Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5C

Orthogroup ID

OG0009922

Physical Location & Seq

Genomic Coordinates Forward (+)

51390837 .. 51393736

Gene Structure 2900 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5CG390100.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 849 bp

ATGGAGGGAAAGCGGTCAAGAGGGAGGTCACAGCCCCGTCCCCGCCATTTGCTAACAAAAATCAAAGAATTTACTCGAGCTCTTGTGAGAGATCTCAGCGTCGGCCGGTCACCGGAGATTCTCATCCATCGCTTCCGAAATTACTGCTCCAATCCCTCCGAAAATTGCTATTGTAGCTCTGATTTGCCGAAAGGGAAGGAGACGCTCACACTTCGTAAAGAAACCCATGTTCGTAGATTAGATGTTCTGCTTAGGGTTCTTGTAATTGTTCAGCAACTTCTGCAAGAAAACAGACATGGGTCTAAGAGAGATATCTATTACATGCACCCTTCAATATTTTCAGATCAGTCAGTTGTAGACCGTGCAATCAATGACATATGCATCCTTCTACAGTGTAGTCGCCACAATTTGAATGTGGTGTCTGTAGGAAAGGGGTTGGTAATGGGCTGGTTAAGGTTCGCAGAGGCTGGAAACATGTTTGATTGCATAAATAGACCAAACACTGCTTACCCTGTTCCAGTTCATGTTGAAGAGGTCAAAGATATTGTTAGTGTTGCCCAGTACATACTTGTTGTGGAGAAAGAATCAGTTTTTCAACGATTGGCAAATGACCAGTTTTGTAACACAAACCACTGCATTGTCATCACTGGATGTGGATATCCTGATATTTCCACAAGAAGGTTTTTGGGGCTCCTTGTTGATACTTTACATATCCCTGTCTATTGCTTGGTAGATTGTGATCCCTACGGTTTTGACATCTTGTCCACATATCGGTTTGGTTCTCTGGTTAGGCCTTCTGATCAGTCTATGAACTTGTTCTCTAAGTTAACAAAGTTAAGGTGCATGTGA

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

282

Amino Acids

32.38

Weight (kDa)

9.09

Isoelectric Point (pI)

51.47

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
TP6A_N	PF04406	78 - 139	1.5e-21	Type IIB DNA topoisomerase
TOP6A-Spo11_Toprim	PF21180	188 - 263	2.9e-32	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

