Basic Information

Type: gene

Biological Identity

Species

rosa_laevigata

Chromosome

Chr5

Orthogroup ID

OG0007476

Physical Location & Seq

Genomic Coordinates Reverse (-)

49613304 .. 49614567

Gene Structure 1264 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

RLM00000025979

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1086 bp

ATGGCGAACAGCTCAAGCTCAGGCTCCCATGGTGGAAACCGTAACGGAGTTCCCAACTGGGAGACACCATCAAGAGTTGAGGTCAACCGTAAATCACAAGAGTTCCTACTTTGGTATAAGACCTCTCGTGAGGTCTACTCCACCCCCAGCGATAAATTTCATAAGATGGTCAAGGTCAGTGAGATGTCTCGAGAGCAAGTATTGGAGGCAATTGAAAAGTATCAGAAAAATATTAAGAACGACGGGCCAAACACAGTCGTTGATCAATCGGCCTCAAACACACGGATCGCCGGTGAGAAGGGGGCCAAACGTCGTATTCTAGAAGACGGTCATGAGAAAGTTTGCCACCCAACACAAAAAACAAGGAAAAGATTGCGACGTGCTCTCGAGCTCCTTCACTCGTTCTGCAAAGAGAAGGTGTACCGCACACTACGCTCATTCTTTTACATGGATGTCTCGCTTTTCAAGGACCAGTCTAAGACTAATAAAGCTATCAATCAAGTCTGTGTTGAACTCCGTTGCACCCGTTCTAGTCTAAACGTCTTTGCAACAGACCGAGGAACCGTCATAGGTCCCCTTTCTTTCAAATTGGAGGGAAGACCAGTCAATTGTAATATTGAAGCGGGTGATGATATTACGTGCAAACTGGGGCAGATTATCCCGCCATTCATGAATCTAGTGACTGAGATGGAGGTTGGAGATGATACTGTGATCGATCCATCGGGCATTGAGATTTCAGCAGTTGTCAAGCACTGTTCGGTGAATATGCCGTATGACAGTCAAAATTTAGCCAGTCCCTTGATGTATTGGTTAGGTATTTGGCCAAGCGATTTGGAAAATCTTAATATACCTTCAGAGGAGTTACTCAAGACAGATTTGAAGAAAATAGCGGAATTGATAAAGGAAGAATTTGTGAATGATGATATGACGCTGAAAAGTGAGCTGGGTCGTATGGCGGAGTTCCAAAAGAAGGCATCCCTTGAAAATTTGAGTGCTCTGGGGACTCACTGCCTGTATAGAAATTATTTGCCATATAAACTGTACAAGACGATGAACCAGATTATGCAAGGTAATACTGGAGCCTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0000228 GO:0000280 GO:0000706 GO:0000729 GO:0001708 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:0008150 GO:0008152 GO:0008544 GO:0009888 GO:0009913 GO:0009957 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:0030154 GO:0030855 GO:0031974 GO:0031981 GO:0032502 GO:0033554 GO:0034641 GO:0035825 GO:0042138 GO:0042623 GO:0042802 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:0045165 GO:0046483 GO:0048285 GO:0048856 GO:0048869 GO:0050896 GO:0051321 GO:0051716 GO:0060429 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

362

Amino Acids

40.96

Weight (kDa)

8.63

Isoelectric Point (pI)

