Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1B

Orthogroup ID

OG0006852

Physical Location & Seq

Genomic Coordinates Forward (+)

46416727 .. 46420542

Gene Structure 3816 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1BG329600.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1728 bp

ATGGAGCTTTCGGTGAAAATTGAAGATGTAGAGTTGACTTCAGATGATGAGGATGATTATGCATCCGCAGATGAAGATGAGTGTAAAATTAAAGTCAAAAGGACAAAGATTACTGATAATTATGCGATATGGGCCACTTTATCTCATAAGGGTCCTATTTTTCCAACTCCATACAAGCCTCATGGGATAAAAGTAAAATATAATGGAGTAGAAGTAGACTTAAATCCTGAACAAGAGGAGCTTGCAACAATGTACGCAGAGTATAGACAAACTCATTTCGGTCATCGTGAGAAGACATTTCAAGAAAATTTTTGGAAAGAATGGCAAGAAATGCTTGGAGGAGAGCATGTAATCAAGGACCTAAGCAGTTGTGACTTTGGAGATATAGAGACATGGCTTGATGATGAGAAGAAGAGGAAAAAAGACATGAAGGACAAAGAGAAGTTGCAAGAAGCGGATGAAGAAATAGAAAATAAATGGGCATATGTGGATGGCAAAAAGATGGAGGTGTCATGCTATCAAATTGAACCACCTGGATTATTTATAGGCCGTGGCAAGCACCCAAAGAATGGAATGTTAAAAAGACGGATCAACCCAAGTGATGTTGTCATCAACATTGGAGATACAAGTCAGACTCCATGTTGTCCAATTCCTGGATGTTGGAAGAAAGTTGTACGCGATCCTCATGTTAAATGGCTCGCATATTGGAAAGATTCAATTTCCGGGAGAAGAAAGTACATGAACTTGAAATATTGCAGCAGTAAGTCTGACATTTCAAAATTTAACACCGCGAGGGAATTAAAGATTAATCAAGCAGAGATCAAGCGACAGTATACAGCGGATTTCACCAGTCTAAATCTTGTGGATAAACAATGTGCAATTGTTACTTATCTTATTGATACATTAGCTTTAAGACCTGGACATGTTAAGGACGAAGAAATTACTGCACCTACTGTTGGATGTTGCACGTTAATGGTGAAAAATGTAATTTTACATGAACCCTCATGTTTGGAGTTTCGCTTTACTGGGAAAGCATCAGTCGACTACGAGAATCAGGTTGAAGTTGAAAACCTTGTGTTTAATTGCATTAAAGAATTCCAGCTTGGAAAATCTCCTGAAGACAATTTGTTTGACAAGTTGGATGCCAAAAAATTGAATGGATATTTACAAAACTTGGGAAAACCTTTTGGCCTCCATTTTACAGCAAAGACATTCCGCACATTTCGAGCATCTGAAATGATGGATGATTTGTTGAACAAGGAAGACTTGAAGGAGAAAACAGAAGAAGATAAGCTTGCTGTTTATTGGGATGCAAACACAGAAGTTGCTATTTTTCTAAATCATCGGAGAGATGTGGCATGTTTTGATTCGAAACAAGTAAATGAGTTTACCGTTCAGATCTTTGAACTAGAGGCGCAAAAATCAAAATTAGAGATTCAAAAAACTCATCCAAGTGATCAATATTATGCCTCTAAAGCGGGAAAACTCTACTTAAACAATGAAATAGAGAAGATAATGAAGAAGATTCATGAGCTGAGTCTAAAAGAGCGTACCATGTCCAGAAGTCACACTTATCGATTAGAAACATCCAGAGAGAATTACCTTGATCCCAGGATTACTGTTGCATGGTGTCTACGACATGGGATTTCAGTTGAAAATATTTTTGACTCGCGTCTCCGAAACAAATTCATTTGGGCAATGGATGTGGAGTCTGATTTTAGATATTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000228 GO:0003674 GO:0003824 GO:0003916 GO:0003917 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005657 GO:0005694 GO:0005730 GO:0006139 GO:0006259 GO:0006260 GO:0006265 GO:0006325 GO:0006338 GO:0006725 GO:0006807 GO:0006996 GO:0007059 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009987 GO:0016020 GO:0016043 GO:0016853 GO:0031298 GO:0031974 GO:0031981 GO:0032991 GO:0034641 GO:0034645 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0043596 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044422 GO:0044424 GO:0044427 GO:0044428 GO:0044446 GO:0044454 GO:0044464 GO:0046483 GO:0051276 GO:0070013 GO:0071103 GO:0071704 GO:0071840 GO:0090304 GO:0140097 GO:1901360 GO:1901576

