Basic Information

Type: gene

Biological Identity

Species

rosa_laevigata

Chromosome

Chr4

Orthogroup ID

OG0007476

Physical Location & Seq

Genomic Coordinates Reverse (-)

1887517 .. 1891052

Gene Structure 3536 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

RLM00000015854

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1101 bp

ATGGCAAAACCCTTTACAAAATTCCCTGCTGGGTCACACCGGATAAAGAGGAGGTTCACAATAGAACAAAGGAGTTCCTTGCGTGGAAGGAGAAAAAAACGTATTGAAGATGGTTGTTCCCTTGAGTTGGTTGATCAATCAACCTCCAATAAAATCTTCGATGAAGGCCAATCTAGGTCTAACAAAGCCGTTAATCAACTCAGTTGTGAAGTAGGTTGCAGTCATACCAGCCTCAATGTCATCGCAGGAGATCGAGGCTTTGTCGTAGGTCCTTTTACTTTCAGTTTAGACGGAAGACCGGTCGATTGTTACAGTGAATCTGGTCCAAATAATAGGGTCAGAGTTGGACAAGTCGTTCCGCCTTATATGAGTTCTGTTAGCGATATGGAGAATAATGGTGCAAAGTTCGTGTTAGTAGTGGAAAGTGTATCTGTTCATCAAACATTGACGGGGGACAACTTTCATAATGATTATGAGTGTATAATCATGATCGAAAAAGTAATGTCTGTTCTAGCACTTAGAGAATTCGCAAAGTATATAATGGACATGTTCGAGATTTCGGGTGTCCGGCCGACCGACTTAACCACACTTGAAATACCATCCGAGAAGTTGAGTTGCGATGACCAGAGAAAAGGTAGAAAATTGTTGAAGAAGGAGTTTGTAACAAGTGATGAGATGTTGGCGAATCAGCTGGACCACATGGTGATGCGCAGAGAAAAGGCAGACATTTTAGCTTTGAATAATTTCGGGCCGTTCTATGGCCTATCTGATTACTTGCTGTATATAGTGATTGACGACGTGAACAAAGAAAGAAAGAGACAAACAACGTTGAAGGTCGGCCTTACAGAACAAAGAATAAAAAGGATTGAAGATGATGTCGACGGAGCTCGTAAAGTTCACGCAGCCATGAAGCGCCTCATGTTAGCCTTCGACGGTGGTAGTAGGCCTGAAGACCTAACAAGGTTGACGGATGGCATACCTGAGGTCGAGATCAGCCAGGCCAAGCGCGTTGAGTATTTGAACAGGACACATGACCAAATTGTAGAGCTAAAACAAAATAGTATCAAAAAGAGAAGCAAAGTGGTCGGAGCTTCCTACTGA

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

367

Amino Acids

41.48

Weight (kDa)

8.87

Isoelectric Point (pI)

