Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3D

Orthogroup ID

OG0009156

Physical Location & Seq

Genomic Coordinates Reverse (-)

25205984 .. 25211439

Gene Structure 5456 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3DG254700.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 792 bp

ATGGAAATCGATTCGGAGAAGAACCTCCATAGAAAACAAGCCTCCTACATCTCACAGGACGACAAGTTTGTGATGAAAGAGGTGTACCAGGGACAGCAGTACAGTCAAATTTACTTTGCGCGCCTCCATCTGATGAGGACCCTCCTCTACTCTCTTCTCCCCAATTGGAAGCCCCATTTACCAGTTTGCACAATTTTGGGATTGGAGGAAGGCAAGGAATGCACCATTGTTGGAACCCTGTACAAGCACATGAAGCTCAAACCTTCCATTCTTGATGAGTACTCTAAGACGGAACAAAACCTTGCATCGCAAATAGTTCATGTTGTAATTGCTGGAAACTCTGTTGAACTTCCTCGTGGACTTCTTAATGGACAGAACTTGGCACCAAAGGATCAATCTAGGCTCTCTTCACCAATTAAGGAGCTGGATATTATGTTGACTCAGATAGCTGCAGGTGTGCCTTTAGATATCATGCCAGGTGTAGATGACCCTGCAAATGCTTCGTTGCCTCAACAGCCTTTAAACAGATGCCTTTTCCCTGGGTCATCAGTTTATAACACGTTTAGATCATGTACTAATCCTCATTCCTTTGATCTTGATGAGATGAGATTTGTTGGAACATCAGGGCAAAATATAGATGACCTTGATAGGTATTCAGAAGCAAAGGATAGACTTGAATATCTTGAAAGAACATTGAGGTGGAGGCATCTGGCACCAACAGCACCAAACACTCTTGCCGCCGTGATCACGGAATGCTCATTTCAAGTTGTTGCTGGAATGAGCATTCAGTAA

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

263

Amino Acids

29.67

Weight (kDa)

5.98

Isoelectric Point (pI)

48.38

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
DNA_pol_D_N	PF18018	33 - 103	7.1e-19	DNA polymerase delta subunit OB-fold domain
DNA_pol_E_B	PF04042	101 - 248	7.3e-38	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

Font Size (px)

Line Width

Align Labels (Cladogram)