46.91

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
TP6A_N	PF04406	125 - 181	2.8e-13	Type IIB DNA topoisomerase
TOP6A-Spo11_Toprim	PF21180	238 - 347	1.4e-23	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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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)
AccI	GTMKAC	1 cut(s)	135
AciI	CCGC	5 cut(s)	424, 623, 662, 890, 956
AclWI	GGATC	2 cut(s)	293, 710
AcoI	YGGCCR	1 cut(s)	821
AcsI	RAATTY	4 cut(s)	155, 784, 908, 985
AcuI	CTGAAG	1 cut(s)	837
AfaI	GTAC	2 cut(s)	422, 1043
AfiI	CCNNNNNNNGG	1 cut(s)	970
AgsI	TTSAA	7 cut(s)	215, 466, 512, 586, 620, 880, 983
AjiI	CACGTC	1 cut(s)	380
AluBI	AGCT	5 cut(s)	12, 18, 391, 491, 943
AluI	AGCT	5 cut(s)	12, 18, 391, 491, 943
Alw21I	GWGCWC	3 cut(s)	385, 393, 997
Alw26I	GTCTC	3 cut(s)	56, 192, 460
AlwI	GGATC	2 cut(s)	293, 710
Ama87I	CYCGRG	2 cut(s)	189, 386
AoxI	GGCC	4 cut(s)	245, 270, 303, 821
ApoI	RAATTY	4 cut(s)	155, 784, 908, 985
AspS9I	GGNCC	4 cut(s)	245, 303, 469, 572
AsuHPI	GGTGA	3 cut(s)	305, 638, 772
AvaI	CYCGRG	2 cut(s)	189, 386
AvaII	GGWCC	2 cut(s)	469, 572
BalI	TGGCCA	1 cut(s)	823
BanII	GRGCYC	1 cut(s)	393
BauI	CACGAG	1 cut(s)	126
BbsI	GAAGAC	2 cut(s)	330, 604
Bbv12I	GWGCWC	3 cut(s)	385, 393, 997
BccI	CCATC	4 cut(s)	76, 160, 682, 727
BceAI	ACGGC	1 cut(s)	754
BclI	TGATCA	1 cut(s)	262
BcoDI	GTCTC	3 cut(s)	56, 192, 460
BfaI	CTAG	3 cut(s)	320, 531, 677
Bme18I	GGWCC	2 cut(s)	469, 572
BmeT110I	CYCGRG	2 cut(s)	189, 386
BmgBI	CACGTC	1 cut(s)	380
BmgT120I	GGNCC	4 cut(s)	245, 303, 469, 572
BmiI	GGNNCC	5 cut(s)	25, 304, 562, 574, 1081
BmrI	ACTGGG	2 cut(s)	67, 656
BmsI	GCATC	1 cut(s)	983
BmuI	ACTGGG	2 cut(s)	67, 656
BpiI	GAAGAC	2 cut(s)	330, 604
BplI	GAGNNNNNCTC	2 cut(s)	122, 154
Bpu10I	CCTNAGC	1 cut(s)	19
BpuEI	CTTGAG	1 cut(s)	851
Bsa29I	ATCGAT	1 cut(s)	714
BsaAI	YACGTR	1 cut(s)	639
BsaJI	CCNNGG	2 cut(s)	28, 556
Bsc4I	CCNNNNNNNGG	1 cut(s)	970
Bse118I	RCCGGY	1 cut(s)	290
Bse1I	ACTGG	6 cut(s)	62, 472, 602, 651, 792, 1081
BseCI	ATCGAT	1 cut(s)	714
BseDI	CCNNGG	2 cut(s)	28, 556
BseGI	GGATG	2 cut(s)	457, 974
BseLI	CCNNNNNNNGG	1 cut(s)	970
BseMII	CTCAG	2 cut(s)	33, 675
BseNI	ACTGG	6 cut(s)	62, 472, 602, 651, 792, 1081
