Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000003

Orthogroup ID

OG0016900

Physical Location & Seq

Genomic Coordinates Reverse (-)

9990764 .. 9994827

Gene Structure 4064 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_3G00226490.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1143 bp

ATGCTGATGATTTCTGAAATGAAAAGAGAGAAGGAGACATATGAGAAAGCAAGGATGCTGAAGGAGTACATAGAAAATATCAGGGCTGCATACACCAAGGATTTTACAAGTGAAGATGGTGAAAAGAGGCAGTTGGCAGTTGCTACCTATCTTGTCGATAAACTTTGTCTGAGGGCTGGAAATGATACGGATGATGATGAAATTGATACTGTCGAGTGCTGCAAATTAAAAGTAGAGAACGTCAAAACAATTCCCCTAGCTCGTTGGAGATGTGAAAATACTGTTGACGTTGAGCTTCCTGTTTACAAGGCAATCGAAGAGTTCCTGGCTGGAAAGAATGGTAGTGAAGGTCTATTTGACAAGTTGGAGAATACCAGTAAATTGAATGCGCATCTAGAGGGACTGATGCCTGGCCTTACAGGAAAAGTATTCCGTACATACAATGCATGCATTACATTGGATGAAATATTGAACAAAGAAACTCCCTCTGGAGCTGTTTCAGAGAAAGCAGGTGTTTATAGCCAGGCAACCAGGGAGGTTGCTATCATCTGTAATTTTCAGCGTACTGTCGCAAGGCCTGGTGGTGTACGGATGTACTGGTTAAAAGAGAACATGAGTGAGTTGCAGGGCACATTGACGGAGCTGAAAACAGATTTGGACAGGGCGGTAATGGGATTACCCCCACTGAGAAATTCTAATGGAAAACCAAATAGAACCCTGACAGATATGGACAGGGCAGTAATGGGATTACCCCCACTGAGAAATTCTAATGGAAAACGAAAGAGAACCCTGACCCCAGAAGAGTTAGAGAGGACGATAGCTGAAACAATTCAGATGATTGAAAAATTGGAACAGGATATGAGAACCCAAGAGAACCAGAAATACACGTCAGTTGGAATGCCCAAAATCAAGTATCTTGACCCTAGGATCGCTGTTGCATGGTGTAAGCGAAATGAAGTTCCTATTAACATGGAGTACATAGAAAATATCAGGACTGCATACACCAAGGATTTTACAAGTGAAGATGGTGAAAAGAGGCGGATGGCGATTGCTACCAATCTTGTCGATAAACTTTGTCCGAGGGCTGGAAATGATACTATCACGCCCCGGATTTTGAATAACGATTTCAAATCTGAAACATGA

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

380

Amino Acids

43.3

Weight (kDa)

6.22

Isoelectric Point (pI)

38.21

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Topoisom_I	PF01028	8 - 218	1.3e-56	Eukaryotic DNA topoisomerase I, catalytic core
Topo_C_assoc	PF14370	279 - 328	3.2e-13	C-terminal topoisomerase domain
Topoisom_I	PF01028	325 - 366	3.9e-06	Eukaryotic DNA topoisomerase I, catalytic core

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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Publication-ready