Image

Tree File

Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready

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

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)	555
AarI	CACCTGC	1 cut(s)	443
Acc36I	ACCTGC	1 cut(s)	443
AccB1I	GGYRCC	2 cut(s)	382, 712
AccII	CGCG	1 cut(s)	121
AciI	CCGC	1 cut(s)	738
AclWI	GGATC	1 cut(s)	399
AcsI	RAATTY	1 cut(s)	108
AfaI	GTAC	5 cut(s)	86, 101, 242, 281, 574
AflIII	ACRYGT	1 cut(s)	558
AgsI	TTSAA	4 cut(s)	347, 677, 686, 764
AjnI	CCWGG	3 cut(s)	87, 475, 538
AluBI	AGCT	3 cut(s)	256, 424, 449
AluI	AGCT	3 cut(s)	256, 424, 449
AlwI	GGATC	1 cut(s)	399
ApeKI	GCWGC	1 cut(s)	449
ApoI	RAATTY	1 cut(s)	108
ArsI	GACNNNNNNTTYG	2 cut(s)	50, 82
AspLEI	GCGC	2 cut(s)	121, 123
AspS9I	GGNCC	1 cut(s)	138
AsuHPI	GGTGA	1 cut(s)	402
AvaII	GGWCC	1 cut(s)	138
BanI	GGYRCC	2 cut(s)	382, 712
BauI	CACGAG	1 cut(s)	354
BbvI	GCAGC	1 cut(s)	436
BccI	CCATC	1 cut(s)	135
BceAI	ACGGC	1 cut(s)	725
BcgI	CGANNNNNNTGC	2 cut(s)	483, 517
BciT130I	CCWGG	3 cut(s)	89, 477, 540
BclI	TGATCA	1 cut(s)	744
BfaI	CTAG	1 cut(s)	399
BfmI	CTRYAG	1 cut(s)	450
BfuAI	ACCTGC	1 cut(s)	443
BisI	GCNGC	2 cut(s)	450, 738
BlsI	GCNGC	2 cut(s)	451, 739
BmcAI	AGTACT	1 cut(s)	281
Bme1390I	CCNGG	3 cut(s)	89, 477, 540
Bme18I	GGWCC	1 cut(s)	138
BmgT120I	GGNCC	1 cut(s)	138
BmiI	GGNNCC	4 cut(s)	140, 235, 384, 714
BmrFI	CCNGG	3 cut(s)	89, 477, 540
BmsI	GCATC	3 cut(s)	314, 518, 715
Bsa29I	ATCGAT	1 cut(s)	9
BsaJI	CCNNGG	3 cut(s)	88, 538, 539
Bse1I	ACTGG	1 cut(s)	182
BseBI	CCWGG	3 cut(s)	89, 477, 540
BseCI	ATCGAT	1 cut(s)	9
BseDI	CCNNGG	3 cut(s)	88, 538, 539
BseMII	CTCAG	1 cut(s)	455
BseNI	ACTGG	1 cut(s)	182
BsePI	GCGCGC	1 cut(s)	119
BseRI	GAGGAG	1 cut(s)	134
BseXI	GCAGC	1 cut(s)	436
Bsh1236I	CGCG	1 cut(s)	121
BshNI	GGYRCC	2 cut(s)	382, 712
BshVI	ATCGAT	1 cut(s)	9
BslFI	GGGAC	1 cut(s)	105
BsmFI	GGGAC	1 cut(s)	105
BsmI	GAATGC	3 cut(s)	224, 758, 783
Bsp1407I	TGTACA	1 cut(s)	240
Bsp143I	GATC	4 cut(s)	391, 566, 592, 744
BspACI	CCGC	1 cut(s)	738
BspCNI	CTCAG	1 cut(s)	454
BspDI	ATCGAT	1 cut(s)	9
BspFNI	CGCG	1 cut(s)	121
BspLI	GGNNCC	4 cut(s)	140, 235, 384, 714
BspMAI	CTGCAG	1 cut(s)	454
BspMI	ACCTGC	1 cut(s)	443
BspPI	GGATC	1 cut(s)	399
BspT107I	GGYRCC	2 cut(s)	382, 712
BsrGI	TGTACA	1 cut(s)	240
BsrI	ACTGG	1 cut(s)	182
BssECI	CCNNGG	3 cut(s)	88, 538, 539
BssHII	GCGCGC	1 cut(s)	119
BssMI	GATC	4 cut(s)	391, 566, 592, 744
BssSI	CACGAG	1 cut(s)	354
Bst2BI	CACGAG	1 cut(s)	354
