Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3C

Orthogroup ID

OG0007476

Physical Location & Seq

Genomic Coordinates Reverse (-)

331085 .. 337062

Gene Structure 5978 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3CG004200.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1149 bp

ATGGCGAACAGCTCAAGCTCAGGCTCCCATGGTGGAAACCATAACGGAGTTCCCAACTGGGAGACACCATCAAGAGTTGAGGTCAACCGTAAATCACAAGAGTTCCTACTTTGGTATAGGACCTCTCGTGAGGTCTACTCCACCCCCAGCGATAAATTTCATAAGATGGTCAAGGTCAGTGAGATGTCTCGAGAGCAAGTATTGGAGGCAATTGAAAAGTATCAGAAAAATATTAAGAACGACGGGCCAAACACAGTCGTTGATCAATCGGCCTCAAACACACGGATCGCCGGTGAGAAGGGGGCCAAACGTCGTATTCTAGAAGACGGTGACAAAGTTTGCCACCCAAGACAAAAAACAAGGAAAAGATTGCGACGTGCTCTCGAGCTCCTTCACTCGTTCTGCAAAGAGAAGGTGTACCGCACACTACGCTCATTCTTTTACATGCTTTTCAAGGACCAGTCTAAGACGAATAAAGCTATCAATCAAGTCTGTATTGAACTCCGTTGCACCCGTTCTAGTCTAAACGTCTTTGCAACAGACCGAGGAACCGTCATAGGTGCCCTTTCTTTCAAATTGGAGGGAAGACTAGTCAATTGTAATATTGAAGCGGGTGATGATATTACGTGCAAACTGGGGCAGATTATCCCGCCATTCATGAATCTAGTGACTGAGATGGATGTTGGAGATGATGTCTGTTTTATCTTATTTGTGGAAAAATATTCAGTTTTTCTAGAATTGACTCTAGAAAACTTCCACAATAAGTACCATTGTATCATCATTACCGGAACAGGCCAGGCCGATGTTGTATCCAGACAACTCACAAAAAAACTAATGGATGATTTCAAGCTACCAGCGTTCTGCCTTGTGGACTGTGATCCATCGGGCATTGAGATTTCAGCAGTTGTCAAGCACGGGTCGGTGAATATGGCGTATGACAGTAAAAATTTAGCCAGTCCCTTGATGTATTGGTTAGGTATTTGGCCAAGCGATTTGGAAAATCTTAATATACCTTCAGAGGTGTTCCACAAAAAAGATAGGAAGAAATTAGCGGAACTGATAAAGCAAGAATTTGTGAATGACGATATGACGCTGAACAGTGAGCTGGATCGATCGTATGGTGGAGCTCAAAAAGAAGGCATCCCTTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0000228 GO:0000280 GO:0000706 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:0005515 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:0007127 GO:0007131 GO:0008094 GO:0008134 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:0030957 GO:0031974 GO:0031981 GO:0033554 GO:0034641 GO:0035825 GO:0042138 GO:0042623 GO:0042802 GO:0042803 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044237 GO:0044238 GO:0044260 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044464 GO:0046483 GO:0046983 GO:0048285 GO:0050896 GO:0051321 GO:0051716 GO:0061505 GO:0061982 GO:0070013 GO:0071704 GO:0071840 GO:0090304 GO:0090305 GO:0097159 GO:0140013 GO:0140097 GO:1901360 GO:1901363 GO:1903046

KEGG Pathways

Metabolic & Signaling

ko04113 map04113

Pfam Domains

Protein Families

TP6A_N

Protein Analysis

382

Amino Acids

43.42

Weight (kDa)

8.55

Isoelectric Point (pI)

47.86

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
TP6A_N	PF04406	124 - 177	2.2e-09	Type IIB DNA topoisomerase
TOP6A-Spo11_Toprim	PF21180	234 - 370	1.6e-40	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: OG0007476)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_1g02062 FvH4_7g23893
rosa_chinensis	RchiOBHm_Chr3g0447681 RchiOBHm_Chr5g0062071
rosa_laevigata	RLG00000015854 RLG00000025979 RLG00000035529
rosa_multiflora	Rmu_sc0002296.1_g000012 Rmu_sc0006064.1_g000010 Rmu_sc0017669.1_g000013
rosa_roxburghii	Rroxscaffold_2G00153710
rosa_rugosa	Rorug01G0475300 Rorug05G0345800
rosa_samantha	Rh2BG027000 Rh2BG028800 Rh3AG004200 Rh3BG003800 Rh3CG004200 Rh3DG004100 Rh5AG407400 Rh5BG420600 Rh5BG420700 Rh5CG444600 Rh5CG444800 Rh5DG435800