52.01

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
TOP6A-Spo11_Toprim	PF21180	188 - 259	6.1e-07	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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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)
Acc16I	TGCGCA	1 cut(s)	710
AccI	GTMKAC	1 cut(s)	879
AccII	CGCG	1 cut(s)	1008
AciI	CCGC	1 cut(s)	359
AclI	AACGTT	1 cut(s)	827
AcoI	YGGCCR	1 cut(s)	569
AcsI	RAATTY	2 cut(s)	20, 524
AcuI	CTGAAG	1 cut(s)	969
AdeI	CACNNNGTG	1 cut(s)	703
AfiI	CCNNNNNNNGG	2 cut(s)	127, 758
AflIII	ACRYGT	1 cut(s)	546
AgeI	ACCGGT	1 cut(s)	298
AgsI	TTSAA	7 cut(s)	107, 593, 649, 739, 832, 869, 1021
AjiI	CACGTC	1 cut(s)	799
AjnI	CCWGG	1 cut(s)	996
AjuI	GAANNNNNNNTTGG	2 cut(s)	140, 172
AloI	GAACNNNNNNTCC	2 cut(s)	339, 371
AluBI	AGCT	5 cut(s)	691, 734, 887, 1048, 1091
AluI	AGCT	5 cut(s)	691, 734, 887, 1048, 1091
Alw21I	GWGCWC	1 cut(s)	889
Alw26I	GTCTC	1 cut(s)	811
AoxI	GGCC	7 cut(s)	166, 569, 749, 760, 838, 944, 999
ApeKI	GCWGC	1 cut(s)	902
ApoI	RAATTY	2 cut(s)	20, 524
AsiGI	ACCGGT	1 cut(s)	298
Asp700I	GAANNNNTTC	1 cut(s)	743
AspLEI	GCGC	3 cut(s)	711, 915, 1008
AspS9I	GGNCC	4 cut(s)	269, 323, 694, 749
AsuHPI	GGTGA	1 cut(s)	715
AvaII	GGWCC	3 cut(s)	269, 323, 694
AxyI	CCTNAGG	1 cut(s)	981
BanII	GRGCYC	1 cut(s)	889
BbsI	GAAGAC	2 cut(s)	301, 957
Bbv12I	GWGCWC	1 cut(s)	889
BbvI	GCAGC	1 cut(s)	914
BccI	CCATC	3 cut(s)	104, 607, 965
BceAI	ACGGC	2 cut(s)	173, 736
BcgI	CGANNNNNNTGC	2 cut(s)	1066, 1100
BciT130I	CCWGG	1 cut(s)	998
BclI	TGATCA	1 cut(s)	133
BcoDI	GTCTC	1 cut(s)	811
BfaI	CTAG	2 cut(s)	174, 512
BfoI	RGCGCY	1 cut(s)	916
BisI	GCNGC	1 cut(s)	903
BlsI	GCNGC	1 cut(s)	904
Bme1390I	CCNGG	1 cut(s)	998
Bme18I	GGWCC	3 cut(s)	269, 323, 694
BmgBI	CACGTC	1 cut(s)	799
BmgT120I	GGNCC	4 cut(s)	269, 323, 694, 749
BmrFI	CCNGG	1 cut(s)	998
BmsI	GCATC	1 cut(s)	696
BpiI	GAAGAC	2 cut(s)	301, 957
BpuEI	CTTGAG	1 cut(s)	143
BsaWI	WCCGGW	2 cut(s)	39, 298
Bsc4I	CCNNNNNNNGG	2 cut(s)	127, 758
Bse118I	RCCGGY	1 cut(s)	298
Bse21I	CCTNAGG	1 cut(s)	981
BseBI	CCWGG	1 cut(s)	998
BseGI	GGATG	2 cut(s)	599, 976
BseLI	CCNNNNNNNGG	2 cut(s)	127, 758
BseMII	CTCAG	2 cut(s)	214, 972
BseRI	GAGGAG	1 cut(s)	64
BseX3I	CGGCCG	1 cut(s)	569