Bst2UI	CCWGG	3 cut(s)	89, 477, 540
Bst4CI	ACNGT	1 cut(s)	104
Bst6I	CTCTTC	2 cut(s)	159, 412
BstAPI	GCANNNNNTGC	1 cut(s)	219
BstAUI	TGTACA	1 cut(s)	240
BstC8I	GCNNGC	1 cut(s)	121
BstDEI	CTNAG	2 cut(s)	285, 441
BstFNI	CGCG	1 cut(s)	121
BstHHI	GCGC	2 cut(s)	121, 123
BstKTI	GATC	4 cut(s)	394, 569, 595, 747
BstMBI	GATC	4 cut(s)	391, 566, 592, 744
BstMWI	GCNNNNNNNGC	4 cut(s)	219, 253, 514, 719
BstNI	CCWGG	3 cut(s)	89, 477, 540
BstSCI	CCNGG	3 cut(s)	87, 475, 538
BstSFI	CTRYAG	1 cut(s)	450
BstUI	CGCG	1 cut(s)	121
BstV1I	GCAGC	1 cut(s)	436
Bsu15I	ATCGAT	1 cut(s)	9
BsuTUI	ATCGAT	1 cut(s)	9
BtgZI	GCGATG	1 cut(s)	291
BveI	ACCTGC	1 cut(s)	443
Cac8I	GCNNGC	1 cut(s)	121
CfoI	GCGC	2 cut(s)	121, 123
Cfr13I	GGNCC	1 cut(s)	138
ClaI	ATCGAT	1 cut(s)	9
Csp6I	GTAC	5 cut(s)	85, 100, 241, 280, 573
CviAII	CATG	4 cut(s)	250, 320, 472, 570
CviJI	RGCY	7 cut(s)	41, 172, 256, 403, 424, 449, 517
CviKI_1	RGCY	7 cut(s)	41, 172, 256, 403, 424, 449, 517
CviQI	GTAC	5 cut(s)	85, 100, 241, 280, 573
DdeI	CTNAG	2 cut(s)	285, 441
DpnI	GATC	4 cut(s)	393, 568, 594, 746
DpnII	GATC	4 cut(s)	391, 566, 592, 744
DraI	TTTAAA	1 cut(s)	522
Eam1104I	CTCTTC	2 cut(s)	159, 412
EarI	CTCTTC	2 cut(s)	159, 412
Eco32I	GATATC	1 cut(s)	469
Eco47I	GGWCC	1 cut(s)	138
EcoO109I	RGGNCCY	1 cut(s)	138
EcoRII	CCWGG	3 cut(s)	87, 475, 538
EcoRV	GATATC	1 cut(s)	469
FaeI	CATG	4 cut(s)	253, 323, 475, 573
FaiI	YATR	8 cut(s)	30, 251, 321, 434, 473, 555, 571, 635
FaqI	GGGAC	1 cut(s)	105
FatI	CATG	4 cut(s)	249, 319, 471, 569
FbaI	TGATCA	1 cut(s)	744
Fnu4HI	GCNGC	2 cut(s)	450, 738
Fsp4HI	GCNGC	2 cut(s)	450, 738
FspBI	CTAG	1 cut(s)	399
GlaI	GCGC	2 cut(s)	120, 122
GluI	GCNGC	2 cut(s)	450, 738
HhaI	GCGC	2 cut(s)	121, 123
Hin1II	CATG	4 cut(s)	253, 323, 475, 573
Hin6I	GCGC	2 cut(s)	119, 121
HinP1I	GCGC	2 cut(s)	119, 121
HincII	GTYRAC	1 cut(s)	438
HindII	GTYRAC	1 cut(s)	438
HinfI	GANTC	2 cut(s)	11, 439
HphI	GGTGA	1 cut(s)	402
Hpy166II	GTNNAC	3 cut(s)	85, 359, 438
Hpy188I	TCNGA	4 cut(s)	16, 132, 444, 658
Hpy188III	TCNNGA	3 cut(s)	272, 596, 683
Hpy8I	GTNNAC	3 cut(s)	85, 359, 438
HpyAV	CCTTC	2 cut(s)	203, 273
HpyCH4III	ACNGT	1 cut(s)	104
HpyCH4IV	ACGT	1 cut(s)	560
HpyCH4V	TGCA	5 cut(s)	189, 222, 305, 452, 494
HpyF10VI	GCNNNNNNNGC	4 cut(s)	219, 253, 514, 719
HpyF3I	CTNAG	2 cut(s)	285, 441
HpySE526I	ACGT	1 cut(s)	560
Hsp92II	CATG	4 cut(s)	253, 323, 475, 573
HspAI	GCGC	2 cut(s)	119, 121
Ksp22I	TGATCA	1 cut(s)	744
