Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5A

Orthogroup ID

OG0009922

Physical Location & Seq

Genomic Coordinates Forward (+)

58436372 .. 58439678

Gene Structure 3307 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5AG353400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 975 bp

ATGGAGGGAAAGCGGTCAAGAGGGAGGTCACAGCCCCGTCCCCGCCATTTGCTAACAAAAATCAAAGAATTTACTCGGGCTCTTGTGAAAGATCTCAGCGACGGACGGTCACCGGAGATTCTCATCCATCGCTTCCGAAATTACTGCTCCAATCCCTCCGCAAATTGCTTTTGTGGCTCTGATTTGCCGAAAGGGAAGGAGACGCTCACACTTCGTAAAGAAACCCATGTTCATAGATTAGATGTTCTGCTTAGGGTTCTTGTAATTGTTCAGCAACTTCTGCAAGAAAACAGACATGGGTCTAAGAGAGATATCTATTACATGCACCCTTCTATATTTTCAGATCAGTCAGTTGTAGACCGTGCAATCAATGACATATGCATCCTTCTGCAGTGTAGTCGCCACAATTTGAATGTGGTGTCTGTAGGAAAGGGGTTGGTAATGGGCTGGTTAAGGTTCGCAGAGGCTGGAAACATGTTTGATTGCATAAATAGACCAAACACTGCCTACCCTGTTCCAGTTCATGTTGAAGAGGTCAAAGATATTGTTAGTGTTGCCCAGTACATACTTGTTGTGGAGAAAGAATCAGTTTTTCAACGATTGGCAAATGACCAGTTTTGTAGCACAAACCACTGCATTGTCATCACTGGACGTGGATATCCTGATATTTCCACAAGAAGGTTTTTGGGGCTCCTTGTTGATACTTTACATATCCCTATCTATTGCTTGGTAGATTGTGATCCCTACGGTTTTGACATCTTGTCCACATATCGGTTTGGTTCTCTGCAAATGGCGTATGATGCAAAATTTCTACGGGTCCCCGAGATAATCTGGCTTGGAGCCTTCCCTTTGGACTCGGAGAAGTACCATCTTCCACACCAATGTCTCCTTCCTTTGACTGCAGAAGACAAGAGGAAAACTGAAGCCATGTTACAGAGATGCTACTTAGAAAGAGAAGTGCCACAGTGGAGGTAA

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

324

Amino Acids

37.4

Weight (kDa)

8.78

Isoelectric Point (pI)

51.73

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
TP6A_N	PF04406	79 - 139	2.4e-21	Type IIB DNA topoisomerase
TOP6A-Spo11_Toprim	PF21180	188 - 324	1.2e-49	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

