Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3A

Orthogroup ID

OG0009156

Physical Location & Seq

Genomic Coordinates Reverse (-)

23502453 .. 23507564

Gene Structure 5112 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3AG228200.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 648 bp

ATGGAAATCGATTCGGAGAAGAACCTCCTTAGAAAACAAGCCTCCTACATCTCACAGGACGACAAGTTTGTGATGAAAGAGGTGTACCAGGGACAGCAGTACAGTCAAATTTACTTTGCGCGCCTCCATCTGATGAGGACCCTCCTCTACTCTCTTCTCCCCAATTGGAAGCCCCATTTACCAGTTTGCACAATTTTGGGATTGGAGGAAGGCAAGGAATGCACCATTGTTGGAACCCTGTACAAGCACATGAAGCTCAAACCTTCCATTCTTGACGAGTACTCTAAGACGGAACAAAACCTTGCATCGCAAATAGTTCATGTTGTAATTGCTGGAAACTCTGTTGAACTTCCTCGTGGACTTCTTAATGGACAGAACTTGGCACCAAAGGATCAATCTAGGCTCTCTTCACCAATTAAGGAGCTGGATATTATGTTGACTCAGATAGCTGCAGGTGTGCCTTTAGATATCATGCCAGGTGTAGATGACCCTGCAAATGCTTCGTTGCCTCAACAGCATTTGTGGAGATCCATTGAAGAGGGAGCTGAATGTGATAAATCTGTGGAGCCACAGCCTGAATGTTTATTTTCTTTTATGAACATTTGCTTGTTGAATATCTTATATCATGTAAGTGGGCTTTTGGAGTAG

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

215

Amino Acids

24.26

Weight (kDa)

5.39

Isoelectric Point (pI)

60.13

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
DNA_pol_D_N	PF18018	33 - 103	4.7e-19	DNA polymerase delta subunit OB-fold domain
DNA_pol_E_B	PF04042	101 - 176	1.7e-12	DNA polymerase alpha/epsilon subunit B

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)

