Basic Information

Type: gene

Biological Identity

Species

rosa_wichuraiana

Chromosome

Contig00066

Orthogroup ID

OG0009922

Physical Location & Seq

Genomic Coordinates Reverse (-)

89979 .. 93441

Gene Structure 3463 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rw0G002140.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1107 bp

ATGGAGGGAAAGCGGTCAAGAGGGAGGTCACAGCCCCGTCCCCGCCATTTGCTAACAAAAATCAAAGAATTTACTCGGGCTCTTGTGAAAGATCTCAGCGATGGACGGTCACCGGAGATTCTCATCCATCGCTTCCGAAATTACTGCTCCAATTCTCAAGTTTTCACAGCAACCTCCTATTGTGGCTCTGATTTGCCGAAAGGGAAGGAGACGCTCACACTTCGTAAAGAAACCCATGTTCATAGATTAGATGTTCTGCTTAGGGTTCTTGTAATTGTTCAGCAACTTCTGCAAGAAAACAGACATGGGTCTAAGAGAGATATCTATTACATGCACCCTTCTATATTTTCAGATCAGTCAGTTGTAGACCGTGCAATCAATGACATATGCATCCTTCTGCAGTGTAGTCGCCACAATTTGAATGTGGTGTCTGTAGGAAAGGGGTTGGTAATGGGCTGGTTAAGGTTCGCAGAGGCTGGAAACATGTTTGATTGCATAAATAGACCAAACACTGCTTACCCTGTTCCAGTTCATGTTGAAGAGGTCAAAGATATTGTTAGTGTTGCCCAGTACATACTTGTTGTGGAGAAAGAATCAGTTTTTCAACGATTGGCAAATGACCAGTTTTGTAACACAAACCACTGCATTGTCATCACTGGACGTGGATATCCTGATATTTCCACAAGAAGGTTTTTGGGGCTCCTTGTTGATACTTTACATATCCCTGTCTATTGCTTGGTAGATTGTGATCCCTACGGTTTTGACATCTTGTCCACATATCGGTTTGGTTCTCTGCAAATGGCGTATGATGCAAAATTTCTACGGGTCCCCGAGATAATCTGGCTTGGAGCCTTCCCTTTGGACTCGGAGAAGTACCATCTTCCACACCAGTGTCTCCTTCCTTTGACTGCAGAAGACAAGAGGAAAACTGAAGCCATGTTACAGAGATGCTACTTAGAAAGAGAAGTGCCACAGTGGAGATTGGAGCTACAGTTGATGCTGGAAAGAGGCGTGAAATTTGAGCTAGAAGCATTGTCTGTGCATGAACTTTCCTTTTTGTCGACCAAGTACATACCATCAAAAATTCAAGGTGGATTGCTCATCTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0000228 GO:0000280 GO:0000706 GO:0000724 GO:0000725 GO:0000729 GO:0003674 GO:0003676 GO:0003677 GO:0003824 GO:0003916 GO:0003918 GO:0004518 GO:0004519 GO:0004520 GO:0004536 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005694 GO:0006139 GO:0006259 GO:0006281 GO:0006302 GO:0006310 GO:0006725 GO:0006807 GO:0006950 GO:0006974 GO:0006996 GO:0007049 GO:0007059 GO:0007127 GO:0007129 GO:0007131 GO:0008094 GO:0008150 GO:0008152 GO:0009987 GO:0016043 GO:0016462 GO:0016787 GO:0016788 GO:0016817 GO:0016818 GO:0016853 GO:0016887 GO:0016889 GO:0016894 GO:0017111 GO:0022402 GO:0022414 GO:0022607 GO:0031974 GO:0031981 GO:0033554 GO:0034641 GO:0035825 GO:0042138 GO:0042623 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044085 GO:0044237 GO:0044238 GO:0044260 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044464 GO:0045132 GO:0045143 GO:0046483 GO:0048285 GO:0050896 GO:0051026 GO:0051276 GO:0051321 GO:0051716 GO:0061505 GO:0061982 GO:0070013 GO:0070192 GO:0071704 GO:0071840 GO:0090304 GO:0090305 GO:0097159 GO:0098813 GO:0140013 GO:0140097 GO:1901360 GO:1901363 GO:1903046

