Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1A

Orthogroup ID

OG0006852

Physical Location & Seq

Genomic Coordinates Forward (+)

60145016 .. 60148484

Gene Structure 3469 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1AG366300.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 957 bp

ATGTTTAAAAGACAAATCAACCCAAGTGATGTTATCATCAACGCTGGAGATACAAGTCACACTCCACGCTGCCCCATTCCTAGACGTTGGAAGAAAGTTGTATGCGATCCTCATCTTAAATGGCTCGCATATTGGAAAGATTCAATTTTCGGGAGAAGAAAGTACATGAACTTGAAATATTGCAGCAGTATGTTTGACAATTCAAAATTTAACACCGCGAGGGAACTAAAGATCAATCAAGCAGAGATCAAGCAACAATACACAGTGGATTTCACCCGTTCAAATCTTGTGGATAAGCAATGTGCAATTGTTACATATCTTATTGATACATTAGCTTTAAGACCTGGACATGTTAAGGACGAAGAAATTACTGCACCTACTGTTGGATGCTGCACTTTAATGGTGAAAAATGTAATTTTGCATGAACCCTCATGTTTGGAGTTTCGCTTTACTGGGAAAGCATCAGTCGACTACGAGAATGAGGTTGAAGTTGAAAACCTTGTGTTTAATTGCGTTAAAGAATTCCAGCTTGGGAAATCTCCTGAAGACAAGTTGGATGCCAAAAAATTGAATAGATATTTACAAAACTTGAGAAAACCTTTTGGCCTCCATTTTACAGCAAAGACATTCCGCACATTTCGAGCATTTGAAATGATGGCTGATTTGGACCAAAAATCAGAACTGGAGATTCAAAGAACTCATCCAAGAGATAAGTATTATGCCTCTGAAGCGGGAAAACTTGAGTTAGACATTGAAATAGAGAAGATAATGGAGAAGATTCATGAGCTGAGTCTACAAGAGCGTACCATAGCCTGTAGTCAAACTTATCGATTAGAAACATTGAGAGAGAATTACCTTGATCCCAGGATTACTGTTGCATGGTGTCTACGACATAGGATTTCAGTTTCTAAGGTGAGCATTTCTTTTGTTGCCGTTGGATATGGGAAAGAAATATGA

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

318

Amino Acids

37.15

Weight (kDa)

8.87

Isoelectric Point (pI)

37.91

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Topoisom_I_N	PF02919	1 - 57	1.1e-12	Eukaryotic DNA topoisomerase I, DNA binding fragment
Topoisom_I	PF01028	65 - 226	2.9e-41	Eukaryotic DNA topoisomerase I, catalytic core
Topo_C_assoc	PF14370	258 - 305	1.6e-08	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)