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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	3 cut(s)	13, 43, 159
AclWI	GGATC	1 cut(s)	734
AcsI	RAATTY	2 cut(s)	68, 806
AcuI	CTGAAG	1 cut(s)	942
AfaI	GTAC	2 cut(s)	563, 866
AfiI	CCNNNNNNNGG	2 cut(s)	678, 771
AflIII	ACRYGT	1 cut(s)	474
AgsI	TTSAA	3 cut(s)	412, 530, 596
AhdI	GACNNNNNGTC	2 cut(s)	106, 760
AjiI	CACGTC	1 cut(s)	653
AjuI	GAANNNNNNNTTGG	2 cut(s)	873, 905
Alw26I	GTCTC	2 cut(s)	194, 890
AlwI	GGATC	1 cut(s)	734
AlwNI	CAGNNNCTG	1 cut(s)	467
Ama87I	CYCGRG	2 cut(s)	75, 821
ApoI	RAATTY	2 cut(s)	68, 806
AspS9I	GGNCC	1 cut(s)	817
AsuHPI	GGTGA	1 cut(s)	102
AvaI	CYCGRG	2 cut(s)	75, 821
AvaII	GGWCC	1 cut(s)	817
BanII	GRGCYC	2 cut(s)	82, 693
BarI	GAAGNNNNNNTAC	2 cut(s)	915, 947
BbsI	GAAGAC	1 cut(s)	912
BccI	CCATC	2 cut(s)	135, 876
BcgI	CGANNNNNNTGC	4 cut(s)	126, 160, 380, 414
BcoDI	GTCTC	2 cut(s)	194, 890
BfmI	CTRYAG	3 cut(s)	389, 423, 900
BglII	AGATCT	1 cut(s)	91
Bme18I	GGWCC	1 cut(s)	817
BmeRI	GACNNNNNGTC	2 cut(s)	106, 760
BmeT110I	CYCGRG	2 cut(s)	75, 821
BmgBI	CACGTC	1 cut(s)	653
BmgT120I	GGNCC	1 cut(s)	817
BmiI	GGNNCC	4 cut(s)	692, 818, 819, 841
BmrI	ACTGGG	1 cut(s)	553
BmsI	GCATC	3 cut(s)	390, 790, 929
BmuI	ACTGGG	1 cut(s)	553
BoxI	GACNNNNGTC	1 cut(s)	298
BpiI	GAAGAC	1 cut(s)	912
Bpu10I	CCTNAGC	1 cut(s)	251
BsaBI	GATNNNNATC	2 cut(s)	122, 738
BsaWI	WCCGGW	1 cut(s)	112
Bsc4I	CCNNNNNNNGG	2 cut(s)	678, 771
Bse1I	ACTGG	4 cut(s)	518, 559, 613, 652
Bse8I	GATNNNNATC	2 cut(s)	122, 738
BseGI	GGATG	2 cut(s)	123, 381
BseJI	GATNNNNATC	2 cut(s)	122, 738
BseLI	CCNNNNNNNGG	2 cut(s)	678, 771
BseMII	CTCAG	1 cut(s)	109
BseNI	ACTGG	4 cut(s)	518, 559, 613, 652
BsiHKCI	CYCGRG	2 cut(s)	75, 821
BsiSI	CCGG	1 cut(s)	113
BslFI	GGGAC	2 cut(s)	24, 803
BslI	CCNNNNNNNGG	2 cut(s)	678, 771
BsmAI	GTCTC	2 cut(s)	194, 890
BsmBI	CGTCTC	1 cut(s)	194
BsmFI	GGGAC	2 cut(s)	24, 803
BsoBI	CYCGRG	2 cut(s)	75, 821
Bsp1286I	GDGCHC	2 cut(s)	82, 693
Bsp143I	GATC	3 cut(s)	91, 343, 739
BspACI	CCGC	3 cut(s)	13, 43, 159
BspCNI	CTCAG	1 cut(s)	108
BspLI	GGNNCC	4 cut(s)	692, 818, 819, 841
BspMAI	CTGCAG	2 cut(s)	393, 904
BspPI	GGATC	1 cut(s)	734
BsrI	ACTGG	4 cut(s)	518, 559, 613, 652
BssMI	GATC	3 cut(s)	91, 343, 739
Bst4CI	ACNGT	4 cut(s)	108, 362, 749, 966
Bst6I	CTCTTC	1 cut(s)	525
BstAPI	GCANNNNNTGC	1 cut(s)	280
BstDEI	CTNAG	4 cut(s)	95, 251, 303, 946