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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	1 cut(s)	357
AciI	CCGC	2 cut(s)	13, 43
AclWI	GGATC	1 cut(s)	734
AcoI	YGGCCR	1 cut(s)	103
AcsI	RAATTY	1 cut(s)	68
AfaI	GTAC	1 cut(s)	563
AfiI	CCNNNNNNNGG	3 cut(s)	112, 678, 771
AflIII	ACRYGT	1 cut(s)	474
AgsI	TTSAA	4 cut(s)	333, 412, 530, 596
AhdI	GACNNNNNGTC	1 cut(s)	760
AluBI	AGCT	2 cut(s)	80, 177
AluI	AGCT	2 cut(s)	80, 177
Alw21I	GWGCWC	1 cut(s)	82
Alw26I	GTCTC	1 cut(s)	194
AlwI	GGATC	1 cut(s)	734
AlwNI	CAGNNNCTG	1 cut(s)	467
Ama87I	CYCGRG	1 cut(s)	75
AoxI	GGCC	2 cut(s)	103, 791
ApoI	RAATTY	1 cut(s)	68
Asp700I	GAANNNNTTC	1 cut(s)	815
AsuHPI	GGTGA	1 cut(s)	102
AvaI	CYCGRG	1 cut(s)	75
BanII	GRGCYC	2 cut(s)	82, 693
Bbv12I	GWGCWC	1 cut(s)	82
BccI	CCATC	1 cut(s)	135
BcgI	CGANNNNNNTGC	2 cut(s)	126, 160
BclI	TGATCA	1 cut(s)	799
BcoDI	GTCTC	1 cut(s)	194
BfmI	CTRYAG	2 cut(s)	389, 423
BglII	AGATCT	1 cut(s)	91
BmeRI	GACNNNNNGTC	1 cut(s)	760
BmeT110I	CYCGRG	1 cut(s)	75
BmiI	GGNNCC	1 cut(s)	692
BmrI	ACTGGG	1 cut(s)	553
BmsI	GCATC	1 cut(s)	390
BmuI	ACTGGG	1 cut(s)	553
BoxI	GACNNNNGTC	1 cut(s)	298
Bpu10I	CCTNAGC	1 cut(s)	251
BsaBI	GATNNNNATC	2 cut(s)	122, 738
BsaWI	WCCGGW	1 cut(s)	112
Bsc4I	CCNNNNNNNGG	3 cut(s)	112, 678, 771
Bse118I	RCCGGY	1 cut(s)	105
Bse1I	ACTGG	4 cut(s)	518, 559, 613, 652
Bse8I	GATNNNNATC	2 cut(s)	122, 738
BseGI	GGATG	3 cut(s)	123, 381, 656
BseJI	GATNNNNATC	2 cut(s)	122, 738
BseLI	CCNNNNNNNGG	3 cut(s)	112, 678, 771
BseMII	CTCAG	1 cut(s)	109
BseNI	ACTGG	4 cut(s)	518, 559, 613, 652
BseX3I	CGGCCG	1 cut(s)	103
Bsh1285I	CGRYCG	1 cut(s)	106
BshFI	GGCC	2 cut(s)	105, 793
BsiEI	CGRYCG	1 cut(s)	106
BsiHKAI	GWGCWC	1 cut(s)	82
BsiHKCI	CYCGRG	1 cut(s)	75
BsiSI	CCGG	2 cut(s)	106, 113
BslFI	GGGAC	1 cut(s)	24
BslI	CCNNNNNNNGG	3 cut(s)	112, 678, 771
BsmAI	GTCTC	1 cut(s)	194
BsmBI	CGTCTC	1 cut(s)	194
BsmFI	GGGAC	1 cut(s)	24
BsnI	GGCC	2 cut(s)	105, 793
BsoBI	CYCGRG	1 cut(s)	75
Bsp1286I	GDGCHC	2 cut(s)	82, 693
Bsp143I	GATC	4 cut(s)	91, 343, 739, 799
BspACI	CCGC	2 cut(s)	13, 43
BspANI	GGCC	2 cut(s)	105, 793
BspCNI	CTCAG	1 cut(s)	108
BspLI	GGNNCC	1 cut(s)	692
BspPI	GGATC	1 cut(s)	734
BsrFI	RCCGGY	1 cut(s)	105
BsrI	ACTGG	4 cut(s)	518, 559, 613, 652
BssAI	RCCGGY	1 cut(s)	105
BssMI	GATC	4 cut(s)	91, 343, 739, 799
Bst4CI	ACNGT	3 cut(s)	362, 393, 749
Bst6I	CTCTTC	1 cut(s)	525
BstAPI	GCANNNNNTGC	1 cut(s)	280
BstDEI	CTNAG	4 cut(s)	95, 251, 303, 822
BstEII	GGTNACC	1 cut(s)	108
BstF5I	GGATG	3 cut(s)	123, 381, 656