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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)
AccI	GTMKAC	3 cut(s)	468, 793, 886
AccII	CGCG	1 cut(s)	218
AciI	CCGC	3 cut(s)	216, 631, 731
AclWI	GGATC	2 cut(s)	101, 854
AcsI	RAATTY	2 cut(s)	206, 521
AcuI	CTGAAG	2 cut(s)	564, 747
AfaI	GTAC	2 cut(s)	164, 805
AfiI	CCNNNNNNNGG	1 cut(s)	383
AflIII	ACRYGT	1 cut(s)	349
AjnI	CCWGG	2 cut(s)	343, 863
AjuI	GAANNNNNNNTTGG	2 cut(s)	513, 545
AluBI	AGCT	3 cut(s)	335, 529, 787
AluI	AGCT	3 cut(s)	335, 529, 787
AlwI	GGATC	2 cut(s)	101, 854
AoxI	GGCC	1 cut(s)	604
ApeKI	GCWGC	3 cut(s)	69, 183, 390
ApoI	RAATTY	2 cut(s)	206, 521
AspS9I	GGNCC	1 cut(s)	667
AsuHPI	GGTGA	3 cut(s)	265, 415, 925
AvaII	GGWCC	1 cut(s)	667
BbsI	GAAGAC	1 cut(s)	552
BbvI	GCAGC	3 cut(s)	56, 195, 377
BccI	CCATC	1 cut(s)	649
BceAI	ACGGC	1 cut(s)	917
BciT130I	CCWGG	2 cut(s)	345, 865
BfaI	CTAG	1 cut(s)	81
BfmI	CTRYAG	1 cut(s)	814
BisI	GCNGC	3 cut(s)	70, 184, 391
BlsI	GCNGC	3 cut(s)	71, 185, 392
Bme1390I	CCNGG	2 cut(s)	345, 865
Bme18I	GGWCC	1 cut(s)	667
BmgT120I	GGNCC	1 cut(s)	667
BmrFI	CCNGG	2 cut(s)	345, 865
BmrI	ACTGGG	1 cut(s)	462
BmsI	GCATC	3 cut(s)	377, 470, 547
BmuI	ACTGGG	1 cut(s)	462
BpiI	GAAGAC	1 cut(s)	552
BpmI	CTGGAG	2 cut(s)	66, 704
BpuEI	CTTGAG	2 cut(s)	610, 761
Bsa29I	ATCGAT	1 cut(s)	829
BsaBI	GATNNNNATC	1 cut(s)	111
BsaJI	CCNNGG	1 cut(s)	863
Bsc4I	CCNNNNNNNGG	1 cut(s)	383
Bse1I	ACTGG	2 cut(s)	457, 687
Bse3DI	GCAATG	1 cut(s)	305
Bse8I	GATNNNNATC	1 cut(s)	111
BseBI	CCWGG	2 cut(s)	345, 865
BseCI	ATCGAT	1 cut(s)	829
BseDI	CCNNGG	1 cut(s)	863
BseGI	GGATG	3 cut(s)	392, 562, 700
BseJI	GATNNNNATC	1 cut(s)	111
BseLI	CCNNNNNNNGG	1 cut(s)	383
BseMI	GCAATG	1 cut(s)	305
BseMII	CTCAG	1 cut(s)	779
BseNI	ACTGG	2 cut(s)	457, 687
BseXI	GCAGC	3 cut(s)	56, 195, 377
BsgI	GTGCAG	2 cut(s)	357, 376
Bsh1236I	CGCG	1 cut(s)	218
BshFI	GGCC	1 cut(s)	606
BshVI	ATCGAT	1 cut(s)	829
BslI	CCNNNNNNNGG	1 cut(s)	383
BsnI	GGCC	1 cut(s)	606
Bsp143I	GATC	4 cut(s)	106, 231, 246, 859
BspACI	CCGC	3 cut(s)	216, 631, 731
BspANI	GGCC	1 cut(s)	606
BspCNI	CTCAG	1 cut(s)	780
BspDI	ATCGAT	1 cut(s)	829
BspFNI	CGCG	1 cut(s)	218
BspHI	TCATGA	1 cut(s)	781
BspPI	GGATC	2 cut(s)	101, 854
BsrDI	GCAATG	1 cut(s)	305
BsrI	ACTGG	2 cut(s)	457, 687
BssECI	CCNNGG	1 cut(s)	863
BssMI	GATC	4 cut(s)	106, 231, 246, 859
