Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000003

Orthogroup ID

OG0016900

Physical Location & Seq

Genomic Coordinates Reverse (-)

9976064 .. 9990746

Gene Structure 14683 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_3G00226480.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 675 bp

ATGAAACGTCTTGAATTTTTTTCTCGTTTGAACTCCCGACCTCTAACACGAAGCCTCTTACTCCCAACCACCGAAGCAAGGACTGCTTCCATTAGAAAGAATGGTAGTGAAGGTCTATTTGACAAGTTGGAGAATACCAGTAAATTGAATGCGCATCTAGAGGGACTGATGCCTGGCCTTACAGGAAAAGTATTCCGTACATACAATGCATGCATTACATTGGATGAAATAGTAAGTTGTACTGGCCGTCTGGCCTCCACCAAATTTTTGAACAAAGAAACTCTCTCTGGAGCAGTTTCAGAGAAACAAGGTGTTTATAGACAGGCAACCAGGGAGGTTGCCATTATCTGCAATTTTCAGCGTACTGTTTCAAGGCCTGATGGTGTACAGATGTACTGGTTAAAAGAGAACATGAGTGAGTTGCAGGGCACATTGACGGAGCTGAAAACTGATTTGGACAGGGCAGTAATGGGATTGCCACCACTGAGAATTTCTAATGGAAAACTAAAGAGAACCCTGACCCCAGAAGAGTTAGAGAGGACGACAGCTGAAACAATTCAGATGATTGAAAAATTGGAACAGGATATGAGGACCCAAGAGAACCAGAAATACACGTCAGTGGGAATGCCCAAAATCAAGTATCTTGACCCTAGGATCACTGTTGCATGGTGTTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

No ontology terms assigned.

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

Topo_C_assoc Topoisom_I Topoisom_I_N

Protein Analysis

224

Amino Acids

25.44

Weight (kDa)

9.39

Isoelectric Point (pI)

37.92

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Topoisom_I	PF01028	32 - 151	9.4e-25	Eukaryotic DNA topoisomerase I, catalytic core
Topo_C_assoc	PF14370	188 - 224	6e-09	C-terminal topoisomerase 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)

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Tree File

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Publication-ready

iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0016900)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_6g41220
rosa_laevigata	RLG00000001192 RLG00000001193 RLG00000001200 RLG00000001202 RLG00000001203
rosa_multiflora	Rmu_sc0000768.1_g000025
rosa_roxburghii	Rroxscaffold_3G00226480 Rroxscaffold_3G00226490 Rroxscaffold_3G00226550
rosa_rugosa	Rorug07G0286300
rosa_samantha	Rh7AG441000 Rh7BG413800 Rh7CG462700