Kzo9I	GATC	4 cut(s)	391, 566, 592, 744
LmnI	GCTCC	1 cut(s)	421
Lsp1109I	GCAGC	1 cut(s)	436
LweI	GCATC	3 cut(s)	314, 518, 715
MaeI	CTAG	1 cut(s)	399
MaeII	ACGT	1 cut(s)	560
MalI	GATC	4 cut(s)	393, 568, 594, 746
MboI	GATC	4 cut(s)	391, 566, 592, 744
MboII	GAAGA	3 cut(s)	31, 146, 399
MfeI	CAATTG	1 cut(s)	163
MluCI	AATT	5 cut(s)	108, 163, 192, 327, 414
MlyI	GAGTC	1 cut(s)	433
MmeI	TCCRAC	2 cut(s)	211, 595
MseI	TTAA	3 cut(s)	366, 417, 521
MslI	CAYNNNNRTG	1 cut(s)	697
MspR9I	CCNGG	3 cut(s)	89, 477, 540
MunI	CAATTG	1 cut(s)	163
Mva1269I	GAATGC	3 cut(s)	224, 758, 783
MvaI	CCWGG	3 cut(s)	89, 477, 540
MvnI	CGCG	1 cut(s)	121
MwoI	GCNNNNNNNGC	4 cut(s)	219, 253, 514, 719
NdeII	GATC	4 cut(s)	391, 566, 592, 744
NlaIII	CATG	4 cut(s)	253, 323, 475, 573
NlaIV	GGNNCC	4 cut(s)	140, 235, 384, 714
PaqCI	CACCTGC	1 cut(s)	443
PasI	CCCWGGG	1 cut(s)	539
PauI	GCGCGC	1 cut(s)	119
PctI	GAATGC	3 cut(s)	224, 758, 783
PfeI	GAWTC	1 cut(s)	11
PkrI	GCNGC	2 cut(s)	451, 739
PleI	GAGTC	1 cut(s)	433
PpsI	GAGTC	1 cut(s)	433
PpuMI	RGGWCCY	1 cut(s)	138
PsiI	TTATAA	1 cut(s)	555
Psp5II	RGGWCCY	1 cut(s)	138
Psp6I	CCWGG	3 cut(s)	87, 475, 538
PspGI	CCWGG	3 cut(s)	87, 475, 538
PspN4I	GGNNCC	4 cut(s)	140, 235, 384, 714
PspPI	GGNCC	1 cut(s)	138
PspPPI	RGGWCCY	1 cut(s)	138
PstI	CTGCAG	1 cut(s)	454
PteI	GCGCGC	1 cut(s)	119
RsaI	GTAC	5 cut(s)	86, 101, 242, 281, 574
RsaNI	GTAC	5 cut(s)	85, 100, 241, 280, 573
RseI	CAYNNNNRTG	1 cut(s)	697
SaqAI	TTAA	3 cut(s)	366, 417, 521
SatI	GCNGC	2 cut(s)	450, 738
Sau3AI	GATC	4 cut(s)	391, 566, 592, 744
Sau96I	GGNCC	1 cut(s)	138
ScaI	AGTACT	1 cut(s)	281
SchI	GAGTC	1 cut(s)	433
ScrFI	CCNGG	3 cut(s)	89, 477, 540
SfaNI	GCATC	3 cut(s)	314, 518, 715
SfcI	CTRYAG	1 cut(s)	450
SinI	GGWCC	1 cut(s)	138
SmiMI	CAYNNNNRTG	1 cut(s)	697
Sse9I	AATT	5 cut(s)	108, 163, 192, 327, 414
SsiI	CCGC	1 cut(s)	738
SspMI	CTAG	1 cut(s)	399
StyD4I	CCNGG	3 cut(s)	87, 475, 538
TaaI	ACNGT	1 cut(s)	104
TaiI	ACGT	1 cut(s)	563
TaqI	TCGA	1 cut(s)	9
TasI	AATT	5 cut(s)	108, 163, 192, 327, 414
TatI	WGTACW	4 cut(s)	99, 240, 279, 572
TauI	GCSGC	1 cut(s)	740
TfiI	GAWTC	1 cut(s)	11
Tru1I	TTAA	3 cut(s)	366, 417, 521
Tru9I	TTAA	3 cut(s)	366, 417, 521
TseI	GCWGC	1 cut(s)	449
TspDTI	ATGAA	3 cut(s)	89, 266, 308
TspGWI	ACGGA	2 cut(s)	305, 764
VpaK11BI	GGWCC	1 cut(s)	138
XapI	RAATTY	1 cut(s)	108
XspI	CTAG	1 cut(s)	399
ZrmI	AGTACT	1 cut(s)	281

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