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

Topo_C_assoc Topoisom_I Topoisom_I_N

Protein Analysis

575

Amino Acids

67.1

Weight (kDa)

6.01

Isoelectric Point (pI)

40.03

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Topoisom_I_N	PF02919	44 - 248	2.5e-68	Eukaryotic DNA topoisomerase I, DNA binding fragment
Topoisom_I	PF01028	254 - 478	9.9e-61	Eukaryotic DNA topoisomerase I, catalytic core
Topo_C_assoc	PF14370	507 - 574	2.3e-20	C-terminal topoisomerase domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0006852)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT4G26701
rosa_chinensis	RchiOBHm_Chr1g0370531 RchiOBHm_Chr4g0420291 RchiOBHm_Chr4g0421651 RchiOBHm_Chr4g0421661
rosa_laevigata	RLG00000007661 RLG00000027031
rosa_multiflora	Rmu_sc0022275.1_g000007 Rmu_sc0026595.1_g000002
rosa_roxburghii	Rroxscaffold_5G00362880 Rroxscaffold_5G00362920
rosa_rugosa	Rorug01G0357400 Rorug04G0161800 Rorug04G0174200
rosa_samantha	Rh1AG366300 Rh1BG328900 Rh1BG329600 Rh1BG329800 Rh1CG342300 Rh1CG342400 Rh1CG343500 Rh1CG343700 Rh4BG236700 Rh4BG236800 Rh4CG248500 Rh4CG248600