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	1 cut(s)	560
AccI	GTMKAC	1 cut(s)	135
AciI	CCGC	4 cut(s)	421, 611, 650, 1052
AclWI	GGATC	3 cut(s)	293, 872, 1116
AcoI	YGGCCR	1 cut(s)	983
AcsI	RAATTY	3 cut(s)	155, 946, 1070
AcuI	CTGAAG	1 cut(s)	999
AfaI	GTAC	2 cut(s)	419, 767
AgsI	TTSAA	6 cut(s)	215, 454, 500, 574, 608, 847
AhlI	ACTAGT	1 cut(s)	589
AjiI	CACGTC	1 cut(s)	377
AjnI	CCWGG	1 cut(s)	795
AluBI	AGCT	7 cut(s)	12, 18, 388, 479, 850, 1105, 1127
AluI	AGCT	7 cut(s)	12, 18, 388, 479, 850, 1105, 1127
Alw21I	GWGCWC	3 cut(s)	382, 390, 1129
Alw26I	GTCTC	2 cut(s)	56, 192
AlwI	GGATC	3 cut(s)	293, 872, 1116
Ama87I	CYCGRG	2 cut(s)	189, 383
AoxI	GGCC	6 cut(s)	245, 270, 303, 793, 798, 983
ApoI	RAATTY	3 cut(s)	155, 946, 1070
AspS9I	GGNCC	4 cut(s)	120, 245, 303, 457
AsuHPI	GGTGA	4 cut(s)	305, 341, 626, 934
AvaI	CYCGRG	2 cut(s)	189, 383
AvaII	GGWCC	2 cut(s)	120, 457
BaeGI	GKGCMC	1 cut(s)	565
BaeI	ACNNNNGTAYC	2 cut(s)	757, 790
BalI	TGGCCA	1 cut(s)	985
BanI	GGYRCC	1 cut(s)	560
BanII	GRGCYC	2 cut(s)	390, 1129
BauI	CACGAG	1 cut(s)	126
BbsI	GAAGAC	2 cut(s)	330, 592
Bbv12I	GWGCWC	3 cut(s)	382, 390, 1129
BccI	CCATC	4 cut(s)	76, 160, 670, 889
BciT130I	CCWGG	1 cut(s)	797
BciVI	GTATCC	1 cut(s)	820
BclI	TGATCA	1 cut(s)	262
BcoDI	GTCTC	2 cut(s)	56, 192
BcuI	ACTAGT	1 cut(s)	589
BfaI	CTAG	6 cut(s)	320, 519, 590, 665, 734, 746
BfuI	GTATCC	1 cut(s)	820
Bme1390I	CCNGG	1 cut(s)	797
Bme18I	GGWCC	2 cut(s)	120, 457
BmeT110I	CYCGRG	2 cut(s)	189, 383
BmgBI	CACGTC	1 cut(s)	377
BmgT120I	GGNCC	4 cut(s)	120, 245, 303, 457
BmiI	GGNNCC	4 cut(s)	25, 304, 550, 562
BmrFI	CCNGG	1 cut(s)	797
BmrI	ACTGGG	2 cut(s)	67, 644
BmuI	ACTGGG	2 cut(s)	67, 644
BpiI	GAAGAC	2 cut(s)	330, 592
BplI	GAGNNNNNCTC	2 cut(s)	122, 154
Bpu10I	CCTNAGC	1 cut(s)	19
Bsa29I	ATCGAT	1 cut(s)	1111
BsaAI	YACGTR	1 cut(s)	627
BsaJI	CCNNGG	2 cut(s)	28, 544
BsaWI	WCCGGW	1 cut(s)	785
BsaXI	ACNNNNNCTCC	2 cut(s)	678, 708
Bse118I	RCCGGY	1 cut(s)	290
Bse1I	ACTGG	4 cut(s)	62, 460, 639, 954
BseBI	CCWGG	1 cut(s)	797
BseCI	ATCGAT	1 cut(s)	1111
BseDI	CCNNGG	2 cut(s)	28, 544
BseGI	GGATG	3 cut(s)	685, 844, 1140
BseMII	CTCAG	2 cut(s)	33, 663
BseNI	ACTGG	4 cut(s)	62, 460, 639, 954
BseSI	GKGCMC	1 cut(s)	565
BseYI	CCCAGC	1 cut(s)	146
Bsh1285I	CGRYCG	1 cut(s)	1115
BshFI	GGCC	6 cut(s)	247, 272, 305, 795, 800, 985