Bst2UI	CCWGG	2 cut(s)	345, 865
Bst4CI	ACNGT	3 cut(s)	265, 382, 874
BstC8I	GCNNGC	1 cut(s)	126
BstDEI	CTNAG	2 cut(s)	788, 909
BstF5I	GGATG	3 cut(s)	392, 562, 700
BstFNI	CGCG	1 cut(s)	218
BstKTI	GATC	4 cut(s)	109, 234, 249, 862
BstMBI	GATC	4 cut(s)	106, 231, 246, 859
BstMWI	GCNNNNNNNGC	1 cut(s)	728
BstNI	CCWGG	2 cut(s)	345, 865
BstNSI	RCATGY	1 cut(s)	353
BstSCI	CCNGG	2 cut(s)	343, 863
BstSFI	CTRYAG	1 cut(s)	814
BstUI	CGCG	1 cut(s)	218
BstV1I	GCAGC	3 cut(s)	56, 195, 377
BstV2I	GAAGAC	1 cut(s)	552
Bsu15I	ATCGAT	1 cut(s)	829
BsuRI	GGCC	1 cut(s)	606
BsuTUI	ATCGAT	1 cut(s)	829
BtsCI	GGATG	3 cut(s)	392, 562, 700
BtsIMutI	CAGTG	1 cut(s)	270
Cac8I	GCNNGC	1 cut(s)	126
CciI	TCATGA	1 cut(s)	781
Cfr13I	GGNCC	1 cut(s)	667
ClaI	ATCGAT	1 cut(s)	829
Csp6I	GTAC	2 cut(s)	163, 804
CspCI	CAANNNNNGTGG	2 cut(s)	270, 305
CviAII	CATG	6 cut(s)	166, 350, 422, 432, 782, 879
CviJI	RGCY	7 cut(s)	124, 335, 529, 606, 659, 787, 812
CviKI_1	RGCY	7 cut(s)	124, 335, 529, 606, 659, 787, 812
CviQI	GTAC	2 cut(s)	163, 804
DdeI	CTNAG	2 cut(s)	788, 909
DpnI	GATC	4 cut(s)	108, 233, 248, 861
DpnII	GATC	4 cut(s)	106, 231, 246, 859
DraI	TTTAAA	1 cut(s)	7
Eco47I	GGWCC	1 cut(s)	667
Eco57I	CTGAAG	2 cut(s)	564, 747
EcoRI	GAATTC	1 cut(s)	521
EcoRII	CCWGG	2 cut(s)	343, 863
FaeI	CATG	6 cut(s)	169, 353, 425, 435, 785, 882
FatI	CATG	6 cut(s)	165, 349, 421, 431, 781, 878
FauI	CCCGC	1 cut(s)	724
FblI	GTMKAC	3 cut(s)	468, 793, 886
Fnu4HI	GCNGC	3 cut(s)	70, 184, 391
FokI	GGATG	3 cut(s)	399, 569, 687
Fsp4HI	GCNGC	3 cut(s)	70, 184, 391
FspBI	CTAG	1 cut(s)	81
GluI	GCNGC	3 cut(s)	70, 184, 391
GsuI	CTGGAG	2 cut(s)	66, 704
HaeIII	GGCC	1 cut(s)	606
Hin1II	CATG	6 cut(s)	169, 353, 425, 435, 785, 882
HincII	GTYRAC	1 cut(s)	469
HindII	GTYRAC	1 cut(s)	469
HinfI	GANTC	4 cut(s)	140, 688, 778, 790
HphI	GGTGA	3 cut(s)	265, 415, 925
Hpy166II	GTNNAC	3 cut(s)	469, 794, 887
Hpy188I	TCNGA	2 cut(s)	679, 727
Hpy188III	TCNNGA	3 cut(s)	151, 542, 782
Hpy8I	GTNNAC	3 cut(s)	469, 794, 887
HpyCH4III	ACNGT	3 cut(s)	265, 382, 874
HpyCH4IV	ACGT	1 cut(s)	85
HpyCH4V	TGCA	6 cut(s)	183, 305, 374, 393, 421, 878
HpyF10VI	GCNNNNNNNGC	1 cut(s)	728
HpyF3I	CTNAG	2 cut(s)	788, 909
HpySE526I	ACGT	1 cut(s)	85
Hsp92II	CATG	6 cut(s)	169, 353, 425, 435, 785, 882
Kzo9I	GATC	4 cut(s)	106, 231, 246, 859
Lsp1109I	GCAGC	3 cut(s)	56, 195, 377
