Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000006

Orthogroup ID

OG0009156

Physical Location & Seq

Genomic Coordinates Forward (+)

24455152 .. 24460557

Gene Structure 5406 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_6G00402060.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1329 bp

ATGGAAATCGATTCGGAGAAGAACCTCCATAGAAAACAAGCCTCCTACATCTCACAGGACGACAAGTTTGTGATGAAAGAGGTGTACCAGGGACAGCAGTACAGTCAAATTTACTTTGCGCGTCTCCATCTGATGAGGACTCTCCTCTATTCCCTTCTCCCCAACTGGAAGCCCCATTTACCAGTTTGCACAATTTTGGGATTGGAGGAAGGCAAGGAATGCACCATTGTTGGAACCCTGTACAAGCACATGAAGCTCAAACCTTCCATTCTTGATGAGTACTCTAAGACGAGATCTGCGGTACCACTTGTCAAGCCTCATAATTTTGTGCACGCTGATGATCATTTGGTTTTGGAGGATGAAAGTGGAAGGGTTAAGCTTGCTGGGACCGTGCTTTCACCTTCTGTATATGTAACAGGGAATATTGTTGGCTTGCACGGAAAAGAGACCGGTGCAGGTGAATTCTTAGTACTAGATGTTCTCGAAGCTGGCTTACCACCCCAGATTGAGCTGCCACTTAAATCAAGAGAAGATAAGTATGTTGTTTTTGTGTCTGGGCTGCATGTTGGAAGCAGCTCTTCAAATCCTCTCTTGTTTCAGCTTCTTGTTGATCATATAACAGGACATTTAGGAGATCAGAAGGAACAAAACCTTGCATCGCAAATAGTTCATGTTGTAATTGCTGGAAACTCTGTTGAACTTCCTCGTGGACTTCTTAATGGACAGAACTTGGCACCAAAGGATCAATCTAGGCTCTCTTCACCAATTAAGGAGCTGGATATTATGTTGACTCAGATAGCTGCAGGTGTGCCTTTAGATATCATGCCAGGTGTAGATGACCCTGCAAATGCTTCGTTGCCTCAACAGCCTTTAAACAGATGCCTTTTCCCTGGGTCATCAGTTTATAACACATTTAGATCATGTACTAATCCTCATTCCTTTGATCTTGATGAAATGAGTCATCTTTTGGTTTTCAGATTTGTTGGAACATCAGGGCAAAATATAGATGATCTTGATAGGTATTCAGAAGCAAAGGATAGACTTGAATATCTTGAAAGAACATTGAGGTGGAGGCATCTGGCACCAACAGCACCAAATACTCTTGAGTGTTATCCTTTCACAGATAGGGATCCCTTCCTGATGGAGAGCTGTCCTTATGTGTACTTCGTTGGGAATCAGGATAAATATGATAGTCGCTTGGTAAAAGGATCTGAAGGGCAGATGGTGAGACTCATTTGCATTCCTAAATTCTGTGAGACAGGAGTTGCTGTTGTGCTAAACATGAGAACCCTTGAATGCCATACACTCAGTTTTGGGACTCAATTCTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000228 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005657 GO:0005694 GO:0006139 GO:0006259 GO:0006260 GO:0006261 GO:0006271 GO:0006725 GO:0006807 GO:0006950 GO:0006974 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009987 GO:0022616 GO:0030894 GO:0031974 GO:0031981 GO:0032991 GO:0032993 GO:0033554 GO:0034641 GO:0034645 GO:0042575 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0043596 GO:0043601 GO:0043625 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:0050896 GO:0051716 GO:0061695 GO:0070013 GO:0071704 GO:0090304 GO:1901360 GO:1901576 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03030 ko03410 ko03420 ko03430 ko03440 ko05166 map00230 map00240 map01100 map03030 map03410 map03420 map03430 map03440 map05166

Pfam Domains

Protein Families

DNA_pol_E_B

Protein Analysis

442

Amino Acids

49.54

Weight (kDa)