BshNI	GGYRCC	1 cut(s)	560
BshVI	ATCGAT	1 cut(s)	1111
BsiEI	CGRYCG	1 cut(s)	1115
BsiHKAI	GWGCWC	3 cut(s)	382, 390, 1129
BsiHKCI	CYCGRG	2 cut(s)	189, 383
BsiSI	CCGG	2 cut(s)	291, 786
BslFI	GGGAC	1 cut(s)	942
BsmAI	GTCTC	2 cut(s)	56, 192
BsmFI	GGGAC	1 cut(s)	942
BsnI	GGCC	6 cut(s)	247, 272, 305, 795, 800, 985
BsoBI	CYCGRG	2 cut(s)	189, 383
Bsp1286I	GDGCHC	4 cut(s)	382, 390, 565, 1129
Bsp143I	GATC	5 cut(s)	262, 285, 877, 1108, 1112
Bsp19I	CCATGG	1 cut(s)	28
BspACI	CCGC	4 cut(s)	421, 611, 650, 1052
BspANI	GGCC	6 cut(s)	247, 272, 305, 795, 800, 985
BspCNI	CTCAG	2 cut(s)	32, 664
BspDI	ATCGAT	1 cut(s)	1111
BspHI	TCATGA	1 cut(s)	657
BspLI	GGNNCC	4 cut(s)	25, 304, 550, 562
BspPI	GGATC	3 cut(s)	293, 872, 1116
BspT107I	GGYRCC	1 cut(s)	560
BsrFI	RCCGGY	1 cut(s)	290
BsrI	ACTGG	4 cut(s)	62, 460, 639, 954
BssAI	RCCGGY	1 cut(s)	290
BssECI	CCNNGG	2 cut(s)	28, 544
BssMI	GATC	5 cut(s)	262, 285, 877, 1108, 1112
BssSI	CACGAG	1 cut(s)	126
BssT1I	CCWWGG	1 cut(s)	28
Bst2BI	CACGAG	1 cut(s)	126
Bst2UI	CCWGG	1 cut(s)	797
Bst4CI	ACNGT	7 cut(s)	89, 256, 329, 553, 875, 941, 1100
BstBAI	YACGTR	1 cut(s)	627
BstDEI	CTNAG	3 cut(s)	19, 465, 672
BstDSI	CCRYGG	1 cut(s)	28
BstF5I	GGATG	3 cut(s)	685, 844, 1140
BstKTI	GATC	5 cut(s)	265, 288, 880, 1111, 1115
BstMAI	GTCTC	2 cut(s)	56, 192
BstMBI	GATC	5 cut(s)	262, 285, 877, 1108, 1112
BstMCI	CGRYCG	1 cut(s)	1115
BstMWI	GCNNNNNNNGC	1 cut(s)	429
BstNI	CCWGG	1 cut(s)	797
BstNSI	RCATGY	1 cut(s)	448
BstSCI	CCNGG	1 cut(s)	795
BstSLI	GKGCMC	1 cut(s)	565
BstV2I	GAAGAC	2 cut(s)	330, 592
Bsu15I	ATCGAT	1 cut(s)	1111
BsuI	GTATCC	1 cut(s)	820
BsuRI	GGCC	6 cut(s)	247, 272, 305, 795, 800, 985
BsuTUI	ATCGAT	1 cut(s)	1111
BtgI	CCRYGG	1 cut(s)	28
BtrI	CACGTC	1 cut(s)	377
BtsCI	GGATG	3 cut(s)	685, 844, 1140
BtsIMutI	CAGTG	2 cut(s)	184, 1105
CciI	TCATGA	1 cut(s)	657
Cfr10I	RCCGGY	1 cut(s)	290
Cfr13I	GGNCC	4 cut(s)	120, 245, 303, 457
ClaI	ATCGAT	1 cut(s)	1111
CseI	GACGC	1 cut(s)	1099
Csp6I	GTAC	2 cut(s)	418, 766
CviAII	CATG	3 cut(s)	29, 445, 658
CviQI	GTAC	2 cut(s)	418, 766
DdeI	CTNAG	3 cut(s)	19, 465, 672
DpnI	GATC	5 cut(s)	264, 287, 879, 1110, 1114
DpnII	GATC	5 cut(s)	262, 285, 877, 1108, 1112
EaeI	YGGCCR	1 cut(s)	983
Ecl136II	GAGCTC	2 cut(s)	388, 1127
Eco130I	CCWWGG	1 cut(s)	28
Eco24I	GRGCYC	2 cut(s)	390, 1129