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB7I	CCANNNNNTGG	2 cut(s)	569, 653
AccI	GTMKAC	4 cut(s)	216, 833, 1041, 1633
AccII	CGCG	3 cut(s)	678, 791, 1672
AciI	CCGC	6 cut(s)	66, 455, 789, 839, 1216, 1478
AclWI	GGATC	3 cut(s)	596, 674, 1601
AcsI	RAATTY	4 cut(s)	307, 779, 1094, 1685
AcuI	CTGAAG	2 cut(s)	24, 1137
AfaI	GTAC	4 cut(s)	254, 675, 737, 1552
AfiI	CCNNNNNNNGG	3 cut(s)	569, 653, 956
AflIII	ACRYGT	1 cut(s)	922
AjnI	CCWGG	4 cut(s)	532, 652, 916, 1610
AjuI	GAANNNNNNNTTGG	2 cut(s)	1086, 1118
AluBI	AGCT	6 cut(s)	7, 241, 908, 1102, 1294, 1534
AluI	AGCT	6 cut(s)	7, 241, 908, 1102, 1294, 1534
Alw26I	GTCTC	2 cut(s)	383, 1679
AlwI	GGATC	3 cut(s)	596, 674, 1601
AoxI	GGCC	3 cut(s)	132, 547, 1189
ApeKI	GCWGC	1 cut(s)	756
ApoI	RAATTY	4 cut(s)	307, 779, 1094, 1685
ArsI	GACNNNNNNTTYG	2 cut(s)	1112, 1144
AseI	ATTAAT	1 cut(s)	807
AspLEI	GCGC	1 cut(s)	1417
AspS9I	GGNCC	3 cut(s)	132, 152, 358
AsuC2I	CCSGG	1 cut(s)	724
AsuHPI	GGTGA	3 cut(s)	25, 838, 988
AsuII	TTCGAA	1 cut(s)	1370
AvaII	GGWCC	2 cut(s)	152, 358
BbsI	GAAGAC	3 cut(s)	299, 1125, 1269
BbvI	GCAGC	1 cut(s)	768
BccI	CCATC	3 cut(s)	485, 496, 1234
BceAI	ACGGC	1 cut(s)	534
BciT130I	CCWGG	4 cut(s)	534, 654, 918, 1612
BclI	TGATCA	1 cut(s)	1456
BcnI	CCSGG	1 cut(s)	724
BcoDI	GTCTC	2 cut(s)	383, 1679
BfaI	CTAG	1 cut(s)	1409
BglII	AGATCT	1 cut(s)	1398
BisI	GCNGC	1 cut(s)	757
BlsI	GCNGC	1 cut(s)	758
Bme1390I	CCNGG	5 cut(s)	534, 654, 724, 918, 1612
Bme18I	GGWCC	2 cut(s)	152, 358
BmgT120I	GGNCC	3 cut(s)	132, 152, 358
BmiI	GGNNCC	1 cut(s)	153
BmrFI	CCNGG	5 cut(s)	534, 654, 724, 918, 1612
BmrI	ACTGGG	1 cut(s)	1035
BmsI	GCATC	5 cut(s)	71, 1043, 1132, 1238, 1300
BmuI	ACTGGG	1 cut(s)	1035
BoxI	GACNNNNGTC	1 cut(s)	1671
BpiI	GAAGAC	3 cut(s)	299, 1125, 1269
Bpu10I	CCTNAGC	1 cut(s)	362
Bpu14I	TTCGAA	1 cut(s)	1370
BpuMI	CCSGG	1 cut(s)	724
Bsa29I	ATCGAT	1 cut(s)	1576
BsaJI	CCNNGG	2 cut(s)	550, 1610
BsaXI	ACNNNNNCTCC	4 cut(s)	198, 228, 333, 363
Bsc4I	CCNNNNNNNGG	3 cut(s)	569, 653, 956
Bse1I	ACTGG	2 cut(s)	849, 1030
Bse3DI	GCAATG	1 cut(s)	1704
BseBI	CCWGG	4 cut(s)	534, 654, 918, 1612
BseCI	ATCGAT	1 cut(s)	1576
BseDI	CCNNGG	2 cut(s)	550, 1610
BseLI	CCNNNNNNNGG	3 cut(s)	569, 653, 956
BseMI	GCAATG	1 cut(s)	1704
BseMII	CTCAG	1 cut(s)	1526
BseNI	ACTGG	2 cut(s)	849, 1030
