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, ycf3
Large subunit of ribosome rpl14, rpl16, rpl2, rpl20, rpl22, rpl23, rpl23_copy2, rpl2_copy2, rpl32, rpl33, rpl36
Small subunit of ribosome rps11, rps12, 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 None
Translational initiation factor infA
Conserved open reading frames ycf1, ycf1_copy2, ycf2, ycf2_copy2, ycf4
Other genes lhbA
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 psbZ
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 accD
Translational initiation factor None
Conserved open reading frames ycf15
Other genes None
2.
Multicopy genes with different lengths:
Genes Length Location
rpl2 825 join{[87103:87494](-), [86018:86452](-)}
rpl2_copy2 828 join{[154407:154800](+), [155448:155883](+)}
ycf1 1887 [110315:112202](+)
ycf1_copy2 5484 [126102:131586](-)
3.
Common intron-contained genes:
Genes exons exon1 exon2 exon3
atpF (2/2) [13671:13829](-) [12575:13036](-)
clpP (3/3) [73668:73736](-) [72511:72801](-) [71659:71889](-)
ndhA (2/2) [123597:124148](-) [121976:122515](-)
ndhB (2/2) [97184:97960](-) [95746:96501](-)
ndhB_copy2 (2/2) [143942:144718](+) [145401:146156](+)
petB (2/2) [76692:76697](+) [77427:78080](+)
petD (2/2) [78259:78266](+) [79021:79495](+)
rpl16 (2/2) [84310:84318](-) [82969:83367](-)
rpl2 (2/2) [87104:87494](-) [86019:86452](-)
rpl2_copy2 (2/2) [154408:154800](+) [155449:155883](+)
rpoC1 (2/2) [24020:24472](-) [21664:23268](-)
rps12 (3/3) [71396:71509](-) [99344:99575](-) [98782:98807](-)
rps16 (2/2) [6370:6409](-) [5253:5494](-)
ycf3 (3/3) [45484:45612](-) [44541:44768](-) [43616:43768](-)
### 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
psbT ATC
rpl22 ATA
rps19 GTG
ndhD ACG
6.
Genes with nonstandard stop codon:
Genes Stop codon
None None
7. Conclusion
This genome has 121 genes (107 unique genes). Including:
84 protein-coding genes (78 are unique)
37 tRNA genes (29 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 [138710:140200](-)
23S ribosomal RNA [133479:136289](-)
4.5S ribosomal RNA [133278:133381](-)
5S ribosomal RNA [132901:133022](-)
84 protein-coding genes (78 are unique)
Genes Length Location
atpA 1524 [10995:12518](-)
atpB 1497 [54634:56130](-)
atpE 402 [54236:54637](-)
atpF 621 [13671:13829](-) [12575:13036](-)
atpH 246 [14281:14526](-)
atpI 744 [15321:16064](-)
ccsA 963 [116721:117683](+)
cemA 696 [62907:63602](+)
clpP 591 [73668:73736](-) [72511:72801](-) [71659:71889](-)
infA 234 [81511:81744](-)
lhbA 189 [37240:37428](+)
matK 1515 [2057:3571](-)
ndhA 1092 [123597:124148](-) [121976:122515](-)
ndhB 1533 [97184:97960](-) [95746:96501](-)
ndhB_copy2 1533 [143942:144718](+) [145401:146156](+)
ndhC 363 [51571:51933](-)
ndhD 1503 [117899:119401](-)
ndhE 306 [120016:120321](-)
ndhF 2262 [112219:114480](-)
ndhG 531 [120525:121055](-)
ndhH 1182 [124150:125331](-)
ndhI 504 [121379:121882](-)
ndhJ 477 [50262:50738](-)
ndhK 678 [50844:51521](-)
petA 963 [63851:64813](+)
petB 660 [76692:76697](+) [77427:78080](+)
petD 483 [78259:78266](+) [79021:79495](+)
petG 114 [67764:67877](+)
petL 96 [67516:67611](+)
petN 90 [29741:29830](+)
psaA 2253 [40885:43137](-)
psaB 2205 [38655:40859](-)
psaC 246 [119516:119761](-)
psaI 111 [61301:61411](+)
psaJ 141 [68741:68881](+)
psbA 1062 [453:1514](-)
psbB 1527 [74188:75714](+)
psbC 1422 [35200:36621](+)
psbD 1062 [34191:35252](+)
psbE 252 [66342:66593](-)
psbF 120 [66213:66332](-)
psbH 240 [76333:76572](+)
psbI 111 [8708:8818](+)
psbJ 123 [65819:65941](-)
psbK 186 [8099:8284](+)
psbL 117 [66074:66190](-)
psbM 117 [30932:31048](-)
psbN 132 [76117:76248](-)