BstKTI	GATC	4 cut(s)	94, 346, 742, 802
BstMAI	GTCTC	1 cut(s)	194
BstMBI	GATC	4 cut(s)	91, 343, 739, 799
BstMCI	CGRYCG	1 cut(s)	106
BstMWI	GCNNNNNNNGC	2 cut(s)	174, 280
BstNSI	RCATGY	3 cut(s)	325, 478, 847
BstPAI	GACNNNNGTC	1 cut(s)	298
BstPI	GGTNACC	1 cut(s)	108
BstSFI	CTRYAG	2 cut(s)	389, 423
BstX2I	RGATCY	1 cut(s)	91
BstYI	RGATCY	1 cut(s)	91
BstZI	CGGCCG	1 cut(s)	103
BsuRI	GGCC	2 cut(s)	105, 793
BtgZI	GCGATG	1 cut(s)	113
BtsCI	GGATG	3 cut(s)	123, 381, 656
BtsI	GCAGTG	2 cut(s)	501, 631
BtsIMutI	CAGTG	4 cut(s)	398, 501, 631, 645
CaiI	CAGNNNCTG	1 cut(s)	467
Cfr10I	RCCGGY	1 cut(s)	105
CseI	GACGC	2 cut(s)	88, 211
Csp6I	GTAC	1 cut(s)	562
CviAII	CATG	6 cut(s)	227, 296, 322, 475, 524, 844
CviJI	RGCY	8 cut(s)	34, 80, 105, 177, 447, 467, 691, 793
CviKI_1	RGCY	8 cut(s)	34, 80, 105, 177, 447, 467, 691, 793
CviQI	GTAC	1 cut(s)	562
DdeI	CTNAG	4 cut(s)	95, 251, 303, 822
DpnI	GATC	4 cut(s)	93, 345, 741, 801
DpnII	GATC	4 cut(s)	91, 343, 739, 799
DriI	GACNNNNNGTC	1 cut(s)	760
EaeI	YGGCCR	1 cut(s)	103
EagI	CGGCCG	1 cut(s)	103
Eam1104I	CTCTTC	1 cut(s)	525
Eam1105I	GACNNNNNGTC	1 cut(s)	760
EarI	CTCTTC	1 cut(s)	525
Ecl136II	GAGCTC	1 cut(s)	80
EclXI	CGGCCG	1 cut(s)	103
Eco147I	AGGCCT	1 cut(s)	793
Eco24I	GRGCYC	2 cut(s)	82, 693
Eco32I	GATATC	2 cut(s)	313, 659
Eco52I	CGGCCG	1 cut(s)	103
Eco53kI	GAGCTC	1 cut(s)	80
Eco88I	CYCGRG	1 cut(s)	75
Eco91I	GGTNACC	1 cut(s)	108
EcoICRI	GAGCTC	1 cut(s)	80
EcoO65I	GGTNACC	1 cut(s)	108
EcoRV	GATATC	2 cut(s)	313, 659
EcoT22I	ATGCAT	1 cut(s)	383
EcoT38I	GRGCYC	2 cut(s)	82, 693
Esp3I	CGTCTC	1 cut(s)	194
FaeI	CATG	6 cut(s)	230, 299, 325, 478, 527, 847
FaqI	GGGAC	1 cut(s)	24
FatI	CATG	6 cut(s)	226, 295, 321, 474, 523, 843
FauI	CCCGC	1 cut(s)	50
FauNDI	CATATG	1 cut(s)	377
FbaI	TGATCA	1 cut(s)	799
FblI	GTMKAC	1 cut(s)	357
FokI	GGATG	3 cut(s)	110, 368, 663
FriOI	GRGCYC	2 cut(s)	82, 693
HaeIII	GGCC	2 cut(s)	105, 793
HapII	CCGG	2 cut(s)	106, 113
HgaI	GACGC	2 cut(s)	88, 211
Hin1II	CATG	6 cut(s)	230, 299, 325, 478, 527, 847
HincII	GTYRAC	1 cut(s)	828
HindII	GTYRAC	1 cut(s)	828
HinfI	GANTC	2 cut(s)	118, 584
HpaI	GTTAAC	1 cut(s)	828
HpaII	CCGG	2 cut(s)	106, 113
HphI	GGTGA	1 cut(s)	102
Hpy166II	GTNNAC	3 cut(s)	358, 765, 828
Hpy188I	TCNGA	5 cut(s)	137, 160, 181, 343, 799
Hpy188III	TCNNGA	2 cut(s)	18, 662
Hpy8I	GTNNAC	3 cut(s)	358, 765, 828
Hpy99I	CGWCG	1 cut(s)	104
HpyAV	CCTTC	5 cut(s)	190, 339, 395, 672, 804
HpyCH4III	ACNGT	3 cut(s)	362, 393, 749
HpyCH4V	TGCA	7 cut(s)	283, 325, 365, 381, 486, 636, 843