5.89

Isoelectric Point (pI)

43.27

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
DNA_pol_D_N	PF18018	33 - 160	3.1e-37	DNA polymerase delta subunit OB-fold domain
DNA_pol_E_B	PF04042	181 - 396	4.3e-48	DNA polymerase alpha/epsilon subunit B

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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Publication-ready

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Orthologous Genes (Group: OG0009156)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT2G42120 AT2G42120
fragaria_vesca	FvH4_6g22330 FvH4_6g22330
malus_domestica	MD12G1057200.v1.1 MD14G1057800.v1.1
prunus_persica	Prupe.7G076900_v2.0.a1 Prupe.7G076900_v2.0.a1 Prupe.7G076900_v2.0.a1
pyrus_communis	pycom14g04690
rosa_chinensis	RchiOBHm_Chr3g0479691
rosa_multiflora	Rmu_sc0003755.1_g000006 Rmu_sc0031395.1_g000006
rosa_roxburghii	Rroxscaffold_6G00402060
rosa_rugosa	Rorug03G0177400 Rorug03G0177500 Rorug03G0177600
rosa_samantha	Rh3AG228200 Rh3BG261400 Rh3CG258500 Rh3DG254700
rosa_wichuraiana	Rw3G020420

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	906
AarI	CACCTGC	2 cut(s)	446, 794
Acc36I	ACCTGC	2 cut(s)	446, 794
Acc65I	GGTACC	1 cut(s)	301
AccB1I	GGYRCC	3 cut(s)	301, 733, 1081
AccII	CGCG	1 cut(s)	121
AciI	CCGC	1 cut(s)	299
AclWI	GGATC	4 cut(s)	750, 1124, 1137, 1216
AcsI	RAATTY	3 cut(s)	108, 461, 1247
AcuI	CTGAAG	1 cut(s)	1233
AfaI	GTAC	8 cut(s)	86, 101, 242, 281, 303, 471, 925, 1163
AgeI	ACCGGT	1 cut(s)	449
AgsI	TTSAA	5 cut(s)	582, 698, 1046, 1055, 1295
AjnI	CCWGG	3 cut(s)	87, 826, 889
AluBI	AGCT	9 cut(s)	256, 379, 488, 511, 576, 601, 775, 800, 1149
AluI	AGCT	9 cut(s)	256, 379, 488, 511, 576, 601, 775, 800, 1149
Alw21I	GWGCWC	1 cut(s)	333
Alw26I	GTCTC	4 cut(s)	128, 440, 1222, 1250
Alw44I	GTGCAC	1 cut(s)	329
AlwI	GGATC	4 cut(s)	750, 1124, 1137, 1216
ApaLI	GTGCAC	1 cut(s)	329
ApeKI	GCWGC	4 cut(s)	511, 559, 573, 800
ApoI	RAATTY	3 cut(s)	108, 461, 1247
ArsI	GACNNNNNNTTYG	2 cut(s)	50, 82
AsiGI	ACCGGT	1 cut(s)	449
Asp718I	GGTACC	1 cut(s)	301
AspLEI	GCGC	1 cut(s)	121
AspS9I	GGNCC	1 cut(s)	387