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc16I	TGCGCA	1 cut(s)	153
AclWI	GGATC	1 cut(s)	662
AcoI	YGGCCR	1 cut(s)	244
AcsI	RAATTY	3 cut(s)	14, 263, 489
AfaI	GTAC	5 cut(s)	199, 241, 364, 387, 395
AfiI	CCNNNNNNNGG	1 cut(s)	78
AflIII	ACRYGT	1 cut(s)	612
AgsI	TTSAA	6 cut(s)	14, 31, 148, 271, 372, 569
AjiI	CACGTC	1 cut(s)	615
AjnI	CCWGG	2 cut(s)	172, 329
AjuI	GAANNNNNNNTTGG	2 cut(s)	437, 469
AleI	CACNNNNGTG	1 cut(s)	617
AluBI	AGCT	2 cut(s)	442, 548
AluI	AGCT	2 cut(s)	442, 548
AlwI	GGATC	1 cut(s)	662
AoxI	GGCC	4 cut(s)	175, 244, 252, 374
ApoI	RAATTY	3 cut(s)	14, 263, 489
Asp700I	GAANNNNTTC	1 cut(s)	555
AspA2I	CCTAGG	1 cut(s)	650
AspLEI	GCGC	1 cut(s)	154
AspS9I	GGNCC	1 cut(s)	591
AvaII	GGWCC	1 cut(s)	591
AvrII	CCTAGG	1 cut(s)	650
BaeGI	GKGCMC	1 cut(s)	431
BccI	CCATC	1 cut(s)	374
BceAI	ACGGC	1 cut(s)	231
BciT130I	CCWGG	2 cut(s)	174, 331
BfaI	CTAG	2 cut(s)	158, 651
BlnI	CCTAGG	1 cut(s)	650
Bme1390I	CCNGG	2 cut(s)	174, 331
Bme18I	GGWCC	1 cut(s)	591
BmgBI	CACGTC	1 cut(s)	615
BmgT120I	GGNCC	1 cut(s)	591
BmiI	GGNNCC	1 cut(s)	593
BmrFI	CCNGG	2 cut(s)	174, 331
BmsI	GCATC	2 cut(s)	159, 163
BpmI	CTGGAG	1 cut(s)	309
BsaJI	CCNNGG	2 cut(s)	330, 650
Bsc4I	CCNNNNNNNGG	1 cut(s)	78
Bse1I	ACTGG	3 cut(s)	138, 247, 401
BseBI	CCWGG	2 cut(s)	174, 331
BseDI	CCNNGG	2 cut(s)	330, 650
BseGI	GGATG	1 cut(s)	229
BseLI	CCNNNNNNNGG	1 cut(s)	78
BseMII	CTCAG	1 cut(s)	476
BseNI	ACTGG	3 cut(s)	138, 247, 401
BseSI	GKGCMC	1 cut(s)	431
BshFI	GGCC	4 cut(s)	177, 246, 254, 376
BslFI	GGGAC	1 cut(s)	177
BslI	CCNNNNNNNGG	1 cut(s)	78
BsmFI	GGGAC	1 cut(s)	177
BsmI	GAATGC	2 cut(s)	154, 630
BsnI	GGCC	4 cut(s)	177, 246, 254, 376
Bsp1286I	GDGCHC	1 cut(s)	431
Bsp1407I	TGTACA	1 cut(s)	385
Bsp143I	GATC	1 cut(s)	654
BspANI	GGCC	4 cut(s)	177, 246, 254, 376
BspCNI	CTCAG	1 cut(s)	477
BspLI	GGNNCC	1 cut(s)	593
BspPI	GGATC	1 cut(s)	662
BsrGI	TGTACA	1 cut(s)	385
BsrI	ACTGG	3 cut(s)	138, 247, 401
BssECI	CCNNGG	2 cut(s)	330, 650
BssMI	GATC	1 cut(s)	654
BssT1I	CCWWGG	1 cut(s)	650
Bst2UI	CCWGG	2 cut(s)	174, 331
Bst4CI	ACNGT	2 cut(s)	367, 661
Bst6I	CTCTTC	1 cut(s)	522
BstAPI	GCANNNNNTGC	1 cut(s)	83
BstAUI	TGTACA	1 cut(s)	385
BstC8I	GCNNGC	1 cut(s)	211
BstDEI	CTNAG	1 cut(s)	485