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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)
AarI	CACCTGC	1 cut(s)	500
Acc16I	TGCGCA	1 cut(s)	390
Acc36I	ACCTGC	1 cut(s)	500
AciI	CCGC	2 cut(s)	665, 1039
AclWI	GGATC	1 cut(s)	935
AcsI	RAATTY	2 cut(s)	691, 763
AcuI	CTGAAG	1 cut(s)	80
AfaI	GTAC	6 cut(s)	68, 436, 565, 588, 596, 977
AfiI	CCNNNNNNNGG	1 cut(s)	1085
AflIII	ACRYGT	1 cut(s)	885
AgsI	TTSAA	5 cut(s)	385, 472, 842, 1117, 1129
AjiI	CACGTC	1 cut(s)	888
AjnI	CCWGG	5 cut(s)	324, 409, 522, 530, 577
AjuI	GAANNNNNNNTTGG	2 cut(s)	638, 670
AluBI	AGCT	5 cut(s)	260, 295, 494, 643, 821
AluI	AGCT	5 cut(s)	260, 295, 494, 643, 821
Alw26I	GTCTC	1 cut(s)	29
AlwI	GGATC	1 cut(s)	935
AoxI	GGCC	2 cut(s)	412, 575
ApeKI	GCWGC	2 cut(s)	86, 219
ApoI	RAATTY	2 cut(s)	691, 763
Asp700I	GAANNNNTTC	1 cut(s)	828
AspA2I	CCTAGG	1 cut(s)	923
AspLEI	GCGC	1 cut(s)	391
AsuC2I	CCSGG	1 cut(s)	1108
AsuHPI	GGTGA	2 cut(s)	131, 1040
AvrII	CCTAGG	1 cut(s)	923
BaeGI	GKGCMC	1 cut(s)	632
BbvI	GCAGC	2 cut(s)	73, 206
BccI	CCATC	3 cut(s)	110, 1019, 1036
BciT130I	CCWGG	5 cut(s)	326, 411, 524, 532, 579
BcnI	CCSGG	1 cut(s)	1108
BcoDI	GTCTC	1 cut(s)	29
BfaI	CTAG	3 cut(s)	257, 395, 924
BfuAI	ACCTGC	1 cut(s)	500
BisI	GCNGC	2 cut(s)	87, 220
BlnI	CCTAGG	1 cut(s)	923
BlsI	GCNGC	2 cut(s)	88, 221
Bme1390I	CCNGG	6 cut(s)	326, 411, 524, 532, 579, 1108
BmgBI	CACGTC	1 cut(s)	888
BmrFI	CCNGG	6 cut(s)	326, 411, 524, 532, 579, 1108
BmsI	GCATC	3 cut(s)	45, 396, 400
BpmI	CTGGAG	1 cut(s)	510
BpuMI	CCSGG	1 cut(s)	1108
BsaJI	CCNNGG	6 cut(s)	96, 531, 923, 1005, 1079, 1106
Bsc4I	CCNNNNNNNGG	1 cut(s)	1085
Bse1I	ACTGG	2 cut(s)	375, 602
BseBI	CCWGG	5 cut(s)	326, 411, 524, 532, 579
BseDI	CCNNGG	6 cut(s)	96, 531, 923, 1005, 1079, 1106
BseGI	GGATG	5 cut(s)	60, 196, 466, 597, 1047
BseLI	CCNNNNNNNGG	1 cut(s)	1085
BseMII	CTCAG	3 cut(s)	161, 677, 749
BseNI	ACTGG	2 cut(s)	375, 602
BseSI	GKGCMC	1 cut(s)	632
BseXI	GCAGC	2 cut(s)	73, 206
BshFI	GGCC	2 cut(s)	414, 577
BsiSI	CCGG	1 cut(s)	1108
BslFI	GGGAC	1 cut(s)	414
BslI	CCNNNNNNNGG	1 cut(s)	1085
BsmAI	GTCTC	1 cut(s)	29
BsmFI	GGGAC	1 cut(s)	414
BsmI	GAATGC	2 cut(s)	391, 903
BsnI	GGCC	2 cut(s)	414, 577
Bsp1286I	GDGCHC	1 cut(s)	632
Bsp143I	GATC	1 cut(s)	927
BspACI	CCGC	2 cut(s)	665, 1039
BspANI	GGCC	2 cut(s)	414, 577
BspCNI	CTCAG	3 cut(s)	162, 678, 750
BspMI	ACCTGC	1 cut(s)	500
BspPI	GGATC	1 cut(s)	935
BsrI	ACTGG	2 cut(s)	375, 602
BssECI	CCNNGG	6 cut(s)	96, 531, 923, 1005, 1079, 1106
BssMI	GATC	1 cut(s)	927
BssT1I	CCWWGG	3 cut(s)	96, 923, 1005