BseRI	GAGGAG	1 cut(s)	872
BseYI	CCCAGC	2 cut(s)	146, 943
BshFI	GGCC	4 cut(s)	247, 272, 305, 823
BshVI	ATCGAT	1 cut(s)	714
BsiHKAI	GWGCWC	3 cut(s)	385, 393, 997
BsiHKCI	CYCGRG	2 cut(s)	189, 386
BsiSI	CCGG	1 cut(s)	291
BslFI	GGGAC	3 cut(s)	558, 780, 1015
BslI	CCNNNNNNNGG	1 cut(s)	970
BsmAI	GTCTC	3 cut(s)	56, 192, 460
BsmFI	GGGAC	3 cut(s)	558, 780, 1015
BsnI	GGCC	4 cut(s)	247, 272, 305, 823
BsoBI	CYCGRG	2 cut(s)	189, 386
Bsp1286I	GDGCHC	3 cut(s)	385, 393, 997
Bsp1407I	TGTACA	1 cut(s)	1041
Bsp143I	GATC	4 cut(s)	262, 285, 711, 715
Bsp19I	CCATGG	1 cut(s)	28
BspACI	CCGC	5 cut(s)	424, 623, 662, 890, 956
BspANI	GGCC	4 cut(s)	247, 272, 305, 823
BspCNI	CTCAG	2 cut(s)	32, 676
BspDI	ATCGAT	1 cut(s)	714
BspHI	TCATGA	2 cut(s)	331, 669
BspLI	GGNNCC	5 cut(s)	25, 304, 562, 574, 1081
BspPI	GGATC	2 cut(s)	293, 710
BsrFI	RCCGGY	1 cut(s)	290
BsrGI	TGTACA	1 cut(s)	1041
BsrI	ACTGG	6 cut(s)	62, 472, 602, 651, 792, 1081
BssAI	RCCGGY	1 cut(s)	290
BssECI	CCNNGG	2 cut(s)	28, 556
BssMI	GATC	4 cut(s)	262, 285, 711, 715
BssSI	CACGAG	1 cut(s)	126
BssT1I	CCWWGG	1 cut(s)	28
Bst2BI	CACGAG	1 cut(s)	126
Bst4CI	ACNGT	9 cut(s)	41, 89, 256, 329, 565, 709, 755, 779, 1041
BstAUI	TGTACA	1 cut(s)	1041
BstBAI	YACGTR	1 cut(s)	639
BstDEI	CTNAG	3 cut(s)	19, 477, 684
BstDSI	CCRYGG	1 cut(s)	28
BstF5I	GGATG	2 cut(s)	457, 974
BstKTI	GATC	4 cut(s)	265, 288, 714, 718
BstMAI	GTCTC	3 cut(s)	56, 192, 460
BstMBI	GATC	4 cut(s)	262, 285, 711, 715
BstMWI	GCNNNNNNNGC	1 cut(s)	432
BstV2I	GAAGAC	2 cut(s)	330, 604
Bsu15I	ATCGAT	1 cut(s)	714
BsuRI	GGCC	4 cut(s)	247, 272, 305, 823
BsuTUI	ATCGAT	1 cut(s)	714
BtgI	CCRYGG	1 cut(s)	28
BtrI	CACGTC	1 cut(s)	380
BtsCI	GGATG	2 cut(s)	457, 974
BtsI	GCAGTG	1 cut(s)	1006
BtsIMutI	CAGTG	3 cut(s)	184, 751, 1006
CciI	TCATGA	2 cut(s)	331, 669
Cfr10I	RCCGGY	1 cut(s)	290
Cfr13I	GGNCC	4 cut(s)	245, 303, 469, 572
ClaI	ATCGAT	1 cut(s)	714
CseI	GACGC	1 cut(s)	937
Csp6I	GTAC	2 cut(s)	421, 1042
CviAII	CATG	4 cut(s)	29, 332, 448, 670
CviQI	GTAC	2 cut(s)	421, 1042
DdeI	CTNAG	3 cut(s)	19, 477, 684
DpnI	GATC	4 cut(s)	264, 287, 713, 717
DpnII	GATC	4 cut(s)	262, 285, 711, 715
EaeI	YGGCCR	1 cut(s)	821
EciI	GGCGGA	1 cut(s)	971
Ecl136II	GAGCTC	1 cut(s)	391