AsuHPI	GGTGA	4 cut(s)	390, 470, 753, 1237
AvaII	GGWCC	1 cut(s)	387
BaeGI	GKGCMC	1 cut(s)	333
BamHI	GGATCC	1 cut(s)	1129
BanI	GGYRCC	3 cut(s)	301, 733, 1081
BarI	GAAGNNNNNNTAC	2 cut(s)	477, 509
BauI	CACGAG	1 cut(s)	705
Bbv12I	GWGCWC	1 cut(s)	333
BbvI	GCAGC	4 cut(s)	498, 546, 585, 787
BccI	CCATC	3 cut(s)	135, 1135, 1216
BcgI	CGANNNNNNTGC	2 cut(s)	834, 868
BciT130I	CCWGG	3 cut(s)	89, 828, 891
BclI	TGATCA	2 cut(s)	340, 610
BcoDI	GTCTC	4 cut(s)	128, 440, 1222, 1250
BfaI	CTAG	2 cut(s)	473, 750
BfmI	CTRYAG	1 cut(s)	801
BfuAI	ACCTGC	2 cut(s)	446, 794
BglII	AGATCT	1 cut(s)	293
BisI	GCNGC	4 cut(s)	512, 560, 574, 801
BlsI	GCNGC	4 cut(s)	513, 561, 575, 802
BmcAI	AGTACT	2 cut(s)	281, 471
Bme1390I	CCNGG	3 cut(s)	89, 828, 891
Bme18I	GGWCC	1 cut(s)	387
BmgT120I	GGNCC	1 cut(s)	387
BmiI	GGNNCC	6 cut(s)	235, 303, 388, 735, 1083, 1131
BmrFI	CCNGG	3 cut(s)	89, 828, 891
BmsI	GCATC	3 cut(s)	665, 869, 1084
BpuEI	CTTGAG	1 cut(s)	1124
Bsa29I	ATCGAT	1 cut(s)	9
BsaBI	GATNNNNATC	1 cut(s)	1128
BsaI	GGTCTC	1 cut(s)	440
BsaJI	CCNNGG	3 cut(s)	88, 889, 890
BsaWI	WCCGGW	1 cut(s)	449
BsaXI	ACNNNNNCTCC	2 cut(s)	1254, 1284
Bse118I	RCCGGY	1 cut(s)	449
Bse1I	ACTGG	2 cut(s)	170, 182
Bse8I	GATNNNNATC	1 cut(s)	1128
BseBI	CCWGG	3 cut(s)	89, 828, 891
BseCI	ATCGAT	1 cut(s)	9
BseDI	CCNNGG	3 cut(s)	88, 889, 890
BseGI	GGATG	1 cut(s)	364
BseJI	GATNNNNATC	1 cut(s)	1128
BseMII	CTCAG	2 cut(s)	806, 1321
BseNI	ACTGG	2 cut(s)	170, 182
BseRI	GAGGAG	1 cut(s)	134
BseSI	GKGCMC	1 cut(s)	333
BseXI	GCAGC	4 cut(s)	498, 546, 585, 787
BseYI	CCCAGC	1 cut(s)	383
BsgI	GTGCAG	1 cut(s)	474
Bsh1236I	CGCG	1 cut(s)	121
BshNI	GGYRCC	3 cut(s)	301, 733, 1081
BshTI	ACCGGT	1 cut(s)	449
BshVI	ATCGAT	1 cut(s)	9
BsiHKAI	GWGCWC	1 cut(s)	333
BsiSI	CCGG	1 cut(s)	450
BslFI	GGGAC	2 cut(s)	105, 400
BsmAI	GTCTC	4 cut(s)	128, 440, 1222, 1250
BsmBI	CGTCTC	1 cut(s)	128
BsmFI	GGGAC	2 cut(s)	105, 400
BsmI	GAATGC	3 cut(s)	224, 1239, 1301
Bso31I	GGTCTC	1 cut(s)	440
Bsp1286I	GDGCHC	1 cut(s)	333
Bsp1407I	TGTACA	1 cut(s)	240
BspACI	CCGC	1 cut(s)	299
BspCNI	CTCAG	2 cut(s)	805, 1320
BspDI	ATCGAT	1 cut(s)	9
BspFNI	CGCG	1 cut(s)	121