Bst2UI	CCWGG	5 cut(s)	326, 411, 524, 532, 579
Bst4CI	ACNGT	3 cut(s)	211, 283, 568
Bst6I	CTCTTC	2 cut(s)	312, 795
BstC8I	GCNNGC	1 cut(s)	448
BstDEI	CTNAG	3 cut(s)	170, 686, 758
BstF5I	GGATG	5 cut(s)	60, 196, 466, 597, 1047
BstHHI	GCGC	1 cut(s)	391
BstKTI	GATC	1 cut(s)	930
BstMAI	GTCTC	1 cut(s)	29
BstMBI	GATC	1 cut(s)	927
BstNI	CCWGG	5 cut(s)	326, 411, 524, 532, 579
BstNSI	RCATGY	1 cut(s)	450
BstSCI	CCNGG	6 cut(s)	324, 409, 522, 530, 577, 1106
BstSLI	GKGCMC	1 cut(s)	632
BstV1I	GCAGC	2 cut(s)	73, 206
BsuRI	GGCC	2 cut(s)	414, 577
BtrI	CACGTC	1 cut(s)	888
BtsCI	GGATG	5 cut(s)	60, 196, 466, 597, 1047
BtsIMutI	CAGTG	2 cut(s)	683, 755
BveI	ACCTGC	1 cut(s)	500
Cac8I	GCNNGC	1 cut(s)	448
CfoI	GCGC	1 cut(s)	391
Csp6I	GTAC	6 cut(s)	67, 435, 564, 587, 595, 976
CviAII	CATG	5 cut(s)	447, 613, 939, 970, 1140
CviQI	GTAC	6 cut(s)	67, 435, 564, 587, 595, 976
DdeI	CTNAG	3 cut(s)	170, 686, 758
DpnI	GATC	1 cut(s)	929
DpnII	GATC	1 cut(s)	927
Eam1104I	CTCTTC	2 cut(s)	312, 795
EarI	CTCTTC	2 cut(s)	312, 795
EciI	GGCGGA	1 cut(s)	1054
Eco130I	CCWWGG	3 cut(s)	96, 923, 1005
Eco147I	AGGCCT	1 cut(s)	577
Eco57I	CTGAAG	1 cut(s)	80
EcoRII	CCWGG	5 cut(s)	324, 409, 522, 530, 577
EcoT14I	CCWWGG	3 cut(s)	96, 923, 1005
EcoT22I	ATGCAT	2 cut(s)	448, 452
ErhI	CCWWGG	3 cut(s)	96, 923, 1005
FaeI	CATG	5 cut(s)	450, 616, 942, 973, 1143
FaqI	GGGAC	1 cut(s)	414
FatI	CATG	5 cut(s)	446, 612, 938, 969, 1139
FauNDI	CATATG	1 cut(s)	40
Fnu4HI	GCNGC	2 cut(s)	87, 220
FokI	GGATG	5 cut(s)	67, 203, 473, 604, 1054
Fsp4HI	GCNGC	2 cut(s)	87, 220
FspAI	RTGCGCAY	1 cut(s)	390
FspBI	CTAG	3 cut(s)	257, 395, 924
FspI	TGCGCA	1 cut(s)	390
GlaI	GCGC	1 cut(s)	390
GluI	GCNGC	2 cut(s)	87, 220
GsuI	CTGGAG	1 cut(s)	510
HaeIII	GGCC	2 cut(s)	414, 577
HapII	CCGG	1 cut(s)	1108
HhaI	GCGC	1 cut(s)	391
Hin1II	CATG	5 cut(s)	450, 616, 942, 973, 1143
Hin6I	GCGC	1 cut(s)	389
HinP1I	GCGC	1 cut(s)	389
HincII	GTYRAC	1 cut(s)	286
HindII	GTYRAC	1 cut(s)	286
HpaII	CCGG	1 cut(s)	1108
HphI	GGTGA	2 cut(s)	131, 1040
Hpy166II	GTNNAC	3 cut(s)	286, 304, 587
Hpy188I	TCNGA	6 cut(s)	16, 171, 502, 834, 1080, 1135
Hpy188III	TCNNGA	4 cut(s)	395, 489, 917, 991
Hpy8I	GTNNAC	3 cut(s)	286, 304, 587
HpyAV	CCTTC	3 cut(s)	25, 55, 341
HpyCH4III	ACNGT	3 cut(s)	211, 283, 568
HpyCH4IV	ACGT	3 cut(s)	240, 288, 887
HpyCH4V	TGCA	7 cut(s)	89, 222, 446, 450, 625, 938, 998
HpyF3I	CTNAG	3 cut(s)	170, 686, 758
HpySE526I	ACGT	3 cut(s)	240, 288, 887
Hsp92II	CATG	5 cut(s)	450, 616, 942, 973, 1143
HspAI	GCGC	1 cut(s)	389
Kzo9I	GATC	1 cut(s)	927