BseRI	GAGGAG	2 cut(s)	251, 354
BseXI	GCAGC	1 cut(s)	768
BsgI	GTGCAG	1 cut(s)	930
Bsh1236I	CGCG	3 cut(s)	678, 791, 1672
BshFI	GGCC	3 cut(s)	134, 549, 1191
BshVI	ATCGAT	1 cut(s)	1576
BsiSI	CCGG	1 cut(s)	723
BslI	CCNNNNNNNGG	3 cut(s)	569, 653, 956
BsmAI	GTCTC	2 cut(s)	383, 1679
BsmBI	CGTCTC	1 cut(s)	1679
BsnI	GGCC	3 cut(s)	134, 549, 1191
Bsp119I	TTCGAA	1 cut(s)	1370
Bsp143I	GATC	6 cut(s)	588, 679, 819, 1398, 1456, 1606
BspACI	CCGC	6 cut(s)	66, 455, 789, 839, 1216, 1478
BspANI	GGCC	3 cut(s)	134, 549, 1191
BspCNI	CTCAG	1 cut(s)	1527
BspDI	ATCGAT	1 cut(s)	1576
BspFNI	CGCG	3 cut(s)	678, 791, 1672
BspHI	TCATGA	1 cut(s)	1528
BspLI	GGNNCC	1 cut(s)	153
BspPI	GGATC	3 cut(s)	596, 674, 1601
BspT104I	TTCGAA	1 cut(s)	1370
BsrDI	GCAATG	1 cut(s)	1704
BsrI	ACTGG	2 cut(s)	849, 1030
BssECI	CCNNGG	2 cut(s)	550, 1610
BssMI	GATC	6 cut(s)	588, 679, 819, 1398, 1456, 1606
BssNAI	GTATAC	1 cut(s)	834
Bst1107I	GTATAC	1 cut(s)	834
Bst2UI	CCWGG	4 cut(s)	534, 654, 918, 1612
Bst4CI	ACNGT	4 cut(s)	831, 955, 1393, 1621
Bst6I	CTCTTC	1 cut(s)	407
BstAPI	GCANNNNNTGC	1 cut(s)	331
BstBI	TTCGAA	1 cut(s)	1370
BstC8I	GCNNGC	4 cut(s)	243, 557, 699, 1296
BstDEI	CTNAG	2 cut(s)	362, 1535
BstDSI	CCRYGG	1 cut(s)	550
BstFNI	CGCG	3 cut(s)	678, 791, 1672
BstHHI	GCGC	1 cut(s)	1417
BstKTI	GATC	6 cut(s)	591, 682, 822, 1401, 1459, 1609
BstMAI	GTCTC	2 cut(s)	383, 1679
BstMBI	GATC	6 cut(s)	588, 679, 819, 1398, 1456, 1606
BstMWI	GCNNNNNNNGC	3 cut(s)	131, 331, 1475
BstNI	CCWGG	4 cut(s)	534, 654, 918, 1612
BstNSI	RCATGY	3 cut(s)	350, 926, 1362
BstPAI	GACNNNNGTC	1 cut(s)	1671
BstSCI	CCNGG	5 cut(s)	532, 652, 722, 916, 1610
BstUI	CGCG	3 cut(s)	678, 791, 1672
BstV1I	GCAGC	1 cut(s)	768
BstV2I	GAAGAC	3 cut(s)	299, 1125, 1269
BstX2I	RGATCY	1 cut(s)	1398
BstYI	RGATCY	1 cut(s)	1398
BstZ17I	GTATAC	1 cut(s)	834
Bsu15I	ATCGAT	1 cut(s)	1576
BsuRI	GGCC	3 cut(s)	134, 549, 1191
BsuTUI	ATCGAT	1 cut(s)	1576
BtgI	CCRYGG	1 cut(s)	550
Cac8I	GCNNGC	4 cut(s)	243, 557, 699, 1296
CciI	TCATGA	1 cut(s)	1528
CfoI	GCGC	1 cut(s)	1417
Cfr13I	GGNCC	3 cut(s)	132, 152, 358
ClaI	ATCGAT	1 cut(s)	1576
CseI	GACGC	1 cut(s)	1661
Csp6I	GTAC	4 cut(s)	253, 674, 736, 1551
CspCI	CAANNNNNGTGG	2 cut(s)	1686, 1721
CviQI	GTAC	4 cut(s)	253, 674, 736, 1551
DdeI	CTNAG	2 cut(s)	362, 1535