BspLI	GGNNCC	6 cut(s)	235, 303, 388, 735, 1083, 1131
BspMAI	CTGCAG	1 cut(s)	805
BspMI	ACCTGC	2 cut(s)	446, 794
BspPI	GGATC	4 cut(s)	750, 1124, 1137, 1216
BspQI	GCTCTTC	1 cut(s)	583
BspT107I	GGYRCC	3 cut(s)	301, 733, 1081
BspTNI	GGTCTC	1 cut(s)	440
BsrFI	RCCGGY	1 cut(s)	449
BsrGI	TGTACA	1 cut(s)	240
BsrI	ACTGG	2 cut(s)	170, 182
BssAI	RCCGGY	1 cut(s)	449
BssECI	CCNNGG	3 cut(s)	88, 889, 890
BssSI	CACGAG	1 cut(s)	705
Bst2BI	CACGAG	1 cut(s)	705
Bst2UI	CCWGG	3 cut(s)	89, 828, 891
Bst4CI	ACNGT	2 cut(s)	104, 391
Bst6I	CTCTTC	2 cut(s)	583, 763
BstAPI	GCANNNNNTGC	1 cut(s)	219
BstAUI	TGTACA	1 cut(s)	240
BstC8I	GCNNGC	4 cut(s)	333, 381, 434, 490
BstDEI	CTNAG	4 cut(s)	285, 466, 792, 1307
BstF5I	GGATG	1 cut(s)	364
BstFNI	CGCG	1 cut(s)	121
BstHHI	GCGC	1 cut(s)	121
BstMAI	GTCTC	4 cut(s)	128, 440, 1222, 1250
BstMWI	GCNNNNNNNGC	4 cut(s)	219, 253, 865, 1088
BstNI	CCWGG	3 cut(s)	89, 828, 891
BstNSI	RCATGY	1 cut(s)	566
BstSCI	CCNGG	3 cut(s)	87, 826, 889
BstSFI	CTRYAG	1 cut(s)	801
BstSLI	GKGCMC	1 cut(s)	333
BstUI	CGCG	1 cut(s)	121
BstV1I	GCAGC	4 cut(s)	498, 546, 585, 787
BstX2I	RGATCY	3 cut(s)	293, 1129, 1208
BstYI	RGATCY	3 cut(s)	293, 1129, 1208
Bsu15I	ATCGAT	1 cut(s)	9
BsuTUI	ATCGAT	1 cut(s)	9
BtgZI	GCGATG	1 cut(s)	642
BtsCI	GGATG	1 cut(s)	364
BveI	ACCTGC	2 cut(s)	446, 794
Cac8I	GCNNGC	4 cut(s)	333, 381, 434, 490
CfoI	GCGC	1 cut(s)	121
Cfr10I	RCCGGY	1 cut(s)	449
Cfr13I	GGNCC	1 cut(s)	387
ClaI	ATCGAT	1 cut(s)	9
CseI	GACGC	1 cut(s)	110
Csp6I	GTAC	8 cut(s)	85, 100, 241, 280, 302, 470, 924, 1162
CspAI	ACCGGT	1 cut(s)	449
CviAII	CATG	6 cut(s)	250, 563, 671, 823, 921, 1282
CviQI	GTAC	8 cut(s)	85, 100, 241, 280, 302, 470, 924, 1162
DdeI	CTNAG	4 cut(s)	285, 466, 792, 1307
DraI	TTTAAA	1 cut(s)	873
Eam1104I	CTCTTC	2 cut(s)	583, 763
EarI	CTCTTC	2 cut(s)	583, 763
Eco31I	GGTCTC	1 cut(s)	440
Eco32I	GATATC	1 cut(s)	820
Eco47I	GGWCC	1 cut(s)	387
Eco57I	CTGAAG	1 cut(s)	1233
EcoRI	GAATTC	1 cut(s)	461
EcoRII	CCWGG	3 cut(s)	87, 826, 889
EcoRV	GATATC	1 cut(s)	820
Esp3I	CGTCTC	1 cut(s)	128
FaeI	CATG	6 cut(s)	253, 566, 674, 826, 924, 1285