BstF5I	GGATG	1 cut(s)	229
BstHHI	GCGC	1 cut(s)	154
BstKTI	GATC	1 cut(s)	657
BstMBI	GATC	1 cut(s)	654
BstMWI	GCNNNNNNNGC	1 cut(s)	83
BstNI	CCWGG	2 cut(s)	174, 331
BstNSI	RCATGY	1 cut(s)	213
BstSCI	CCNGG	2 cut(s)	172, 329
BstSLI	GKGCMC	1 cut(s)	431
BsuRI	GGCC	4 cut(s)	177, 246, 254, 376
BtrI	CACGTC	1 cut(s)	615
BtsCI	GGATG	1 cut(s)	229
BtsIMutI	CAGTG	3 cut(s)	482, 624, 657
Cac8I	GCNNGC	1 cut(s)	211
CfoI	GCGC	1 cut(s)	154
Cfr13I	GGNCC	1 cut(s)	591
Csp6I	GTAC	5 cut(s)	198, 240, 363, 386, 394
CviAII	CATG	3 cut(s)	210, 412, 666
CviJI	RGCY	7 cut(s)	54, 177, 246, 254, 376, 442, 548
CviKI_1	RGCY	7 cut(s)	54, 177, 246, 254, 376, 442, 548
CviQI	GTAC	5 cut(s)	198, 240, 363, 386, 394
DdeI	CTNAG	1 cut(s)	485
DpnI	GATC	1 cut(s)	656
DpnII	GATC	1 cut(s)	654
EaeI	YGGCCR	1 cut(s)	244
Eam1104I	CTCTTC	1 cut(s)	522
EarI	CTCTTC	1 cut(s)	522
Eco130I	CCWWGG	1 cut(s)	650
Eco147I	AGGCCT	1 cut(s)	376
Eco47I	GGWCC	1 cut(s)	591
EcoO109I	RGGNCCY	1 cut(s)	591
EcoRII	CCWGG	2 cut(s)	172, 329
EcoT14I	CCWWGG	1 cut(s)	650
EcoT22I	ATGCAT	2 cut(s)	211, 215
ErhI	CCWWGG	1 cut(s)	650
FaeI	CATG	3 cut(s)	213, 415, 669
FaiI	YATR	6 cut(s)	202, 211, 318, 413, 587, 667
FalI	AAGNNNNNCTT	2 cut(s)	70, 102
FaqI	GGGAC	1 cut(s)	177
FatI	CATG	3 cut(s)	209, 411, 665
FokI	GGATG	1 cut(s)	236
FspAI	RTGCGCAY	1 cut(s)	153
FspBI	CTAG	2 cut(s)	158, 651
FspI	TGCGCA	1 cut(s)	153
GlaI	GCGC	1 cut(s)	153
GsuI	CTGGAG	1 cut(s)	309
HaeIII	GGCC	4 cut(s)	177, 246, 254, 376
HhaI	GCGC	1 cut(s)	154
Hin1II	CATG	3 cut(s)	213, 415, 669
Hin6I	GCGC	1 cut(s)	152
HinP1I	GCGC	1 cut(s)	152
Hpy166II	GTNNAC	1 cut(s)	386
Hpy188I	TCNGA	2 cut(s)	301, 561
Hpy188III	TCNNGA	5 cut(s)	11, 36, 158, 288, 644
Hpy8I	GTNNAC	1 cut(s)	386
HpyAV	CCTTC	1 cut(s)	104
HpyCH4III	ACNGT	2 cut(s)	367, 661
HpyCH4IV	ACGT	2 cut(s)	7, 614
HpyCH4V	TGCA	5 cut(s)	209, 213, 351, 424, 665
HpyF10VI	GCNNNNNNNGC	1 cut(s)	83
HpyF3I	CTNAG	1 cut(s)	485
HpySE526I	ACGT	2 cut(s)	7, 614
Hsp92II	CATG	3 cut(s)	213, 415, 669
HspAI	GCGC	1 cut(s)	152
Kzo9I	GATC	1 cut(s)	654
LmnI	GCTCC	2 cut(s)	290, 439
LweI	GCATC	2 cut(s)	159, 163
MaeI	CTAG	2 cut(s)	158, 651
MaeII	ACGT	2 cut(s)	7, 614
MalI	GATC	1 cut(s)	656
MboI	GATC	1 cut(s)	654
MboII	GAAGA	1 cut(s)	539
MhlI	GDGCHC	1 cut(s)	431