KEGG Pathways

Metabolic & Signaling

ko04113 map04113

Pfam Domains

Protein Families

TP6A_N

Protein Analysis

368

Amino Acids

42.41

Weight (kDa)

8.68

Isoelectric Point (pI)

47.9

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
TP6A_N	PF04406	82 - 142	2.9e-21	Type IIB DNA topoisomerase
TOP6A-Spo11_Toprim	PF21180	191 - 362	1.1e-64	Topoisomerase 6 subunit A/Spo11, Toprim domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

Font Size (px)

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0009922)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G13170 AT3G13170 AT3G13170
fragaria_vesca	FvH4_3g29420
malus_domestica	MD03G1184400.v1.1 MD03G1184700.v1.1
prunus_persica	Prupe.4G241800_v2.0.a1 Prupe.4G241800_v2.0.a1
pyrus_communis	pycom03g13780
rosa_chinensis	RchiOBHm_Chr5g0053841
rosa_laevigata	RLG00000034906
rosa_multiflora	Rmu_sc0007356.1_g000010
rosa_roxburghii	Rroxscaffold_1G00026760
rosa_rugosa	Rorug05G0283600 Rorug05G0283700
rosa_samantha	Rh5AG353400 Rh5BG365000 Rh5CG390100 Rh5DG380000
rosa_wichuraiana	Rw0G002140 Rw0G009550