BseXI	GCAGC	1 cut(s)	914
BseYI	CCCAGC	1 cut(s)	29
Bsh1236I	CGCG	1 cut(s)	1008
Bsh1285I	CGRYCG	3 cut(s)	303, 572, 576
BshFI	GGCC	7 cut(s)	168, 571, 751, 762, 840, 946, 1001
BshTI	ACCGGT	1 cut(s)	298
BsiEI	CGRYCG	3 cut(s)	303, 572, 576
BsiHKAI	GWGCWC	1 cut(s)	889
BsiSI	CCGG	3 cut(s)	40, 299, 568
BslFI	GGGAC	1 cut(s)	467
BslI	CCNNNNNNNGG	2 cut(s)	127, 758
BsmAI	GTCTC	1 cut(s)	811
BsmFI	GGGAC	1 cut(s)	467
BsnI	GGCC	7 cut(s)	168, 571, 751, 762, 840, 946, 1001
Bsp1286I	GDGCHC	1 cut(s)	889
Bsp143I	GATC	4 cut(s)	133, 250, 489, 990
BspACI	CCGC	1 cut(s)	359
BspANI	GGCC	7 cut(s)	168, 571, 751, 762, 840, 946, 1001
BspCNI	CTCAG	2 cut(s)	213, 973
BspFNI	CGCG	1 cut(s)	1008
BspHI	TCATGA	1 cut(s)	486
BsrFI	RCCGGY	1 cut(s)	298
BssAI	RCCGGY	1 cut(s)	298
BssMI	GATC	4 cut(s)	133, 250, 489, 990
Bst2UI	CCWGG	1 cut(s)	998
Bst4CI	ACNGT	2 cut(s)	314, 935
BstDEI	CTNAG	3 cut(s)	200, 518, 981
BstF5I	GGATG	2 cut(s)	599, 976
BstFNI	CGCG	1 cut(s)	1008
BstH2I	RGCGCY	1 cut(s)	916
BstHHI	GCGC	3 cut(s)	711, 915, 1008
BstKTI	GATC	4 cut(s)	136, 253, 492, 993
BstMAI	GTCTC	1 cut(s)	811
BstMBI	GATC	4 cut(s)	133, 250, 489, 990
BstMCI	CGRYCG	3 cut(s)	303, 572, 576
BstNI	CCWGG	1 cut(s)	998
BstNSI	RCATGY	1 cut(s)	550
BstSCI	CCNGG	1 cut(s)	996
BstUI	CGCG	1 cut(s)	1008
BstV1I	GCAGC	1 cut(s)	914
BstV2I	GAAGAC	2 cut(s)	301, 957
BstZI	CGGCCG	1 cut(s)	569
Bsu36I	CCTNAGG	1 cut(s)	981
BsuRI	GGCC	7 cut(s)	168, 571, 751, 762, 840, 946, 1001
BtgZI	GCGATG	2 cut(s)	226, 633
BtrI	CACGTC	1 cut(s)	799
BtsCI	GGATG	2 cut(s)	599, 976
BtsIMutI	CAGTG	1 cut(s)	319
CciI	TCATGA	1 cut(s)	486
CfoI	GCGC	3 cut(s)	711, 915, 1008
Cfr10I	RCCGGY	1 cut(s)	298
Cfr13I	GGNCC	4 cut(s)	269, 323, 694, 749
CspAI	ACCGGT	1 cut(s)	298
CviAII	CATG	6 cut(s)	487, 547, 700, 907, 919, 1031
DdeI	CTNAG	3 cut(s)	200, 518, 981
DpnI	GATC	4 cut(s)	135, 252, 491, 992
DpnII	GATC	4 cut(s)	133, 250, 489, 990
DraIII	CACNNNGTG	1 cut(s)	703
EaeI	YGGCCR	1 cut(s)	569
EagI	CGGCCG	1 cut(s)	569
EciI	GGCGGA	1 cut(s)	348
Ecl136II	GAGCTC	1 cut(s)	887
EclXI	CGGCCG	1 cut(s)	569
Eco147I	AGGCCT	1 cut(s)	946
Eco24I	GRGCYC	1 cut(s)	889
Eco47I	GGWCC	3 cut(s)	269, 323, 694
Eco52I	CGGCCG	1 cut(s)	569
Eco53kI	GAGCTC	1 cut(s)	887