Eco47I	GGWCC	2 cut(s)	120, 457
Eco53kI	GAGCTC	2 cut(s)	388, 1127
Eco57I	CTGAAG	1 cut(s)	999
Eco88I	CYCGRG	2 cut(s)	189, 383
EcoICRI	GAGCTC	2 cut(s)	388, 1127
EcoO109I	RGGNCCY	1 cut(s)	120
EcoRII	CCWGG	1 cut(s)	795
EcoT14I	CCWWGG	1 cut(s)	28
EcoT38I	GRGCYC	2 cut(s)	390, 1129
ErhI	CCWWGG	1 cut(s)	28
FaeI	CATG	3 cut(s)	32, 448, 661
FaqI	GGGAC	1 cut(s)	942
FatI	CATG	3 cut(s)	28, 444, 657
FauI	CCCGC	2 cut(s)	604, 657
FbaI	TGATCA	1 cut(s)	262
FblI	GTMKAC	1 cut(s)	135
FokI	GGATG	3 cut(s)	692, 851, 1127
FriOI	GRGCYC	2 cut(s)	390, 1129
FspBI	CTAG	6 cut(s)	320, 519, 590, 665, 734, 746
GsaI	CCCAGC	1 cut(s)	150
HaeIII	GGCC	6 cut(s)	247, 272, 305, 795, 800, 985
HapII	CCGG	2 cut(s)	291, 786
HgaI	GACGC	1 cut(s)	1099
Hin1II	CATG	3 cut(s)	32, 448, 661
HincII	GTYRAC	1 cut(s)	85
HindII	GTYRAC	1 cut(s)	85
HinfI	GANTC	2 cut(s)	661, 742
HpaII	CCGG	2 cut(s)	291, 786
HphI	GGTGA	4 cut(s)	305, 341, 626, 934
Hpy166II	GTNNAC	4 cut(s)	85, 136, 418, 871
Hpy188I	TCNGA	2 cut(s)	225, 1018
Hpy8I	GTNNAC	4 cut(s)	85, 136, 418, 871
Hpy99I	CGWCG	3 cut(s)	245, 315, 378
HpyAV	CCTTC	5 cut(s)	292, 401, 406, 1023, 1130
HpyCH4III	ACNGT	7 cut(s)	89, 256, 329, 553, 875, 941, 1100
HpyCH4IV	ACGT	4 cut(s)	310, 376, 528, 626
HpyCH4V	TGCA	4 cut(s)	405, 510, 536, 630
HpyF10VI	GCNNNNNNNGC	1 cut(s)	429
HpyF3I	CTNAG	3 cut(s)	19, 465, 672
HpySE526I	ACGT	4 cut(s)	310, 376, 528, 626
Hsp92II	CATG	3 cut(s)	32, 448, 661
Ksp22I	TGATCA	1 cut(s)	262
Kzo9I	GATC	5 cut(s)	262, 285, 877, 1108, 1112
LmnI	GCTCC	3 cut(s)	29, 393, 1124
MaeI	CTAG	6 cut(s)	320, 519, 590, 665, 734, 746
MaeII	ACGT	4 cut(s)	310, 376, 528, 626
MaeIII	GTNAC	2 cut(s)	329, 667
MalI	GATC	5 cut(s)	264, 287, 879, 1110, 1114
MboI	GATC	5 cut(s)	262, 285, 877, 1108, 1112
MboII	GAAGA	3 cut(s)	335, 597, 1054
MfeI	CAATTG	2 cut(s)	210, 595
MhlI	GDGCHC	4 cut(s)	382, 390, 565, 1129
MlsI	TGGCCA	1 cut(s)	985
MluCI	AATT	8 cut(s)	155, 210, 575, 595, 737, 946, 1046, 1070
MluNI	TGGCCA	1 cut(s)	985
MlyI	GAGTC	1 cut(s)	736
MmeI	TCCRAC	1 cut(s)	664
MnlI	CCTC	8 cut(s)	73, 124, 133, 199, 283, 539, 574, 1012
Mox20I	TGGCCA	1 cut(s)	985
MscI	TGGCCA	1 cut(s)	985
MseI	TTAA	2 cut(s)	234, 1005
Msp20I	TGGCCA	1 cut(s)	985
MspI	CCGG	2 cut(s)	291, 786
MspR9I	CCNGG	1 cut(s)	797
MunI	CAATTG	2 cut(s)	210, 595
MvaI	CCWGG	1 cut(s)	797