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccI	GTMKAC	2 cut(s)	366, 1061
AciI	CCGC	2 cut(s)	13, 43
AclWI	GGATC	1 cut(s)	743
AcsI	RAATTY	4 cut(s)	68, 815, 1016, 1083
AcuI	CTGAAG	1 cut(s)	951
AfaI	GTAC	3 cut(s)	572, 875, 1070
AfiI	CCNNNNNNNGG	2 cut(s)	687, 780
AflIII	ACRYGT	1 cut(s)	483
AgsI	TTSAA	4 cut(s)	421, 539, 605, 1088
AhdI	GACNNNNNGTC	1 cut(s)	769
AjiI	CACGTC	1 cut(s)	662
AleI	CACNNNNGTG	1 cut(s)	889
AluBI	AGCT	2 cut(s)	988, 1024
AluI	AGCT	2 cut(s)	988, 1024
Alw26I	GTCTC	2 cut(s)	203, 899
AlwI	GGATC	1 cut(s)	743
AlwNI	CAGNNNCTG	1 cut(s)	476
Ama87I	CYCGRG	2 cut(s)	75, 830
ApoI	RAATTY	4 cut(s)	68, 815, 1016, 1083
AspS9I	GGNCC	1 cut(s)	826
AsuHPI	GGTGA	1 cut(s)	102
AvaI	CYCGRG	2 cut(s)	75, 830
AvaII	GGWCC	1 cut(s)	826
BanII	GRGCYC	2 cut(s)	82, 702
BarI	GAAGNNNNNNTAC	2 cut(s)	924, 956
BbsI	GAAGAC	1 cut(s)	921
BccI	CCATC	4 cut(s)	95, 135, 885, 1084
BcgI	CGANNNNNNTGC	4 cut(s)	126, 160, 389, 423
BcoDI	GTCTC	2 cut(s)	203, 899
BfaI	CTAG	1 cut(s)	1025
BfmI	CTRYAG	4 cut(s)	398, 432, 909, 989
BglII	AGATCT	1 cut(s)	91
Bme18I	GGWCC	1 cut(s)	826
BmeRI	GACNNNNNGTC	1 cut(s)	769
BmeT110I	CYCGRG	2 cut(s)	75, 830
BmgBI	CACGTC	1 cut(s)	662
BmgT120I	GGNCC	1 cut(s)	826
BmiI	GGNNCC	4 cut(s)	701, 827, 828, 850
BmrI	ACTGGG	1 cut(s)	562
BmsI	GCATC	4 cut(s)	399, 799, 938, 987
BmuI	ACTGGG	1 cut(s)	562
BoxI	GACNNNNGTC	1 cut(s)	307
BpiI	GAAGAC	1 cut(s)	921
Bpu10I	CCTNAGC	1 cut(s)	260
BpuEI	CTTGAG	1 cut(s)	141
BsaBI	GATNNNNATC	2 cut(s)	122, 747
BsaWI	WCCGGW	1 cut(s)	112
BsaXI	ACNNNNNCTCC	2 cut(s)	977, 1007
Bsc4I	CCNNNNNNNGG	2 cut(s)	687, 780
Bse1I	ACTGG	5 cut(s)	527, 568, 622, 661, 889
Bse8I	GATNNNNATC	2 cut(s)	122, 747
BseGI	GGATG	2 cut(s)	123, 390
BseJI	GATNNNNATC	2 cut(s)	122, 747
BseLI	CCNNNNNNNGG	2 cut(s)	687, 780
BseMII	CTCAG	1 cut(s)	109
BseNI	ACTGG	5 cut(s)	527, 568, 622, 661, 889
BsiHKCI	CYCGRG	2 cut(s)	75, 830
BsiSI	CCGG	1 cut(s)	113
BslFI	GGGAC	2 cut(s)	24, 812
BslI	CCNNNNNNNGG	2 cut(s)	687, 780
BsmAI	GTCTC	2 cut(s)	203, 899
BsmBI	CGTCTC	1 cut(s)	203
BsmFI	GGGAC	2 cut(s)	24, 812
BsoBI	CYCGRG	2 cut(s)	75, 830
Bsp1286I	GDGCHC	2 cut(s)	82, 702
Bsp143I	GATC	3 cut(s)	91, 352, 748
BspACI	CCGC	2 cut(s)	13, 43
BspCNI	CTCAG	1 cut(s)	108
BspLI	GGNNCC	4 cut(s)	701, 827, 828, 850
BspMAI	CTGCAG	2 cut(s)	402, 913
BspPI	GGATC	1 cut(s)	743
BsrI	ACTGG	5 cut(s)	527, 568, 622, 661, 889
BssMI	GATC	3 cut(s)	91, 352, 748
Bst4CI	ACNGT	5 cut(s)	108, 371, 758, 975, 993
Bst6I	CTCTTC	1 cut(s)	534
BstAPI	GCANNNNNTGC	1 cut(s)	289
BstDEI	CTNAG	4 cut(s)	95, 260, 312, 955