DpnI	GATC	6 cut(s)	590, 681, 821, 1400, 1458, 1608
DpnII	GATC	6 cut(s)	588, 679, 819, 1398, 1456, 1606
Eam1104I	CTCTTC	1 cut(s)	407
EarI	CTCTTC	1 cut(s)	407
Eco47I	GGWCC	2 cut(s)	152, 358
Eco57I	CTGAAG	2 cut(s)	24, 1137
EcoO109I	RGGNCCY	2 cut(s)	152, 358
EcoRI	GAATTC	1 cut(s)	1094
EcoRII	CCWGG	4 cut(s)	532, 652, 916, 1610
EcoT22I	ATGCAT	1 cut(s)	64
Esp3I	CGTCTC	1 cut(s)	1679
FauI	CCCGC	1 cut(s)	1471
FauNDI	CATATG	1 cut(s)	484
FbaI	TGATCA	1 cut(s)	1456
FblI	GTMKAC	4 cut(s)	216, 833, 1041, 1633
Fnu4HI	GCNGC	1 cut(s)	757
Fsp4HI	GCNGC	1 cut(s)	757
FspBI	CTAG	1 cut(s)	1409
GlaI	GCGC	1 cut(s)	1416
GluI	GCNGC	1 cut(s)	757
HaeIII	GGCC	3 cut(s)	134, 549, 1191
HapII	CCGG	1 cut(s)	723
HgaI	GACGC	1 cut(s)	1661
HhaI	GCGC	1 cut(s)	1417
Hin6I	GCGC	1 cut(s)	1415
HinP1I	GCGC	1 cut(s)	1415
HincII	GTYRAC	2 cut(s)	36, 1042
HindII	GTYRAC	2 cut(s)	36, 1042
HindIII	AAGCTT	1 cut(s)	1292
HinfI	GANTC	9 cut(s)	634, 713, 1051, 1367, 1435, 1525, 1537, 1667, 1709
HpaII	CCGG	1 cut(s)	723
HphI	GGTGA	3 cut(s)	25, 838, 988
Hpy166II	GTNNAC	6 cut(s)	36, 217, 834, 1042, 1389, 1634
Hpy188I	TCNGA	8 cut(s)	43, 633, 769, 1234, 1347, 1398, 1679, 1714
Hpy188III	TCNNGA	7 cut(s)	227, 287, 302, 1115, 1529, 1560, 1590
Hpy8I	GTNNAC	6 cut(s)	36, 217, 834, 1042, 1389, 1634
HpyAV	CCTTC	2 cut(s)	424, 1264
HpyCH4III	ACNGT	4 cut(s)	831, 955, 1393, 1621
HpyCH4IV	ACGT	1 cut(s)	968
HpyF10VI	GCNNNNNNNGC	3 cut(s)	131, 331, 1475
HpyF3I	CTNAG	2 cut(s)	362, 1535
HpySE526I	ACGT	1 cut(s)	968
HspAI	GCGC	1 cut(s)	1415
Ksp22I	TGATCA	1 cut(s)	1456
Kzo9I	GATC	6 cut(s)	588, 679, 819, 1398, 1456, 1606
LmnI	GCTCC	2 cut(s)	4, 238
Lsp1109I	GCAGC	1 cut(s)	768
LweI	GCATC	5 cut(s)	71, 1043, 1132, 1238, 1300
MaeI	CTAG	1 cut(s)	1409
MaeII	ACGT	1 cut(s)	968
MaeIII	GTNAC	3 cut(s)	371, 883, 1565
MalI	GATC	6 cut(s)	590, 681, 821, 1400, 1458, 1608
MboI	GATC	6 cut(s)	588, 679, 819, 1398, 1456, 1606
MfeI	CAATTG	1 cut(s)	879
MflI	RGATCY	1 cut(s)	1398
MlyI	GAGTC	4 cut(s)	628, 1546, 1661, 1718
MmeI	TCCRAC	4 cut(s)	188, 641, 937, 1119
Mph1103I	ATGCAT	1 cut(s)	64
MslI	CAYNNNNRTG	2 cut(s)	971, 1452
MspA1I	CMGCKG	1 cut(s)	839
MspI	CCGG	1 cut(s)	723
MspR9I	CCNGG	5 cut(s)	534, 654, 724, 918, 1612
MunI	CAATTG	1 cut(s)	879
MvaI	CCWGG	4 cut(s)	534, 654, 918, 1612
MvnI	CGCG	3 cut(s)	678, 791, 1672