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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)
AarI	CACCTGC	1 cut(s)	443
Acc36I	ACCTGC	1 cut(s)	443
AccB1I	GGYRCC	1 cut(s)	382
AccII	CGCG	1 cut(s)	121
AclWI	GGATC	2 cut(s)	399, 522
AcsI	RAATTY	1 cut(s)	108
AfaI	GTAC	4 cut(s)	86, 101, 242, 281
AgsI	TTSAA	3 cut(s)	347, 536, 613
AjnI	CCWGG	2 cut(s)	87, 475
AluBI	AGCT	4 cut(s)	256, 424, 449, 545
AluI	AGCT	4 cut(s)	256, 424, 449, 545
AlwI	GGATC	2 cut(s)	399, 522
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	1 cut(s)	382
BauI	CACGAG	1 cut(s)	354
BbvI	GCAGC	1 cut(s)	436
BccI	CCATC	1 cut(s)	135
BcgI	CGANNNNNNTGC	2 cut(s)	483, 517
BciT130I	CCWGG	2 cut(s)	89, 477
BfaI	CTAG	1 cut(s)	399
BfmI	CTRYAG	1 cut(s)	450
BfuAI	ACCTGC	1 cut(s)	443
BisI	GCNGC	1 cut(s)	450
BlsI	GCNGC	1 cut(s)	451
BmcAI	AGTACT	1 cut(s)	281
Bme1390I	CCNGG	2 cut(s)	89, 477
Bme18I	GGWCC	1 cut(s)	138
BmgT120I	GGNCC	1 cut(s)	138
BmiI	GGNNCC	4 cut(s)	140, 235, 384, 567
BmrFI	CCNGG	2 cut(s)	89, 477
BmsI	GCATC	1 cut(s)	314
Bsa29I	ATCGAT	1 cut(s)	9
BsaJI	CCNNGG	1 cut(s)	88
Bse1I	ACTGG	1 cut(s)	182
BseBI	CCWGG	2 cut(s)	89, 477
BseCI	ATCGAT	1 cut(s)	9
BseDI	CCNNGG	1 cut(s)	88
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	1 cut(s)	382
BshVI	ATCGAT	1 cut(s)	9
BslFI	GGGAC	1 cut(s)	105
BsmFI	GGGAC	1 cut(s)	105
BsmI	GAATGC	1 cut(s)	224
Bsp1407I	TGTACA	1 cut(s)	240
Bsp143I	GATC	2 cut(s)	391, 527
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, 567
BspMAI	CTGCAG	1 cut(s)	454
BspMI	ACCTGC	1 cut(s)	443
BspPI	GGATC	2 cut(s)	399, 522
BspT107I	GGYRCC	1 cut(s)	382
BsrGI	TGTACA	1 cut(s)	240
BsrI	ACTGG	1 cut(s)	182
BssECI	CCNNGG	1 cut(s)	88
BssHII	GCGCGC	1 cut(s)	119
BssMI	GATC	2 cut(s)	391, 527
BssSI	CACGAG	1 cut(s)	354
Bst2BI	CACGAG	1 cut(s)	354
Bst2UI	CCWGG	2 cut(s)	89, 477
Bst4CI	ACNGT	1 cut(s)	104
Bst6I	CTCTTC	3 cut(s)	159, 412, 531
BstAPI	GCANNNNNTGC	1 cut(s)	219
BstAUI	TGTACA	1 cut(s)	240
BstC8I	GCNNGC	1 cut(s)	121
BstDEI	CTNAG	3 cut(s)	29, 285, 441
BstFNI	CGCG	1 cut(s)	121
BstHHI	GCGC	2 cut(s)	121, 123
BstKTI	GATC	2 cut(s)	394, 530
BstMBI	GATC	2 cut(s)	391, 527
BstMWI	GCNNNNNNNGC	3 cut(s)	219, 253, 514
BstNI	CCWGG	2 cut(s)	89, 477
BstSCI	CCNGG	2 cut(s)	87, 475
BstSFI	CTRYAG	1 cut(s)	450
BstUI	CGCG	1 cut(s)	121
BstV1I	GCAGC	1 cut(s)	436
BstX2I	RGATCY	1 cut(s)	527
BstYI	RGATCY	1 cut(s)	527
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	4 cut(s)	85, 100, 241, 280
CviAII	CATG	4 cut(s)	250, 320, 472, 626
CviQI	GTAC	4 cut(s)	85, 100, 241, 280
DdeI	CTNAG	3 cut(s)	29, 285, 441
DpnI	GATC	2 cut(s)	393, 529
DpnII	GATC	2 cut(s)	391, 527
Eam1104I	CTCTTC	3 cut(s)	159, 412, 531
EarI	CTCTTC	3 cut(s)	159, 412, 531
Eco32I	GATATC	1 cut(s)	469
Eco47I	GGWCC	1 cut(s)	138
EcoO109I	RGGNCCY	1 cut(s)	138
EcoRII	CCWGG	2 cut(s)	87, 475
EcoRV	GATATC	1 cut(s)	469