BstEII	GGTNACC	1 cut(s)	108
BstF5I	GGATG	2 cut(s)	123, 390
BstKTI	GATC	3 cut(s)	94, 355, 751
BstMAI	GTCTC	2 cut(s)	203, 899
BstMBI	GATC	3 cut(s)	91, 352, 748
BstMWI	GCNNNNNNNGC	2 cut(s)	289, 809
BstNSI	RCATGY	2 cut(s)	334, 487
BstPAI	GACNNNNGTC	1 cut(s)	307
BstPI	GGTNACC	1 cut(s)	108
BstSFI	CTRYAG	4 cut(s)	398, 432, 909, 989
BstV2I	GAAGAC	1 cut(s)	921
BstX2I	RGATCY	1 cut(s)	91
BstYI	RGATCY	1 cut(s)	91
BtgZI	GCGATG	2 cut(s)	113, 114
BtrI	CACGTC	1 cut(s)	662
BtsCI	GGATG	2 cut(s)	123, 390
BtsI	GCAGTG	3 cut(s)	407, 510, 640
BtsIMutI	CAGTG	6 cut(s)	407, 510, 640, 654, 896, 980
CaiI	CAGNNNCTG	1 cut(s)	476
Cfr13I	GGNCC	1 cut(s)	826
CseI	GACGC	1 cut(s)	220
Csp6I	GTAC	3 cut(s)	571, 874, 1069
CviAII	CATG	7 cut(s)	236, 305, 331, 484, 533, 937, 1043
CviQI	GTAC	3 cut(s)	571, 874, 1069
DdeI	CTNAG	4 cut(s)	95, 260, 312, 955
DpnI	GATC	3 cut(s)	93, 354, 750
DpnII	GATC	3 cut(s)	91, 352, 748
DriI	GACNNNNNGTC	1 cut(s)	769
Eam1104I	CTCTTC	1 cut(s)	534
Eam1105I	GACNNNNNGTC	1 cut(s)	769
EarI	CTCTTC	1 cut(s)	534
Eco24I	GRGCYC	2 cut(s)	82, 702
Eco32I	GATATC	2 cut(s)	322, 668
Eco47I	GGWCC	1 cut(s)	826
Eco57I	CTGAAG	1 cut(s)	951
Eco88I	CYCGRG	2 cut(s)	75, 830
Eco91I	GGTNACC	1 cut(s)	108
EcoO109I	RGGNCCY	1 cut(s)	826
EcoO65I	GGTNACC	1 cut(s)	108
EcoRV	GATATC	2 cut(s)	322, 668
EcoT22I	ATGCAT	1 cut(s)	392
EcoT38I	GRGCYC	2 cut(s)	82, 702
Esp3I	CGTCTC	1 cut(s)	203
FaeI	CATG	7 cut(s)	239, 308, 334, 487, 536, 940, 1046
FaqI	GGGAC	2 cut(s)	24, 812
FatI	CATG	7 cut(s)	235, 304, 330, 483, 532, 936, 1042
FauI	CCCGC	1 cut(s)	50
FauNDI	CATATG	1 cut(s)	386
FblI	GTMKAC	2 cut(s)	366, 1061
FokI	GGATG	2 cut(s)	110, 377
FriOI	GRGCYC	2 cut(s)	82, 702
FspBI	CTAG	1 cut(s)	1025
HapII	CCGG	1 cut(s)	113
HgaI	GACGC	1 cut(s)	220
Hin1II	CATG	7 cut(s)	239, 308, 334, 487, 536, 940, 1046
HincII	GTYRAC	1 cut(s)	1062
HindII	GTYRAC	1 cut(s)	1062
HinfI	GANTC	3 cut(s)	118, 593, 863
HpaII	CCGG	1 cut(s)	113
HphI	GGTGA	1 cut(s)	102
Hpy166II	GTNNAC	3 cut(s)	367, 774, 1062
Hpy188I	TCNGA	4 cut(s)	137, 190, 352, 868
Hpy188III	TCNNGA	2 cut(s)	18, 671
Hpy8I	GTNNAC	3 cut(s)	367, 774, 1062
HpyAV	CCTTC	6 cut(s)	199, 348, 404, 681, 862, 908
HpyCH4III	ACNGT	5 cut(s)	108, 371, 758, 975, 993
HpyCH4IV	ACGT	1 cut(s)	661
HpyF10VI	GCNNNNNNNGC	2 cut(s)	289, 809
HpyF3I	CTNAG	4 cut(s)	95, 260, 312, 955
HpySE526I	ACGT	1 cut(s)	661
Hsp92II	CATG	7 cut(s)	239, 308, 334, 487, 536, 940, 1046
KflI	GGGWCCC	1 cut(s)	826
Kzo9I	GATC	3 cut(s)	91, 352, 748
LmnI	GCTCC	4 cut(s)	152, 705, 848, 985
LweI	GCATC	4 cut(s)	399, 799, 938, 987
MaeI	CTAG	1 cut(s)	1025