LweI	GCATC	3 cut(s)	377, 470, 547
MaeI	CTAG	1 cut(s)	81
MaeII	ACGT	1 cut(s)	85
MaeIII	GTNAC	2 cut(s)	56, 310
MalI	GATC	4 cut(s)	108, 233, 248, 861
MboI	GATC	4 cut(s)	106, 231, 246, 859
MboII	GAAGA	6 cut(s)	103, 168, 374, 557, 775, 787
MfeI	CAATTG	1 cut(s)	306
MlyI	GAGTC	1 cut(s)	799
MmeI	TCCRAC	4 cut(s)	68, 364, 534, 916
MnlI	CCTC	6 cut(s)	120, 213, 439, 475, 617, 733
MseI	TTAA	8 cut(s)	6, 117, 210, 338, 354, 398, 507, 516
MslI	CAYNNNNRTG	1 cut(s)	398
MspR9I	CCNGG	2 cut(s)	345, 865
MunI	CAATTG	1 cut(s)	306
MvaI	CCWGG	2 cut(s)	345, 865
MvnI	CGCG	1 cut(s)	218
MwoI	GCNNNNNNNGC	1 cut(s)	728
NdeII	GATC	4 cut(s)	106, 231, 246, 859
NlaIII	CATG	6 cut(s)	169, 353, 425, 435, 785, 882
NmuCI	GTSAC	1 cut(s)	56
NspI	RCATGY	1 cut(s)	353
PagI	TCATGA	1 cut(s)	781
PciI	ACATGT	1 cut(s)	349
PfeI	GAWTC	3 cut(s)	140, 688, 778
PkrI	GCNGC	3 cut(s)	71, 185, 392
PleI	GAGTC	1 cut(s)	798
PpsI	GAGTC	1 cut(s)	798
PscI	ACATGT	1 cut(s)	349
Psp6I	CCWGG	2 cut(s)	343, 863
PspGI	CCWGG	2 cut(s)	343, 863
PspPI	GGNCC	1 cut(s)	667
RsaI	GTAC	2 cut(s)	164, 805
RsaNI	GTAC	2 cut(s)	163, 804
RseI	CAYNNNNRTG	1 cut(s)	398
SalI	GTCGAC	1 cut(s)	467
SaqAI	TTAA	8 cut(s)	6, 117, 210, 338, 354, 398, 507, 516
SatI	GCNGC	3 cut(s)	70, 184, 391
Sau3AI	GATC	4 cut(s)	106, 231, 246, 859
Sau96I	GGNCC	1 cut(s)	667
SchI	GAGTC	1 cut(s)	799
ScrFI	CCNGG	2 cut(s)	345, 865
SfaNI	GCATC	3 cut(s)	377, 470, 547
SfcI	CTRYAG	1 cut(s)	814
SinI	GGWCC	1 cut(s)	667
SmiMI	CAYNNNNRTG	1 cut(s)	398
SmlI	CTYRAG	2 cut(s)	589, 740
SmoI	CTYRAG	2 cut(s)	589, 740
SsiI	CCGC	3 cut(s)	216, 631, 731
SspI	AATATT	1 cut(s)	179
SspMI	CTAG	1 cut(s)	81
StyD4I	CCNGG	2 cut(s)	343, 863
TaaI	ACNGT	3 cut(s)	265, 382, 874
TaiI	ACGT	1 cut(s)	88
TaqI	TCGA	3 cut(s)	468, 640, 829
TatI	WGTACW	1 cut(s)	162
TfiI	GAWTC	3 cut(s)	140, 688, 778
Tru1I	TTAA	8 cut(s)	6, 117, 210, 338, 354, 398, 507, 516
Tru9I	TTAA	8 cut(s)	6, 117, 210, 338, 354, 398, 507, 516
TscAI	CASTG	1 cut(s)	270
TseFI	GTSAC	1 cut(s)	56
TseI	GCWGC	3 cut(s)	69, 183, 390
Tsp45I	GTSAC	1 cut(s)	56
TspDTI	ATGAA	3 cut(s)	182, 438, 770
TspRI	CASTG	1 cut(s)	270
VpaK11BI	GGWCC	1 cut(s)	667
XapI	RAATTY	2 cut(s)	206, 521
XceI	RCATGY	1 cut(s)	353
XmiI	GTMKAC	3 cut(s)	468, 793, 886
XspI	CTAG	1 cut(s)	81

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