Eco130I	CCWWGG	1 cut(s)	28
Eco24I	GRGCYC	1 cut(s)	393
Eco47I	GGWCC	2 cut(s)	469, 572
Eco53kI	GAGCTC	1 cut(s)	391
Eco57I	CTGAAG	1 cut(s)	837
Eco88I	CYCGRG	2 cut(s)	189, 386
EcoICRI	GAGCTC	1 cut(s)	391
EcoO109I	RGGNCCY	1 cut(s)	572
EcoT14I	CCWWGG	1 cut(s)	28
EcoT38I	GRGCYC	1 cut(s)	393
ErhI	CCWWGG	1 cut(s)	28
FaeI	CATG	4 cut(s)	32, 335, 451, 673
FaqI	GGGAC	3 cut(s)	558, 780, 1015
FatI	CATG	4 cut(s)	28, 331, 447, 669
FauI	CCCGC	2 cut(s)	616, 669
FbaI	TGATCA	1 cut(s)	262
FblI	GTMKAC	1 cut(s)	135
FokI	GGATG	2 cut(s)	464, 961
FriOI	GRGCYC	1 cut(s)	393
FspBI	CTAG	3 cut(s)	320, 531, 677
GsaI	CCCAGC	2 cut(s)	150, 947
HaeIII	GGCC	4 cut(s)	247, 272, 305, 823
HapII	CCGG	1 cut(s)	291
HgaI	GACGC	1 cut(s)	937
Hin1II	CATG	4 cut(s)	32, 335, 451, 673
HincII	GTYRAC	1 cut(s)	85
HindII	GTYRAC	1 cut(s)	85
HinfI	GANTC	2 cut(s)	673, 1003
HpaII	CCGG	1 cut(s)	291
HphI	GGTGA	3 cut(s)	305, 638, 772
Hpy166II	GTNNAC	3 cut(s)	85, 136, 421
Hpy188I	TCNGA	2 cut(s)	225, 856
Hpy188III	TCNNGA	9 cut(s)	72, 128, 189, 191, 320, 332, 386, 670, 868
Hpy8I	GTNNAC	3 cut(s)	85, 136, 421
Hpy99I	CGWCG	3 cut(s)	245, 315, 381
HpyAV	CCTTC	5 cut(s)	292, 404, 409, 861, 964
HpyCH4III	ACNGT	9 cut(s)	41, 89, 256, 329, 565, 709, 755, 779, 1041
HpyCH4IV	ACGT	4 cut(s)	310, 379, 540, 638
HpyCH4V	TGCA	5 cut(s)	408, 522, 548, 642, 1066
HpyF10VI	GCNNNNNNNGC	1 cut(s)	432
HpyF3I	CTNAG	3 cut(s)	19, 477, 684
HpySE526I	ACGT	4 cut(s)	310, 379, 540, 638
Hsp92II	CATG	4 cut(s)	32, 335, 451, 673
Ksp22I	TGATCA	1 cut(s)	262
Kzo9I	GATC	4 cut(s)	262, 285, 711, 715
LmnI	GCTCC	3 cut(s)	29, 396, 1079
LweI	GCATC	1 cut(s)	983
MaeI	CTAG	3 cut(s)	320, 531, 677
MaeII	ACGT	4 cut(s)	310, 379, 540, 638
MaeIII	GTNAC	3 cut(s)	41, 679, 861
MalI	GATC	4 cut(s)	264, 287, 713, 717
MboI	GATC	4 cut(s)	262, 285, 711, 715
MboII	GAAGA	4 cut(s)	335, 609, 892, 917
MfeI	CAATTG	2 cut(s)	210, 607
MhlI	GDGCHC	3 cut(s)	385, 393, 997
MlsI	TGGCCA	1 cut(s)	823
MluCI	AATT	9 cut(s)	155, 210, 587, 607, 784, 893, 908, 985, 1021
MluNI	TGGCCA	1 cut(s)	823
MlyI	GAGTC	1 cut(s)	997
MmeI	TCCRAC	1 cut(s)	676
MnlI	CCTC	9 cut(s)	73, 124, 133, 199, 283, 551, 586, 685, 850
Mox20I	TGGCCA	1 cut(s)	823
MscI	TGGCCA	1 cut(s)	823
MseI	TTAA	2 cut(s)	234, 843