BstEII	GGTNACC	1 cut(s)	108
BstF5I	GGATG	2 cut(s)	123, 381
BstKTI	GATC	3 cut(s)	94, 346, 742
BstMAI	GTCTC	2 cut(s)	194, 890
BstMBI	GATC	3 cut(s)	91, 343, 739
BstMWI	GCNNNNNNNGC	3 cut(s)	174, 280, 800
BstNSI	RCATGY	2 cut(s)	325, 478
BstPAI	GACNNNNGTC	1 cut(s)	298
BstPI	GGTNACC	1 cut(s)	108
BstSFI	CTRYAG	3 cut(s)	389, 423, 900
BstV2I	GAAGAC	1 cut(s)	912
BstX2I	RGATCY	1 cut(s)	91
BstYI	RGATCY	1 cut(s)	91
BtgZI	GCGATG	1 cut(s)	113
BtrI	CACGTC	1 cut(s)	653
BtsCI	GGATG	2 cut(s)	123, 381
BtsI	GCAGTG	3 cut(s)	398, 501, 631
BtsIMutI	CAGTG	5 cut(s)	398, 501, 631, 645, 971
CaiI	CAGNNNCTG	1 cut(s)	467
Cfr13I	GGNCC	1 cut(s)	817
CseI	GACGC	1 cut(s)	211
Csp6I	GTAC	2 cut(s)	562, 865
CviAII	CATG	6 cut(s)	227, 296, 322, 475, 524, 928
CviJI	RGCY	9 cut(s)	34, 80, 177, 447, 467, 691, 835, 842, 926
CviKI_1	RGCY	9 cut(s)	34, 80, 177, 447, 467, 691, 835, 842, 926
CviQI	GTAC	2 cut(s)	562, 865
DdeI	CTNAG	4 cut(s)	95, 251, 303, 946
DpnI	GATC	3 cut(s)	93, 345, 741
DpnII	GATC	3 cut(s)	91, 343, 739
DriI	GACNNNNNGTC	2 cut(s)	106, 760
Eam1104I	CTCTTC	1 cut(s)	525
Eam1105I	GACNNNNNGTC	2 cut(s)	106, 760
EarI	CTCTTC	1 cut(s)	525
Eco24I	GRGCYC	2 cut(s)	82, 693
Eco32I	GATATC	2 cut(s)	313, 659
Eco47I	GGWCC	1 cut(s)	817
Eco57I	CTGAAG	1 cut(s)	942
Eco88I	CYCGRG	2 cut(s)	75, 821
Eco91I	GGTNACC	1 cut(s)	108
EcoO109I	RGGNCCY	1 cut(s)	817
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, 931
FaqI	GGGAC	2 cut(s)	24, 803
FatI	CATG	6 cut(s)	226, 295, 321, 474, 523, 927
FauI	CCCGC	1 cut(s)	50
FauNDI	CATATG	1 cut(s)	377
FblI	GTMKAC	1 cut(s)	357
FokI	GGATG	2 cut(s)	110, 368
FriOI	GRGCYC	2 cut(s)	82, 693
HapII	CCGG	1 cut(s)	113
HgaI	GACGC	1 cut(s)	211
Hin1II	CATG	6 cut(s)	230, 299, 325, 478, 527, 931
HinfI	GANTC	3 cut(s)	118, 584, 854
HpaII	CCGG	1 cut(s)	113
HphI	GGTGA	1 cut(s)	102
Hpy166II	GTNNAC	2 cut(s)	358, 765
Hpy188I	TCNGA	4 cut(s)	137, 181, 343, 859
Hpy188III	TCNNGA	2 cut(s)	18, 662
Hpy8I	GTNNAC	2 cut(s)	358, 765
Hpy99I	CGWCG	1 cut(s)	104
HpyAV	CCTTC	6 cut(s)	190, 339, 395, 672, 853, 899
HpyCH4III	ACNGT	4 cut(s)	108, 362, 749, 966
HpyCH4IV	ACGT	1 cut(s)	652
HpyF10VI	GCNNNNNNNGC	3 cut(s)	174, 280, 800
HpyF3I	CTNAG	4 cut(s)	95, 251, 303, 946
HpySE526I	ACGT	1 cut(s)	652
Hsp92II	CATG	6 cut(s)	230, 299, 325, 478, 527, 931
KflI	GGGWCCC	1 cut(s)	817
Kzo9I	GATC	3 cut(s)	91, 343, 739