MwoI	GCNNNNNNNGC	1 cut(s)	429
NcoI	CCATGG	1 cut(s)	28
NdeII	GATC	5 cut(s)	262, 285, 877, 1108, 1112
NlaIII	CATG	3 cut(s)	32, 448, 661
NlaIV	GGNNCC	4 cut(s)	25, 304, 550, 562
NmuCI	GTSAC	2 cut(s)	329, 667
NspI	RCATGY	1 cut(s)	448
PaeR7I	CTCGAG	2 cut(s)	189, 383
PagI	TCATGA	1 cut(s)	657
PfeI	GAWTC	1 cut(s)	661
Ple19I	CGATCG	1 cut(s)	1115
PleI	GAGTC	1 cut(s)	736
PpsI	GAGTC	1 cut(s)	736
Ppu21I	YACGTR	1 cut(s)	627
PpuMI	RGGWCCY	1 cut(s)	120
Psp124BI	GAGCTC	2 cut(s)	390, 1129
Psp5II	RGGWCCY	1 cut(s)	120
Psp6I	CCWGG	1 cut(s)	795
PspFI	CCCAGC	1 cut(s)	146
PspGI	CCWGG	1 cut(s)	795
PspN4I	GGNNCC	4 cut(s)	25, 304, 550, 562
PspPI	GGNCC	4 cut(s)	120, 245, 303, 457
PspPPI	RGGWCCY	1 cut(s)	120
PvuI	CGATCG	1 cut(s)	1115
RsaI	GTAC	2 cut(s)	419, 767
RsaNI	GTAC	2 cut(s)	418, 766
SacI	GAGCTC	2 cut(s)	390, 1129
SaqAI	TTAA	2 cut(s)	234, 1005
Sau3AI	GATC	5 cut(s)	262, 285, 877, 1108, 1112
Sau96I	GGNCC	4 cut(s)	120, 245, 303, 457
SchI	GAGTC	1 cut(s)	736
ScrFI	CCNGG	1 cut(s)	797
SduI	GDGCHC	4 cut(s)	382, 390, 565, 1129
Sfr274I	CTCGAG	2 cut(s)	189, 383
SgrAI	CRCCGGYG	1 cut(s)	290
SinI	GGWCC	2 cut(s)	120, 457
SlaI	CTCGAG	2 cut(s)	189, 383
SmlI	CTYRAG	3 cut(s)	13, 189, 383
SmoI	CTYRAG	3 cut(s)	13, 189, 383
SpeI	ACTAGT	1 cut(s)	589
Sse9I	AATT	8 cut(s)	155, 210, 575, 595, 737, 946, 1046, 1070
SsiI	CCGC	4 cut(s)	421, 611, 650, 1052
SspI	AATATT	3 cut(s)	232, 604, 722
SspMI	CTAG	6 cut(s)	320, 519, 590, 665, 734, 746
SstI	GAGCTC	2 cut(s)	390, 1129
StyD4I	CCNGG	1 cut(s)	795
StyI	CCWWGG	1 cut(s)	28
TaaI	ACNGT	7 cut(s)	89, 256, 329, 553, 875, 941, 1100
TaiI	ACGT	4 cut(s)	313, 379, 531, 629
TaqI	TCGA	3 cut(s)	190, 384, 1111
TaqII	GACCGA	1 cut(s)	558
TasI	AATT	8 cut(s)	155, 210, 575, 595, 737, 946, 1046, 1070
TfiI	GAWTC	1 cut(s)	661
Tru1I	TTAA	2 cut(s)	234, 1005
Tru9I	TTAA	2 cut(s)	234, 1005
TscAI	CASTG	2 cut(s)	184, 1105
TseFI	GTSAC	2 cut(s)	329, 667
Tsp45I	GTSAC	2 cut(s)	329, 667
TspDTI	ATGAA	3 cut(s)	149, 646, 674
TspGWI	ACGGA	3 cut(s)	60, 298, 494
TspRI	CASTG	2 cut(s)	184, 1105
VpaK11BI	GGWCC	2 cut(s)	120, 457
XapI	RAATTY	3 cut(s)	155, 946, 1070
XbaI	TCTAGA	3 cut(s)	319, 733, 745
XceI	RCATGY	1 cut(s)	448
XhoI	CTCGAG	2 cut(s)	189, 383
XmiI	GTMKAC	1 cut(s)	135
XspI	CTAG	6 cut(s)	320, 519, 590, 665, 734, 746

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