96848](-) [94617:95372](-)
ndhA [116730:117281](+) [118361:118900](+)
ndhB_copy2 [141069:141845](+) [142545:143300](+)
rpl2_copy2 [152208:152594](+) [153256:153687](+)
trnK-UUU [4022:4058](-) [1436:1470](-)
trnG-UCC [8772:8795](+) [9572:9619](+)
trnL-UAA [47457:47491](+) [48028:48077](+)
trnV-UAC [52189:52227](-) [51566:51602](-)
trnI-GAU [102470:102511](+) [103459:103493](+)
trnA-UGC [103558:103595](+) [104388:104422](+)
trnA-UGC_copy2 [134322:134359](-) [133495:133529](-)
trnI-GAU_copy2 [135406:135447](-) [134424:134458](-)
4 gene(s) have 2 intron(s)
Genes Exons
rps12 [69375:69488](-) [98265:98495](-) [97692:97718](-)
ycf3 [44751:44876](-) [43789:44016](-) [42881:43039](-)
rps12_copy2 [69375:69488](-) [139422:139652](+) [140199:140225](+)
clpP [71547:71615](-) [70506:70796](-) [69621:69872](-)