LmnI	GCTCC	3 cut(s)	152, 696, 839
LweI	GCATC	3 cut(s)	390, 790, 929
MaeII	ACGT	1 cut(s)	652
MaeIII	GTNAC	3 cut(s)	27, 108, 930
MalI	GATC	3 cut(s)	93, 345, 741
MboI	GATC	3 cut(s)	91, 343, 739
MboII	GAAGA	3 cut(s)	542, 863, 917
MflI	RGATCY	1 cut(s)	91
MhlI	GDGCHC	2 cut(s)	82, 693
MluCI	AATT	6 cut(s)	68, 139, 163, 264, 406, 806
MlyI	GAGTC	1 cut(s)	848
MnlI	CCTC	7 cut(s)	14, 18, 166, 457, 526, 906, 963
Mph1103I	ATGCAT	1 cut(s)	383
MseI	TTAA	1 cut(s)	452
MslI	CAYNNNNRTG	1 cut(s)	880
MspI	CCGG	1 cut(s)	113
MwoI	GCNNNNNNNGC	3 cut(s)	174, 280, 800
NdeI	CATATG	1 cut(s)	377
NdeII	GATC	3 cut(s)	91, 343, 739
NlaIII	CATG	6 cut(s)	230, 299, 325, 478, 527, 931
NlaIV	GGNNCC	4 cut(s)	692, 818, 819, 841
NmuCI	GTSAC	2 cut(s)	27, 108
NsiI	ATGCAT	1 cut(s)	383
NspI	RCATGY	2 cut(s)	325, 478
PciI	ACATGT	1 cut(s)	474
PfeI	GAWTC	2 cut(s)	118, 584
PleI	GAGTC	1 cut(s)	848
PpsI	GAGTC	1 cut(s)	848
PpuMI	RGGWCCY	1 cut(s)	817
PscI	ACATGT	1 cut(s)	474
PshAI	GACNNNNGTC	1 cut(s)	298
Psp5II	RGGWCCY	1 cut(s)	817
PspEI	GGTNACC	1 cut(s)	108
PspN4I	GGNNCC	4 cut(s)	692, 818, 819, 841
PspPI	GGNCC	1 cut(s)	817
PspPPI	RGGWCCY	1 cut(s)	817
PstI	CTGCAG	2 cut(s)	393, 904
PstNI	CAGNNNCTG	1 cut(s)	467
PsuI	RGATCY	1 cut(s)	91
RsaI	GTAC	2 cut(s)	563, 866
RsaNI	GTAC	2 cut(s)	562, 865
RseI	CAYNNNNRTG	1 cut(s)	880
SaqAI	TTAA	1 cut(s)	452
Sau3AI	GATC	3 cut(s)	91, 343, 739
Sau96I	GGNCC	1 cut(s)	817
SchI	GAGTC	1 cut(s)	848
SduI	GDGCHC	2 cut(s)	82, 693
SetI	ASST	6 cut(s)	29, 458, 537, 655, 683, 974
SfaNI	GCATC	3 cut(s)	390, 790, 929
SfcI	CTRYAG	3 cut(s)	389, 423, 900
SinI	GGWCC	1 cut(s)	817
SmiMI	CAYNNNNRTG	1 cut(s)	880
Sse9I	AATT	6 cut(s)	68, 139, 163, 264, 406, 806
SsiI	CCGC	3 cut(s)	13, 43, 159
TaaI	ACNGT	4 cut(s)	108, 362, 749, 966
TaiI	ACGT	1 cut(s)	655
TasI	AATT	6 cut(s)	68, 139, 163, 264, 406, 806
TatI	WGTACW	1 cut(s)	561
TfiI	GAWTC	2 cut(s)	118, 584
Tru1I	TTAA	1 cut(s)	452
Tru9I	TTAA	1 cut(s)	452
TscAI	CASTG	5 cut(s)	398, 508, 638, 652, 971
TseFI	GTSAC	2 cut(s)	27, 108
Tsp45I	GTSAC	2 cut(s)	27, 108
TspDTI	ATGAA	2 cut(s)	221, 512
TspGWI	ACGGA	1 cut(s)	117
TspRI	CASTG	5 cut(s)	398, 508, 638, 652, 971
VpaK11BI	GGWCC	1 cut(s)	817
XapI	RAATTY	2 cut(s)	68, 806
XceI	RCATGY	2 cut(s)	325, 478
XmiI	GTMKAC	1 cut(s)	357
Zsp2I	ATGCAT	1 cut(s)	383

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