FalI	AAGNNNNNCTT	2 cut(s)	562, 594
FaqI	GGGAC	2 cut(s)	105, 400
FatI	CATG	6 cut(s)	249, 562, 670, 822, 920, 1281
FbaI	TGATCA	2 cut(s)	340, 610
Fnu4HI	GCNGC	4 cut(s)	512, 560, 574, 801
FokI	GGATG	1 cut(s)	371
Fsp4HI	GCNGC	4 cut(s)	512, 560, 574, 801
FspBI	CTAG	2 cut(s)	473, 750
GlaI	GCGC	1 cut(s)	120
GluI	GCNGC	4 cut(s)	512, 560, 574, 801
GsaI	CCCAGC	1 cut(s)	387
HapII	CCGG	1 cut(s)	450
HgaI	GACGC	1 cut(s)	110
HhaI	GCGC	1 cut(s)	121
Hin1II	CATG	6 cut(s)	253, 566, 674, 826, 924, 1285
Hin6I	GCGC	1 cut(s)	119
HinP1I	GCGC	1 cut(s)	119
HincII	GTYRAC	1 cut(s)	789
HindII	GTYRAC	1 cut(s)	789
HindIII	AAGCTT	1 cut(s)	377
HinfI	GANTC	7 cut(s)	11, 139, 790, 958, 1174, 1230, 1318
HpaII	CCGG	1 cut(s)	450
HphI	GGTGA	4 cut(s)	390, 470, 753, 1237
Hpy166II	GTNNAC	5 cut(s)	85, 331, 710, 789, 1162
Hpy188I	TCNGA	7 cut(s)	16, 132, 639, 795, 977, 1027, 1213
Hpy188III	TCNNGA	9 cut(s)	272, 482, 525, 947, 1013, 1052, 1103, 1138, 1178
Hpy8I	GTNNAC	5 cut(s)	85, 331, 710, 789, 1162
HpyAV	CCTTC	8 cut(s)	164, 203, 273, 363, 411, 634, 1144, 1208
HpyCH4III	ACNGT	2 cut(s)	104, 391
HpyF10VI	GCNNNNNNNGC	4 cut(s)	219, 253, 865, 1088
HpyF3I	CTNAG	4 cut(s)	285, 466, 792, 1307
Hsp92II	CATG	6 cut(s)	253, 566, 674, 826, 924, 1285
HspAI	GCGC	1 cut(s)	119
KpnI	GGTACC	1 cut(s)	305
Ksp22I	TGATCA	2 cut(s)	340, 610
LguI	GCTCTTC	1 cut(s)	583
LmnI	GCTCC	1 cut(s)	772
Lsp1109I	GCAGC	4 cut(s)	498, 546, 585, 787
LweI	GCATC	3 cut(s)	665, 869, 1084
MaeI	CTAG	2 cut(s)	473, 750
MaeIII	GTNAC	1 cut(s)	412
MboII	GAAGA	4 cut(s)	31, 542, 570, 750
MflI	RGATCY	3 cut(s)	293, 1129, 1208
MhlI	GDGCHC	1 cut(s)	333
MluCI	AATT	8 cut(s)	108, 192, 322, 461, 678, 765, 1247, 1322
MlyI	GAGTC	5 cut(s)	133, 784, 967, 1224, 1312
MmeI	TCCRAC	3 cut(s)	211, 547, 964
MseI	TTAA	5 cut(s)	375, 519, 717, 768, 872
MslI	CAYNNNNRTG	2 cut(s)	336, 1066
MspI	CCGG	1 cut(s)	450
MspR9I	CCNGG	3 cut(s)	89, 828, 891
Mva1269I	GAATGC	3 cut(s)	224, 1239, 1301
MvaI	CCWGG	3 cut(s)	89, 828, 891
MvnI	CGCG	1 cut(s)	121
MwoI	GCNNNNNNNGC	4 cut(s)	219, 253, 865, 1088
NlaIII	CATG	6 cut(s)	253, 566, 674, 826, 924, 1285