psbT 111 [75915:76025](+)
rbcL 1428 [56906:58333](+)
rpl14 369 [82468:82836](-)
rpl16 408 [84310:84318](-) [82969:83367](-)
rpl2 825 [87104:87494](-) [86019:86452](-)
rpl20 387 [70252:70638](-)
rpl22 480 [85115:85594](-)
rpl23 282 [87513:87794](-)
rpl23_copy2 282 [154108:154389](+)
rpl2_copy2 828 [154408:154800](+) [155449:155883](+)
rpl32 165 [115715:115879](+)
rpl33 201 [69349:69549](+)
rpl36 114 [81285:81398](-)
rpoA 1077 [79617:80693](-)
rpoB 3213 [24478:27690](-)
rpoC1 2058 [24020:24472](-) [21664:23268](-)
rpoC2 4122 [17325:21446](-)
rps11 417 [80773:81189](-)
rps12 372 [71396:71509](-) [99344:99575](-) [98782:98807](-)
rps14 303 [38224:38526](-)
rps15 273 [125424:125696](-)
rps16 282 [6370:6409](-) [5253:5494](-)
rps18 306 [69714:70019](+)
rps19 279 [85683:85961](-)
rps2 711 [16329:17039](-)
rps3 657 [84474:85130](-)
rps4 606 [47105:47710](-)
rps7 468 [98259:98726](-)
rps7_copy2 468 [143176:143643](+)
rps8 399 [81866:82264](-)
ycf1 1887 [110316:112202](+)
ycf1_copy2 5484 [126103:131586](-)
ycf2 6303 [88122:94424](+)
ycf2_copy2 6303 [147478:153780](-)
ycf3 510 [45484:45612](-) [44541:44768](-) [43616:43768](-)
ycf4 555 [61798:62352](+)
37 tRNA genes (29 are unique)
Genes Location
trnH-GUG [26:100](-)
trnK-UUU [4298:4334](-) [1730:1764](-)
trnQ-UUG [7676:7747](-)
trnS-GCU [8962:9049](-)
trnG-UCC [9815:9837](+) [10544:10591](+)
trnR-UCU [10812:10883](+)
trnC-GCA [28940:29020](+)
trnD-GUC [31741:31814](-)
trnY-GUA [31925:32008](-)
trnE-UUC [32094:32166](-)
trnT-GGU [32905:32976](+)
trnS-UGA [36861:36953](-)
trnG-UCC_copy2 [37751:37821](+)
trnfM-CAU [37995:38068](-)
trnS-GGA [46488:46573](+)
trnT-UGU [48080:48152](-)
trnL-UAA [48873:48909](+) [49410:49459](+)
trnF-GAA [49813:49885](+)
trnV-UAC [53736:53774](-) [53131:53167](-)
trnM-CAU [53950:54022](+)
trnW-CCA [68024:68097](-)
trnP-UGG [68233:68307](-)
trnI-CAU [87960:88033](-)
trnL-CAA [95101:95181](-)
trnV-GAC [101402:101473](+)
trnI-GAU [103489:103530](+) [104473:104507](+)
trnA-UGC [104572:104609](+) [105426:105460](+)
trnR-ACG [109257:109330](+)
trnN-GUU [109917:109988](-)
trnL-UAG [116554:116633](+)
trnN-GUU_copy2 [131914:131985](+)
trnR-ACG_copy2 [132572:132645](-)
trnA-UGC_copy2 [137293:137330](-) [136442:136476](-)
trnI-GAU_copy2 [138372:138413](-) [137395:137429](-)
trnV-GAC_copy2 [140429:140500](-)
trnL-CAA_copy2 [146721:146801](+)
trnI-CAU_copy2 [153869:153942](+)
0 rRNA genes (0 are unique)
Genes Location
This genome has 22 genes with intron(s).
Details are as follows:
19 gene(s) have 1 intron(s)
Genes Exons
rps16 [6370:6409](-) [5253:5494](-)
atpF [13671:13829](-) [12575:13036](-)
rpoC1 [24020:24472](-) [21664:23268](-)
petB [76692:76697](+) [77427:78080](+)
petD [78259:78266](+) [79021:79495](+)
rpl16 [84310:84318](-) [82969:83367](-)
rpl2 [87104:87494](-) [86019:86452](-)
ndhB [97184:97960](-) [95746:96501](-)
ndhA [123597:124148](-) [121976:122515](-)
ndhB_copy2 [143942:144718](+) [145401:146156](+)
rpl2_copy2 [154408:154800](+) [155449:155883](+)
trnK-UUU [4298:4334](-) [1730:1764](-)
trnG-UCC [9815:9837](+) [10544:10591](+)
trnL-UAA [48873:48909](+) [49410:49459](+)
trnV-UAC [53736:53774](-) [53131:53167](-)
trnI-GAU [103489:103530](+) [104473:104507](+)
trnA-UGC [104572:104609](+) [105426:105460](+)
trnA-UGC_copy2 [137293:137330](-) [136442:136476](-)
trnI-GAU_copy2 [138372:138413](-) [137395:137429](-)
3 gene(s) have 2 intron(s)
Genes Exons
rps12 [71396:71509](-) [99344:99575](-) [98782:98807](-)
ycf3 [45484:45612](-) [44541:44768](-) [43616:43768](-)
clpP [73668:73736](-) [72511:72801](-) [71659:71889](-)