Eco57I	CTGAAG	1 cut(s)	969
Eco81I	CCTNAGG	1 cut(s)	981
EcoICRI	GAGCTC	1 cut(s)	887
EcoO109I	RGGNCCY	1 cut(s)	269
EcoRI	GAATTC	1 cut(s)	524
EcoRII	CCWGG	1 cut(s)	996
EcoT38I	GRGCYC	1 cut(s)	889
FaeI	CATG	6 cut(s)	490, 550, 703, 910, 922, 1034
FaqI	GGGAC	1 cut(s)	467
FatI	CATG	6 cut(s)	486, 546, 699, 906, 918, 1030
FbaI	TGATCA	1 cut(s)	133
FblI	GTMKAC	1 cut(s)	879
Fnu4HI	GCNGC	1 cut(s)	903
FokI	GGATG	2 cut(s)	586, 983
FriOI	GRGCYC	1 cut(s)	889
Fsp4HI	GCNGC	1 cut(s)	903
FspBI	CTAG	2 cut(s)	174, 512
FspI	TGCGCA	1 cut(s)	710
GlaI	GCGC	3 cut(s)	710, 914, 1007
GluI	GCNGC	1 cut(s)	903
GsaI	CCCAGC	1 cut(s)	33
HaeII	RGCGCY	1 cut(s)	916
HaeIII	GGCC	7 cut(s)	168, 571, 751, 762, 840, 946, 1001
HapII	CCGG	3 cut(s)	40, 299, 568
HhaI	GCGC	3 cut(s)	711, 915, 1008
Hin1II	CATG	6 cut(s)	490, 550, 703, 910, 922, 1034
Hin6I	GCGC	3 cut(s)	709, 913, 1006
HinP1I	GCGC	3 cut(s)	709, 913, 1006
HincII	GTYRAC	2 cut(s)	880, 966
HindII	GTYRAC	2 cut(s)	880, 966
HinfI	GANTC	2 cut(s)	317, 685
HpaII	CCGG	3 cut(s)	40, 299, 568
HphI	GGTGA	1 cut(s)	715
Hpy166II	GTNNAC	5 cut(s)	57, 802, 880, 898, 966
Hpy188I	TCNGA	4 cut(s)	341, 604, 769, 1088
Hpy188III	TCNNGA	3 cut(s)	487, 553, 988
Hpy8I	GTNNAC	5 cut(s)	57, 802, 880, 898, 966
Hpy99I	CGWCG	3 cut(s)	800, 884, 935
HpyAV	CCTTC	5 cut(s)	81, 158, 646, 826, 937
HpyCH4III	ACNGT	2 cut(s)	314, 935
HpyCH4IV	ACGT	3 cut(s)	100, 798, 827
HpyCH4V	TGCA	2 cut(s)	219, 401
HpyF3I	CTNAG	3 cut(s)	200, 518, 981
HpySE526I	ACGT	3 cut(s)	100, 798, 827
Hsp92II	CATG	6 cut(s)	490, 550, 703, 910, 922, 1034
HspAI	GCGC	3 cut(s)	709, 913, 1006
Ksp22I	TGATCA	1 cut(s)	133
Kzo9I	GATC	4 cut(s)	133, 250, 489, 990
LmnI	GCTCC	2 cut(s)	884, 1088
Lsp1109I	GCAGC	1 cut(s)	914
LweI	GCATC	1 cut(s)	696
MaeI	CTAG	2 cut(s)	174, 512
MaeII	ACGT	3 cut(s)	100, 798, 827
MaeIII	GTNAC	3 cut(s)	33, 308, 661
MalI	GATC	4 cut(s)	135, 252, 491, 992
MboI	GATC	4 cut(s)	133, 250, 489, 990
MboII	GAAGA	6 cut(s)	119, 148, 306, 661, 881, 962
MhlI	GDGCHC	1 cut(s)	889
MluCI	AATT	5 cut(s)	20, 524, 641, 742, 1038
MmeI	TCCRAC	2 cut(s)	325, 1066
MnlI	CCTC	7 cut(s)	42, 45, 154, 242, 248, 926, 976
MroXI	GAANNNNTTC	1 cut(s)	743
MseI	TTAA	2 cut(s)	192, 581