HpyF10VI	GCNNNNNNNGC	2 cut(s)	174, 280
HpyF3I	CTNAG	4 cut(s)	95, 251, 303, 822
Hsp92II	CATG	6 cut(s)	230, 299, 325, 478, 527, 847
Ksp22I	TGATCA	1 cut(s)	799
KspAI	GTTAAC	1 cut(s)	828
Kzo9I	GATC	4 cut(s)	91, 343, 739, 799
LmnI	GCTCC	2 cut(s)	152, 696
LweI	GCATC	1 cut(s)	390
MaeIII	GTNAC	3 cut(s)	27, 108, 620
MalI	GATC	4 cut(s)	93, 345, 741, 801
MboI	GATC	4 cut(s)	91, 343, 739, 799
MboII	GAAGA	1 cut(s)	542
MflI	RGATCY	1 cut(s)	91
MhlI	GDGCHC	2 cut(s)	82, 693
MluCI	AATT	5 cut(s)	68, 139, 163, 264, 406
MnlI	CCTC	5 cut(s)	14, 18, 166, 457, 526
Mph1103I	ATGCAT	1 cut(s)	383
MroXI	GAANNNNTTC	1 cut(s)	815
MseI	TTAA	3 cut(s)	452, 827, 836
MspI	CCGG	2 cut(s)	106, 113
MwoI	GCNNNNNNNGC	2 cut(s)	174, 280
NdeI	CATATG	1 cut(s)	377
NdeII	GATC	4 cut(s)	91, 343, 739, 799
NlaIII	CATG	6 cut(s)	230, 299, 325, 478, 527, 847
NlaIV	GGNNCC	1 cut(s)	692
NmuCI	GTSAC	2 cut(s)	27, 108
NsiI	ATGCAT	1 cut(s)	383
NspI	RCATGY	3 cut(s)	325, 478, 847
PaeR7I	CTCGAG	1 cut(s)	75
PceI	AGGCCT	1 cut(s)	793
PciI	ACATGT	1 cut(s)	474
PdmI	GAANNNNTTC	1 cut(s)	815
PfeI	GAWTC	2 cut(s)	118, 584
PscI	ACATGT	1 cut(s)	474
PshAI	GACNNNNGTC	1 cut(s)	298
Psp124BI	GAGCTC	1 cut(s)	82
PspEI	GGTNACC	1 cut(s)	108
PspN4I	GGNNCC	1 cut(s)	692
PspXI	VCTCGAGB	1 cut(s)	75
PstNI	CAGNNNCTG	1 cut(s)	467
PsuI	RGATCY	1 cut(s)	91
RsaI	GTAC	1 cut(s)	563
RsaNI	GTAC	1 cut(s)	562
SacI	GAGCTC	1 cut(s)	82
SaqAI	TTAA	3 cut(s)	452, 827, 836
Sau3AI	GATC	4 cut(s)	91, 343, 739, 799
SduI	GDGCHC	2 cut(s)	82, 693
SetI	ASST	7 cut(s)	29, 82, 179, 458, 537, 683, 842
SfaNI	GCATC	1 cut(s)	390
SfcI	CTRYAG	2 cut(s)	389, 423
Sfr274I	CTCGAG	1 cut(s)	75
SlaI	CTCGAG	1 cut(s)	75
SmlI	CTYRAG	1 cut(s)	75
SmoI	CTYRAG	1 cut(s)	75
Sse9I	AATT	5 cut(s)	68, 139, 163, 264, 406
SseBI	AGGCCT	1 cut(s)	793
SsiI	CCGC	2 cut(s)	13, 43
SspI	AATATT	1 cut(s)	336
SstI	GAGCTC	1 cut(s)	82
StuI	AGGCCT	1 cut(s)	793
TaaI	ACNGT	3 cut(s)	362, 393, 749
TaqI	TCGA	1 cut(s)	76
TasI	AATT	5 cut(s)	68, 139, 163, 264, 406
TatI	WGTACW	1 cut(s)	561
TfiI	GAWTC	2 cut(s)	118, 584
Tru1I	TTAA	3 cut(s)	452, 827, 836
Tru9I	TTAA	3 cut(s)	452, 827, 836
TscAI	CASTG	4 cut(s)	398, 508, 638, 652
TseFI	GTSAC	2 cut(s)	27, 108
Tsp45I	GTSAC	2 cut(s)	27, 108
TspDTI	ATGAA	2 cut(s)	512, 824
TspRI	CASTG	4 cut(s)	398, 508, 638, 652
XapI	RAATTY	1 cut(s)	68
XceI	RCATGY	3 cut(s)	325, 478, 847
XhoI	CTCGAG	1 cut(s)	75
XmiI	GTMKAC	1 cut(s)	357
XmnI	GAANNNNTTC	1 cut(s)	815
Zsp2I	ATGCAT	1 cut(s)	383

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