FaeI	CATG	4 cut(s)	253, 323, 475, 629
FaiI	YATR	7 cut(s)	251, 321, 434, 473, 596, 622, 627
FaqI	GGGAC	1 cut(s)	105
FatI	CATG	4 cut(s)	249, 319, 471, 625
Fnu4HI	GCNGC	1 cut(s)	450
Fsp4HI	GCNGC	1 cut(s)	450
FspBI	CTAG	1 cut(s)	399
GlaI	GCGC	2 cut(s)	120, 122
GluI	GCNGC	1 cut(s)	450
HhaI	GCGC	2 cut(s)	121, 123
Hin1II	CATG	4 cut(s)	253, 323, 475, 629
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	3 cut(s)	16, 132, 444
Hpy188III	TCNNGA	1 cut(s)	272
Hpy8I	GTNNAC	3 cut(s)	85, 359, 438
HpyAV	CCTTC	2 cut(s)	203, 273
HpyCH4III	ACNGT	1 cut(s)	104
HpyCH4V	TGCA	5 cut(s)	189, 222, 305, 452, 494
HpyF10VI	GCNNNNNNNGC	3 cut(s)	219, 253, 514
HpyF3I	CTNAG	3 cut(s)	29, 285, 441
Hsp92II	CATG	4 cut(s)	253, 323, 475, 629
HspAI	GCGC	2 cut(s)	119, 121
Kzo9I	GATC	2 cut(s)	391, 527
LmnI	GCTCC	3 cut(s)	421, 542, 565
Lsp1109I	GCAGC	1 cut(s)	436
LweI	GCATC	1 cut(s)	314
MaeI	CTAG	1 cut(s)	399
MalI	GATC	2 cut(s)	393, 529
MboI	GATC	2 cut(s)	391, 527
MboII	GAAGA	4 cut(s)	31, 146, 399, 548
MfeI	CAATTG	1 cut(s)	163
MflI	RGATCY	1 cut(s)	527
MluCI	AATT	5 cut(s)	108, 163, 192, 327, 414
MlyI	GAGTC	1 cut(s)	433
MmeI	TCCRAC	1 cut(s)	211
MseI	TTAA	2 cut(s)	366, 417
MslI	CAYNNNNRTG	1 cut(s)	630
MspR9I	CCNGG	2 cut(s)	89, 477
MunI	CAATTG	1 cut(s)	163
Mva1269I	GAATGC	1 cut(s)	224
MvaI	CCWGG	2 cut(s)	89, 477
MvnI	CGCG	1 cut(s)	121
MwoI	GCNNNNNNNGC	3 cut(s)	219, 253, 514
NdeII	GATC	2 cut(s)	391, 527
NlaIII	CATG	4 cut(s)	253, 323, 475, 629
NlaIV	GGNNCC	4 cut(s)	140, 235, 384, 567
PaqCI	CACCTGC	1 cut(s)	443
PauI	GCGCGC	1 cut(s)	119
PctI	GAATGC	1 cut(s)	224
PfeI	GAWTC	1 cut(s)	11
PkrI	GCNGC	1 cut(s)	451
PleI	GAGTC	1 cut(s)	433
PpsI	GAGTC	1 cut(s)	433
PpuMI	RGGWCCY	1 cut(s)	138
Psp5II	RGGWCCY	1 cut(s)	138
Psp6I	CCWGG	2 cut(s)	87, 475
PspGI	CCWGG	2 cut(s)	87, 475
PspN4I	GGNNCC	4 cut(s)	140, 235, 384, 567
PspPI	GGNCC	1 cut(s)	138
PspPPI	RGGWCCY	1 cut(s)	138
PstI	CTGCAG	1 cut(s)	454
PsuI	RGATCY	1 cut(s)	527
PteI	GCGCGC	1 cut(s)	119
RsaI	GTAC	4 cut(s)	86, 101, 242, 281
RsaNI	GTAC	4 cut(s)	85, 100, 241, 280
RseI	CAYNNNNRTG	1 cut(s)	630
SaqAI	TTAA	2 cut(s)	366, 417
SatI	GCNGC	1 cut(s)	450
Sau3AI	GATC	2 cut(s)	391, 527
Sau96I	GGNCC	1 cut(s)	138
ScaI	AGTACT	1 cut(s)	281
SchI	GAGTC	1 cut(s)	433
ScrFI	CCNGG	2 cut(s)	89, 477
SfaNI	GCATC	1 cut(s)	314
SfcI	CTRYAG	1 cut(s)	450
SinI	GGWCC	1 cut(s)	138
SmiMI	CAYNNNNRTG	1 cut(s)	630
Sse9I	AATT	5 cut(s)	108, 163, 192, 327, 414
SspMI	CTAG	1 cut(s)	399
StyD4I	CCNGG	2 cut(s)	87, 475
TaaI	ACNGT	1 cut(s)	104
TaqI	TCGA	1 cut(s)	9
TasI	AATT	5 cut(s)	108, 163, 192, 327, 414
TatI	WGTACW	3 cut(s)	99, 240, 279
TfiI	GAWTC	1 cut(s)	11
Tru1I	TTAA	2 cut(s)	366, 417
Tru9I	TTAA	2 cut(s)	366, 417
TseI	GCWGC	1 cut(s)	449
TspDTI	ATGAA	4 cut(s)	89, 266, 308, 611
TspGWI	ACGGA	1 cut(s)	305
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.