MwoI	GCNNNNNNNGC	3 cut(s)	131, 331, 1475
NciI	CCSGG	1 cut(s)	724
NdeI	CATATG	1 cut(s)	484
NdeII	GATC	6 cut(s)	588, 679, 819, 1398, 1456, 1606
NlaIV	GGNNCC	1 cut(s)	153
NmuCI	GTSAC	2 cut(s)	371, 1565
NsiI	ATGCAT	1 cut(s)	64
NspI	RCATGY	3 cut(s)	350, 926, 1362
NspV	TTCGAA	1 cut(s)	1370
PagI	TCATGA	1 cut(s)	1528
PciI	ACATGT	1 cut(s)	922
PfeI	GAWTC	5 cut(s)	713, 1051, 1367, 1435, 1525
PflMI	CCANNNNNTGG	2 cut(s)	569, 653
PfoI	TCCNGGA	2 cut(s)	652, 722
PkrI	GCNGC	1 cut(s)	758
PleI	GAGTC	4 cut(s)	628, 1545, 1661, 1717
PpsI	GAGTC	4 cut(s)	628, 1545, 1661, 1717
PpuMI	RGGWCCY	2 cut(s)	152, 358
PscI	ACATGT	1 cut(s)	922
PshAI	GACNNNNGTC	1 cut(s)	1671
PshBI	ATTAAT	1 cut(s)	807
Psp5II	RGGWCCY	2 cut(s)	152, 358
Psp6I	CCWGG	4 cut(s)	532, 652, 916, 1610
PspGI	CCWGG	4 cut(s)	532, 652, 916, 1610
PspN4I	GGNNCC	1 cut(s)	153
PspPI	GGNCC	3 cut(s)	132, 152, 358
PspPPI	RGGWCCY	2 cut(s)	152, 358
PsuI	RGATCY	1 cut(s)	1398
RsaI	GTAC	4 cut(s)	254, 675, 737, 1552
RsaNI	GTAC	4 cut(s)	253, 674, 736, 1551
RseI	CAYNNNNRTG	2 cut(s)	971, 1452
SalI	GTCGAC	1 cut(s)	1040
SatI	GCNGC	1 cut(s)	757
Sau3AI	GATC	6 cut(s)	588, 679, 819, 1398, 1456, 1606
Sau96I	GGNCC	3 cut(s)	132, 152, 358
SchI	GAGTC	4 cut(s)	628, 1546, 1661, 1718
ScrFI	CCNGG	5 cut(s)	534, 654, 724, 918, 1612
SfaNI	GCATC	5 cut(s)	71, 1043, 1132, 1238, 1300
SfuI	TTCGAA	1 cut(s)	1370
SinI	GGWCC	2 cut(s)	152, 358
SmiMI	CAYNNNNRTG	2 cut(s)	971, 1452
SsiI	CCGC	6 cut(s)	66, 455, 789, 839, 1216, 1478
SspI	AATATT	3 cut(s)	752, 1463, 1660
SspMI	CTAG	1 cut(s)	1409
StyD4I	CCNGG	5 cut(s)	532, 652, 722, 916, 1610
TaaI	ACNGT	4 cut(s)	831, 955, 1393, 1621
TaiI	ACGT	1 cut(s)	971
TaqI	TCGA	4 cut(s)	1041, 1225, 1370, 1576
TaqII	GACCGA	1 cut(s)	269
TatI	WGTACW	1 cut(s)	735
TfiI	GAWTC	5 cut(s)	713, 1051, 1367, 1435, 1525
TseFI	GTSAC	2 cut(s)	371, 1565
TseI	GCWGC	1 cut(s)	756
Tsp45I	GTSAC	2 cut(s)	371, 1565
TspDTI	ATGAA	9 cut(s)	87, 443, 474, 755, 1011, 1515, 1517, 1532, 1678
TspGWI	ACGGA	1 cut(s)	601
Van91I	CCANNNNNTGG	2 cut(s)	569, 653
VpaK11BI	GGWCC	2 cut(s)	152, 358
VspI	ATTAAT	1 cut(s)	807
XapI	RAATTY	4 cut(s)	307, 779, 1094, 1685
XceI	RCATGY	3 cut(s)	350, 926, 1362
XmiI	GTMKAC	4 cut(s)	216, 833, 1041, 1633
XspI	CTAG	1 cut(s)	1409
Zsp2I	ATGCAT	1 cut(s)	64

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