MluCI	AATT	7 cut(s)	14, 143, 263, 352, 489, 555, 572
MmeI	TCCRAC	1 cut(s)	108
MnlI	CCTC	7 cut(s)	51, 65, 154, 265, 328, 531, 582
Mph1103I	ATGCAT	2 cut(s)	211, 215
MroXI	GAANNNNTTC	1 cut(s)	555
MseI	TTAA	1 cut(s)	401
MslI	CAYNNNNRTG	1 cut(s)	617
MspA1I	CMGCKG	1 cut(s)	548
MspR9I	CCNGG	2 cut(s)	174, 331
Mva1269I	GAATGC	2 cut(s)	154, 630
MvaI	CCWGG	2 cut(s)	174, 331
MwoI	GCNNNNNNNGC	1 cut(s)	83
NdeII	GATC	1 cut(s)	654
NlaIII	CATG	3 cut(s)	213, 415, 669
NlaIV	GGNNCC	1 cut(s)	593
NsbI	TGCGCA	1 cut(s)	153
NsiI	ATGCAT	2 cut(s)	211, 215
NspI	RCATGY	1 cut(s)	213
OliI	CACNNNNGTG	1 cut(s)	617
PaeI	GCATGC	1 cut(s)	213
PceI	AGGCCT	1 cut(s)	376
PctI	GAATGC	2 cut(s)	154, 630
PdmI	GAANNNNTTC	1 cut(s)	555
PpuMI	RGGWCCY	1 cut(s)	591
Psp5II	RGGWCCY	1 cut(s)	591
Psp6I	CCWGG	2 cut(s)	172, 329
PspGI	CCWGG	2 cut(s)	172, 329
PspN4I	GGNNCC	1 cut(s)	593
PspPI	GGNCC	1 cut(s)	591
PspPPI	RGGWCCY	1 cut(s)	591
PsrI	GAACNNNNNNTAC	2 cut(s)	593, 625
PvuII	CAGCTG	1 cut(s)	548
RsaI	GTAC	5 cut(s)	199, 241, 364, 387, 395
RsaNI	GTAC	5 cut(s)	198, 240, 363, 386, 394
RseI	CAYNNNNRTG	1 cut(s)	617
SaqAI	TTAA	1 cut(s)	401
Sau3AI	GATC	1 cut(s)	654
Sau96I	GGNCC	1 cut(s)	591
ScrFI	CCNGG	2 cut(s)	174, 331
SduI	GDGCHC	1 cut(s)	431
SetI	ASST	8 cut(s)	10, 43, 115, 313, 339, 444, 550, 617
SfaNI	GCATC	2 cut(s)	159, 163
SinI	GGWCC	1 cut(s)	591
SmiMI	CAYNNNNRTG	1 cut(s)	617
SphI	GCATGC	1 cut(s)	213
Sse9I	AATT	7 cut(s)	14, 143, 263, 352, 489, 555, 572
SseBI	AGGCCT	1 cut(s)	376
SspMI	CTAG	2 cut(s)	158, 651
StuI	AGGCCT	1 cut(s)	376
StyD4I	CCNGG	2 cut(s)	172, 329
StyI	CCWWGG	1 cut(s)	650
TaaI	ACNGT	2 cut(s)	367, 661
TaiI	ACGT	2 cut(s)	10, 617
TasI	AATT	7 cut(s)	14, 143, 263, 352, 489, 555, 572
TatI	WGTACW	3 cut(s)	239, 385, 393
Tru1I	TTAA	1 cut(s)	401
Tru9I	TTAA	1 cut(s)	401
TscAI	CASTG	3 cut(s)	489, 624, 664
TspDTI	ATGAA	2 cut(s)	17, 240
TspGWI	ACGGA	2 cut(s)	185, 452
TspRI	CASTG	3 cut(s)	489, 624, 664
VpaK11BI	GGWCC	1 cut(s)	591
XapI	RAATTY	3 cut(s)	14, 263, 489
XbaI	TCTAGA	1 cut(s)	157
XceI	RCATGY	1 cut(s)	213
XmaJI	CCTAGG	1 cut(s)	650
XmnI	GAANNNNTTC	1 cut(s)	555
XspI	CTAG	2 cut(s)	158, 651
Zsp2I	ATGCAT	2 cut(s)	211, 215

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