NlaIV	GGNNCC	6 cut(s)	235, 303, 388, 735, 1083, 1131
NspI	RCATGY	1 cut(s)	566
PaqCI	CACCTGC	2 cut(s)	446, 794
PasI	CCCWGGG	1 cut(s)	890
PciSI	GCTCTTC	1 cut(s)	583
PctI	GAATGC	3 cut(s)	224, 1239, 1301
PfeI	GAWTC	2 cut(s)	11, 1174
PinAI	ACCGGT	1 cut(s)	449
PkrI	GCNGC	4 cut(s)	513, 561, 575, 802
PleI	GAGTC	5 cut(s)	133, 784, 966, 1224, 1312
PpsI	GAGTC	5 cut(s)	133, 784, 966, 1224, 1312
PsiI	TTATAA	1 cut(s)	906
Psp6I	CCWGG	3 cut(s)	87, 826, 889
PspFI	CCCAGC	1 cut(s)	383
PspGI	CCWGG	3 cut(s)	87, 826, 889
PspN4I	GGNNCC	6 cut(s)	235, 303, 388, 735, 1083, 1131
PspPI	GGNCC	1 cut(s)	387
PsrI	GAACNNNNNNTAC	2 cut(s)	462, 494
PstI	CTGCAG	1 cut(s)	805
PsuI	RGATCY	3 cut(s)	293, 1129, 1208
RsaI	GTAC	8 cut(s)	86, 101, 242, 281, 303, 471, 925, 1163
RsaNI	GTAC	8 cut(s)	85, 100, 241, 280, 302, 470, 924, 1162
RseI	CAYNNNNRTG	2 cut(s)	336, 1066
SapI	GCTCTTC	1 cut(s)	583
SaqAI	TTAA	5 cut(s)	375, 519, 717, 768, 872
SatI	GCNGC	4 cut(s)	512, 560, 574, 801
Sau96I	GGNCC	1 cut(s)	387
ScaI	AGTACT	2 cut(s)	281, 471
SchI	GAGTC	5 cut(s)	133, 784, 967, 1224, 1312
ScrFI	CCNGG	3 cut(s)	89, 828, 891
SduI	GDGCHC	1 cut(s)	333
SfaNI	GCATC	3 cut(s)	665, 869, 1084
SfcI	CTRYAG	1 cut(s)	801
SinI	GGWCC	1 cut(s)	387
SmiMI	CAYNNNNRTG	2 cut(s)	336, 1066
SmlI	CTYRAG	1 cut(s)	1103
SmoI	CTYRAG	1 cut(s)	1103
Sse9I	AATT	8 cut(s)	108, 192, 322, 461, 678, 765, 1247, 1322
SsiI	CCGC	1 cut(s)	299
SspI	AATATT	1 cut(s)	424
SspMI	CTAG	2 cut(s)	473, 750
StyD4I	CCNGG	3 cut(s)	87, 826, 889
TaaI	ACNGT	2 cut(s)	104, 391
TaqI	TCGA	2 cut(s)	9, 483
TasI	AATT	8 cut(s)	108, 192, 322, 461, 678, 765, 1247, 1322
TatI	WGTACW	6 cut(s)	99, 240, 279, 469, 923, 1161
TfiI	GAWTC	2 cut(s)	11, 1174
Tru1I	TTAA	5 cut(s)	375, 519, 717, 768, 872
Tru9I	TTAA	5 cut(s)	375, 519, 717, 768, 872
TseI	GCWGC	4 cut(s)	511, 559, 573, 800
TspDTI	ATGAA	5 cut(s)	89, 266, 375, 659, 966
TspGWI	ACGGA	1 cut(s)	453
VneI	GTGCAC	1 cut(s)	329
VpaK11BI	GGWCC	1 cut(s)	387
XapI	RAATTY	3 cut(s)	108, 461, 1247
XceI	RCATGY	1 cut(s)	566
XspI	CTAG	2 cut(s)	473, 750
ZrmI	AGTACT	2 cut(s)	281, 471

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