LmnI	GCTCC	2 cut(s)	491, 640
Lsp1109I	GCAGC	2 cut(s)	73, 206
LweI	GCATC	3 cut(s)	45, 396, 400
MaeI	CTAG	3 cut(s)	257, 395, 924
MaeII	ACGT	3 cut(s)	240, 288, 887
MalI	GATC	1 cut(s)	929
MboI	GATC	1 cut(s)	927
MboII	GAAGA	4 cut(s)	125, 329, 812, 1034
MhlI	GDGCHC	1 cut(s)	632
MluCI	AATT	9 cut(s)	201, 224, 249, 380, 553, 691, 763, 828, 845
MmeI	TCCRAC	3 cut(s)	245, 345, 874
MnlI	CCTC	8 cut(s)	120, 165, 391, 496, 529, 804, 1029, 1074
Mph1103I	ATGCAT	2 cut(s)	448, 452
MroXI	GAANNNNTTC	1 cut(s)	828
MseI	TTAA	3 cut(s)	227, 602, 966
MspI	CCGG	1 cut(s)	1108
MspR9I	CCNGG	6 cut(s)	326, 411, 524, 532, 579, 1108
Mva1269I	GAATGC	2 cut(s)	391, 903
MvaI	CCWGG	5 cut(s)	326, 411, 524, 532, 579
NciI	CCSGG	1 cut(s)	1108
NdeI	CATATG	1 cut(s)	40
NdeII	GATC	1 cut(s)	927
NlaIII	CATG	5 cut(s)	450, 616, 942, 973, 1143
NsbI	TGCGCA	1 cut(s)	390
NsiI	ATGCAT	2 cut(s)	448, 452
NspI	RCATGY	1 cut(s)	450
PaeI	GCATGC	1 cut(s)	450
PaqCI	CACCTGC	1 cut(s)	500
PceI	AGGCCT	1 cut(s)	577
PctI	GAATGC	2 cut(s)	391, 903
PdmI	GAANNNNTTC	1 cut(s)	828
PkrI	GCNGC	2 cut(s)	88, 221
Psp6I	CCWGG	5 cut(s)	324, 409, 522, 530, 577
PspGI	CCWGG	5 cut(s)	324, 409, 522, 530, 577
PsrI	GAACNNNNNNTAC	2 cut(s)	866, 898
RsaI	GTAC	6 cut(s)	68, 436, 565, 588, 596, 977
RsaNI	GTAC	6 cut(s)	67, 435, 564, 587, 595, 976
SaqAI	TTAA	3 cut(s)	227, 602, 966
SatI	GCNGC	2 cut(s)	87, 220
Sau3AI	GATC	1 cut(s)	927
ScrFI	CCNGG	6 cut(s)	326, 411, 524, 532, 579, 1108
SduI	GDGCHC	1 cut(s)	632
SfaNI	GCATC	3 cut(s)	45, 396, 400
SphI	GCATGC	1 cut(s)	450
Sse9I	AATT	9 cut(s)	201, 224, 249, 380, 553, 691, 763, 828, 845
SseBI	AGGCCT	1 cut(s)	577
SsiI	CCGC	2 cut(s)	665, 1039
SspI	AATATT	1 cut(s)	468
SspMI	CTAG	3 cut(s)	257, 395, 924
StuI	AGGCCT	1 cut(s)	577
StyD4I	CCNGG	6 cut(s)	324, 409, 522, 530, 577, 1106
StyI	CCWWGG	3 cut(s)	96, 923, 1005
TaaI	ACNGT	3 cut(s)	211, 283, 568
TaiI	ACGT	3 cut(s)	243, 291, 890
TaqI	TCGA	4 cut(s)	156, 213, 315, 1065
TasI	AATT	9 cut(s)	201, 224, 249, 380, 553, 691, 763, 828, 845
TatI	WGTACW	3 cut(s)	66, 594, 975
Tru1I	TTAA	3 cut(s)	227, 602, 966
Tru9I	TTAA	3 cut(s)	227, 602, 966
TscAI	CASTG	2 cut(s)	690, 762
TseI	GCWGC	2 cut(s)	86, 219
TspDTI	ATGAA	4 cut(s)	35, 213, 477, 969
TspGWI	ACGGA	4 cut(s)	203, 422, 604, 653
TspRI	CASTG	2 cut(s)	690, 762
XapI	RAATTY	2 cut(s)	691, 763
XbaI	TCTAGA	1 cut(s)	394
XceI	RCATGY	1 cut(s)	450
XmaJI	CCTAGG	1 cut(s)	923
XmnI	GAANNNNTTC	1 cut(s)	828
XspI	CTAG	3 cut(s)	257, 395, 924
Zsp2I	ATGCAT	2 cut(s)	448, 452

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