MslI	CAYNNNNRTG	1 cut(s)	704
MspA1I	CMGCKG	1 cut(s)	691
MspI	CCGG	3 cut(s)	40, 299, 568
MspR9I	CCNGG	1 cut(s)	998
MvaI	CCWGG	1 cut(s)	998
MvnI	CGCG	1 cut(s)	1008
NdeII	GATC	4 cut(s)	133, 250, 489, 990
NlaIII	CATG	6 cut(s)	490, 550, 703, 910, 922, 1034
NmuCI	GTSAC	1 cut(s)	33
NsbI	TGCGCA	1 cut(s)	710
NspI	RCATGY	1 cut(s)	550
PagI	TCATGA	1 cut(s)	486
PceI	AGGCCT	1 cut(s)	946
PciI	ACATGT	1 cut(s)	546
PdmI	GAANNNNTTC	1 cut(s)	743
PfeI	GAWTC	2 cut(s)	317, 685
PinAI	ACCGGT	1 cut(s)	298
PkrI	GCNGC	1 cut(s)	904
PpuMI	RGGWCCY	1 cut(s)	269
PscI	ACATGT	1 cut(s)	546
Psp124BI	GAGCTC	1 cut(s)	889
Psp1406I	AACGTT	1 cut(s)	827
Psp5II	RGGWCCY	1 cut(s)	269
Psp6I	CCWGG	1 cut(s)	996
PspFI	CCCAGC	1 cut(s)	29
PspGI	CCWGG	1 cut(s)	996
PspPI	GGNCC	4 cut(s)	269, 323, 694, 749
PspPPI	RGGWCCY	1 cut(s)	269
PsrI	GAACNNNNNNTAC	2 cut(s)	492, 524
PvuII	CAGCTG	1 cut(s)	691
RseI	CAYNNNNRTG	1 cut(s)	704
SacI	GAGCTC	1 cut(s)	889
SalI	GTCGAC	1 cut(s)	878
SaqAI	TTAA	2 cut(s)	192, 581
SatI	GCNGC	1 cut(s)	903
Sau3AI	GATC	4 cut(s)	133, 250, 489, 990
Sau96I	GGNCC	4 cut(s)	269, 323, 694, 749
ScrFI	CCNGG	1 cut(s)	998
SduI	GDGCHC	1 cut(s)	889
SfaNI	GCATC	1 cut(s)	696
SinI	GGWCC	3 cut(s)	269, 323, 694
SmiMI	CAYNNNNRTG	1 cut(s)	704
SmlI	CTYRAG	1 cut(s)	122
SmoI	CTYRAG	1 cut(s)	122
Sse9I	AATT	5 cut(s)	20, 524, 641, 742, 1038
SseBI	AGGCCT	1 cut(s)	946
SsiI	CCGC	1 cut(s)	359
SspMI	CTAG	2 cut(s)	174, 512
SstI	GAGCTC	1 cut(s)	889
StuI	AGGCCT	1 cut(s)	946
StyD4I	CCNGG	1 cut(s)	996
TaaI	ACNGT	2 cut(s)	314, 935
TaiI	ACGT	3 cut(s)	103, 801, 830
TaqI	TCGA	8 cut(s)	159, 253, 303, 492, 552, 879, 930, 987
TaqII	GACCGA	1 cut(s)	590
TasI	AATT	5 cut(s)	20, 524, 641, 742, 1038
TfiI	GAWTC	2 cut(s)	317, 685
Tru1I	TTAA	2 cut(s)	192, 581
Tru9I	TTAA	2 cut(s)	192, 581
TscAI	CASTG	1 cut(s)	319
TseFI	GTSAC	1 cut(s)	33
TseI	GCWGC	1 cut(s)	902
Tsp45I	GTSAC	1 cut(s)	33
TspDTI	ATGAA	4 cut(s)	177, 425, 452, 923
TspGWI	ACGGA	3 cut(s)	306, 897, 983
TspRI	CASTG	1 cut(s)	319
VpaK11BI	GGWCC	3 cut(s)	269, 323, 694
XapI	RAATTY	2 cut(s)	20, 524
XceI	RCATGY	1 cut(s)	550
XmiI	GTMKAC	1 cut(s)	879
XmnI	GAANNNNTTC	1 cut(s)	743
XspI	CTAG	2 cut(s)	174, 512

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