Msp20I	TGGCCA	1 cut(s)	823
MspI	CCGG	1 cut(s)	291
MunI	CAATTG	2 cut(s)	210, 607
MwoI	GCNNNNNNNGC	1 cut(s)	432
NcoI	CCATGG	1 cut(s)	28
NdeII	GATC	4 cut(s)	262, 285, 711, 715
NlaIII	CATG	4 cut(s)	32, 335, 451, 673
NlaIV	GGNNCC	5 cut(s)	25, 304, 562, 574, 1081
NmuCI	GTSAC	1 cut(s)	679
PaeR7I	CTCGAG	2 cut(s)	189, 386
PagI	TCATGA	2 cut(s)	331, 669
PfeI	GAWTC	1 cut(s)	673
PleI	GAGTC	1 cut(s)	997
PpsI	GAGTC	1 cut(s)	997
Ppu21I	YACGTR	1 cut(s)	639
PpuMI	RGGWCCY	1 cut(s)	572
Psp124BI	GAGCTC	1 cut(s)	393
Psp5II	RGGWCCY	1 cut(s)	572
PspFI	CCCAGC	2 cut(s)	146, 943
PspN4I	GGNNCC	5 cut(s)	25, 304, 562, 574, 1081
PspPI	GGNCC	4 cut(s)	245, 303, 469, 572
PspPPI	RGGWCCY	1 cut(s)	572
RsaI	GTAC	2 cut(s)	422, 1043
RsaNI	GTAC	2 cut(s)	421, 1042
SacI	GAGCTC	1 cut(s)	393
SaqAI	TTAA	2 cut(s)	234, 843
Sau3AI	GATC	4 cut(s)	262, 285, 711, 715
Sau96I	GGNCC	4 cut(s)	245, 303, 469, 572
SchI	GAGTC	1 cut(s)	997
SduI	GDGCHC	3 cut(s)	385, 393, 997
SfaNI	GCATC	1 cut(s)	983
Sfr274I	CTCGAG	2 cut(s)	189, 386
SgrAI	CRCCGGYG	1 cut(s)	290
SinI	GGWCC	2 cut(s)	469, 572
SlaI	CTCGAG	2 cut(s)	189, 386
SmlI	CTYRAG	4 cut(s)	13, 189, 386, 866
SmoI	CTYRAG	4 cut(s)	13, 189, 386, 866
Sse9I	AATT	9 cut(s)	155, 210, 587, 607, 784, 893, 908, 985, 1021
SsiI	CCGC	5 cut(s)	424, 623, 662, 890, 956
SspI	AATATT	2 cut(s)	232, 616
SspMI	CTAG	3 cut(s)	320, 531, 677
SstI	GAGCTC	1 cut(s)	393
StyI	CCWWGG	1 cut(s)	28
TaaI	ACNGT	9 cut(s)	41, 89, 256, 329, 565, 709, 755, 779, 1041
TaiI	ACGT	4 cut(s)	313, 382, 543, 641
TaqI	TCGA	3 cut(s)	190, 387, 714
TaqII	GACCGA	1 cut(s)	570
TasI	AATT	9 cut(s)	155, 210, 587, 607, 784, 893, 908, 985, 1021
TatI	WGTACW	1 cut(s)	1041
TfiI	GAWTC	1 cut(s)	673
Tru1I	TTAA	2 cut(s)	234, 843
Tru9I	TTAA	2 cut(s)	234, 843
TscAI	CASTG	3 cut(s)	184, 758, 1013
TseFI	GTSAC	1 cut(s)	679
Tsp45I	GTSAC	1 cut(s)	679
TspDTI	ATGAA	4 cut(s)	149, 658, 686, 1067
TspGWI	ACGGA	3 cut(s)	60, 298, 506
TspRI	CASTG	3 cut(s)	184, 758, 1013
VpaK11BI	GGWCC	2 cut(s)	469, 572
XapI	RAATTY	4 cut(s)	155, 784, 908, 985
XbaI	TCTAGA	1 cut(s)	319
XhoI	CTCGAG	2 cut(s)	189, 386
XmiI	GTMKAC	1 cut(s)	135
XspI	CTAG	3 cut(s)	320, 531, 677

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