MaeII	ACGT	1 cut(s)	661
MaeIII	GTNAC	4 cut(s)	27, 108, 629, 939
MalI	GATC	3 cut(s)	93, 354, 750
MboI	GATC	3 cut(s)	91, 352, 748
MboII	GAAGA	3 cut(s)	551, 872, 926
MflI	RGATCY	1 cut(s)	91
MhlI	GDGCHC	2 cut(s)	82, 702
MluCI	AATT	8 cut(s)	68, 139, 151, 273, 415, 815, 1016, 1083
MlyI	GAGTC	1 cut(s)	857
MnlI	CCTC	7 cut(s)	14, 18, 184, 466, 535, 915, 1001
Mph1103I	ATGCAT	1 cut(s)	392
MseI	TTAA	1 cut(s)	461
MslI	CAYNNNNRTG	1 cut(s)	889
MspI	CCGG	1 cut(s)	113
MwoI	GCNNNNNNNGC	2 cut(s)	289, 809
NdeI	CATATG	1 cut(s)	386
NdeII	GATC	3 cut(s)	91, 352, 748
NlaIII	CATG	7 cut(s)	239, 308, 334, 487, 536, 940, 1046
NlaIV	GGNNCC	4 cut(s)	701, 827, 828, 850
NmuCI	GTSAC	2 cut(s)	27, 108
NsiI	ATGCAT	1 cut(s)	392
NspI	RCATGY	2 cut(s)	334, 487
OliI	CACNNNNGTG	1 cut(s)	889
PciI	ACATGT	1 cut(s)	483
PfeI	GAWTC	2 cut(s)	118, 593
PleI	GAGTC	1 cut(s)	857
PpsI	GAGTC	1 cut(s)	857
PpuMI	RGGWCCY	1 cut(s)	826
PscI	ACATGT	1 cut(s)	483
PshAI	GACNNNNGTC	1 cut(s)	307
Psp5II	RGGWCCY	1 cut(s)	826
PspEI	GGTNACC	1 cut(s)	108
PspN4I	GGNNCC	4 cut(s)	701, 827, 828, 850
PspPI	GGNCC	1 cut(s)	826
PspPPI	RGGWCCY	1 cut(s)	826
PstI	CTGCAG	2 cut(s)	402, 913
PstNI	CAGNNNCTG	1 cut(s)	476
PsuI	RGATCY	1 cut(s)	91
RsaI	GTAC	3 cut(s)	572, 875, 1070
RsaNI	GTAC	3 cut(s)	571, 874, 1069
RseI	CAYNNNNRTG	1 cut(s)	889
SalI	GTCGAC	1 cut(s)	1060
SaqAI	TTAA	1 cut(s)	461
Sau3AI	GATC	3 cut(s)	91, 352, 748
Sau96I	GGNCC	1 cut(s)	826
SchI	GAGTC	1 cut(s)	857
SduI	GDGCHC	2 cut(s)	82, 702
SetI	ASST	9 cut(s)	29, 176, 467, 546, 664, 692, 990, 1026, 1093
SfaNI	GCATC	4 cut(s)	399, 799, 938, 987
SfcI	CTRYAG	4 cut(s)	398, 432, 909, 989
SinI	GGWCC	1 cut(s)	826
SmiMI	CAYNNNNRTG	1 cut(s)	889
SmlI	CTYRAG	1 cut(s)	156
SmoI	CTYRAG	1 cut(s)	156
Sse9I	AATT	8 cut(s)	68, 139, 151, 273, 415, 815, 1016, 1083
SsiI	CCGC	2 cut(s)	13, 43
SspMI	CTAG	1 cut(s)	1025
TaaI	ACNGT	5 cut(s)	108, 371, 758, 975, 993
TaiI	ACGT	1 cut(s)	664
TaqI	TCGA	1 cut(s)	1061
TasI	AATT	8 cut(s)	68, 139, 151, 273, 415, 815, 1016, 1083
TatI	WGTACW	2 cut(s)	570, 1068
TfiI	GAWTC	2 cut(s)	118, 593
Tru1I	TTAA	1 cut(s)	461
Tru9I	TTAA	1 cut(s)	461
TscAI	CASTG	6 cut(s)	407, 517, 647, 661, 896, 980
TseFI	GTSAC	2 cut(s)	27, 108
Tsp45I	GTSAC	2 cut(s)	27, 108
TspDTI	ATGAA	3 cut(s)	230, 521, 1059
TspRI	CASTG	6 cut(s)	407, 517, 647, 661, 896, 980
VpaK11BI	GGWCC	1 cut(s)	826
XapI	RAATTY	4 cut(s)	68, 815, 1016, 1083
XceI	RCATGY	2 cut(s)	334, 487
XmiI	GTMKAC	2 cut(s)	366, 1061
XspI	CTAG	1 cut(s)	1025
Zsp2I	ATGCAT	1 cut(s)	392

Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.