Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3A

Orthogroup ID

OG0004695

Physical Location & Seq

Genomic Coordinates Forward (+)

2572576 .. 2579058

Gene Structure 6483 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3AG038500.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 768 bp

ATGGCCGTCGGCAAGAACAAGCGGATTTCGAAGGGGAAGAAGGCTGGGAAAAAGAAGGCAGCTGACCCTTTTGCGAAGAAGGATTGGTATGATATCAAGGCACCTAATCTCTTCCATGTAAGGCAGGTTGGCAAAACCCTCGTCACCAGAACTCAGGGAACTAAGATTGCTTCTGAAGGACTCAAACATCGAGTGTTCGAGGTTTCTCTGGCTGATCTCCAGAAGGATGAGGATCATGCTTACAGAAAGATCCGTCTAAGAGCAGAGGATGTGCAAGGGAAGGATGTACTAACAAACTTCTGGGGGATGGATTTCACCACTGACAAGCTGAGGTCATTGGTCCGAAAGTGGCAGACACTGATTGAGGCTCATGTGGATGTAAAGACTACCGATAACTATACCCTTAGGATGTTCTGTATTGCTTTTACCAAGAGACGCGCAAATCAGGTCAAGCGTACCTGCTATGCTCAATCCAGTCAGATTCGTCAGATTCGCCGCAAGATGAGAGAAATTATGGTAAACCAAGCTTCAGCCTGTGATCTGAAGGAGTTGGTGCAAAAATTCATTCCTGAGATGATTGGTAGAGAGATTGAAAAGGCTACATCCAGCATCTACCCACTGCAGAATGTTTTCATTCGAAAAGCCAAGCTCTTGAAAGCTCCCAAATTCGATCTTGGCAAGTTGATGGAGGTTCATGAGAAAAAAGAGGATGTTGGTGTGAAAATTGAGAGACCAGCTGAAGAAATTGTGCCCGAGGAGACCACCTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0002181 GO:0003674 GO:0003676 GO:0003723 GO:0003729 GO:0003735 GO:0005198 GO:0005488 GO:0005575 GO:0005618 GO:0005622 GO:0005623 GO:0005634 GO:0005730 GO:0005737 GO:0005829 GO:0005840 GO:0005844 GO:0005886 GO:0005911 GO:0006412 GO:0006518 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009506 GO:0009507 GO:0009536 GO:0009987 GO:0010467 GO:0015935 GO:0016020 GO:0019538 GO:0022626 GO:0022627 GO:0030054 GO:0030312 GO:0031974 GO:0031981 GO:0032991 GO:0034641 GO:0034645 GO:0042788 GO:0043043 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0043603 GO:0043604 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044267 GO:0044271 GO:0044391 GO:0044422 GO:0044424 GO:0044428 GO:0044444 GO:0044445 GO:0044446 GO:0044464 GO:0055044 GO:0070013 GO:0071704 GO:0071944 GO:0097159 GO:1901363 GO:1901564 GO:1901566 GO:1901576 GO:1990904

KEGG Pathways

Metabolic & Signaling

ko00030 ko00710 ko01100 ko01110 ko01120 ko01130 ko01200 ko01230 ko03010 map00030 map00710 map01100 map01110 map01120 map01130 map01200 map01230 map03010

Pfam Domains

Protein Families

Ribosomal_S3Ae

Protein Analysis

255

Amino Acids

29.51

Weight (kDa)

9.9

Isoelectric Point (pI)

42.55

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Ribosomal_S3Ae	PF01015	16 - 221	3.3e-81	Ribosomal S3Ae family

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: OG0004695)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G04840 AT4G34670
fragaria_vesca	FvH4_4g00850 FvH4_6g03341
malus_domestica	MD13G1198000.v1.1 MD16G1198000.v1.1
prunus_persica	Prupe.1G019500_v2.0.a1 Prupe.6G340700_v2.0.a1
pyrus_communis	pycom16g16690
rosa_chinensis	RchiOBHm_Chr3g0451851 RchiOBHm_Chr4g0387481
rosa_laevigata	RLG00000010119 RLG00000025643
rosa_multiflora	Rmu_sc0002901.1_g000009 Rmu_sc0006510.1_g000011 Rmu_sc0009161.1_g000004 Rmu_sc0011414.1_g000002
rosa_roxburghii	Rroxscaffold_164G00436260 Rroxscaffold_5G00334160 Rroxscaffold_6G00429030
rosa_rugosa	Rorug02G0636600 Rorug03G0309800
rosa_samantha	Rh3AG038500 Rh3BG039800 Rh3CG038300 Rh3DG039100 Rh4BG010800 Rh4CG017300 Rh4DG012000
rosa_wichuraiana	Rw3G002870 Rw4G001020

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc36I	ACCTGC	2 cut(s)	115, 467
AccB1I	GGYRCC	1 cut(s)	100
AccII	CGCG	1 cut(s)	438
AciI	CCGC	2 cut(s)	22, 496
AclWI	GGATC	2 cut(s)	240, 244
AcoI	YGGCCR	1 cut(s)	3
AcsI	RAATTY	2 cut(s)	560, 665
AcuI	CTGAAG	4 cut(s)	195, 513, 563, 759
AfaI	GTAC	2 cut(s)	288, 457
AgsI	TTSAA	2 cut(s)	593, 655
AluBI	AGCT	6 cut(s)	62, 328, 527, 649, 659, 737
AluI	AGCT	6 cut(s)	62, 328, 527, 649, 659, 737
Alw26I	GTCTC	3 cut(s)	427, 724, 752
AlwI	GGATC	2 cut(s)	240, 244
AlwNI	CAGNNNCTG	1 cut(s)	358
Ama87I	CYCGRG	1 cut(s)	752
AoxI	GGCC	1 cut(s)	3
ApeKI	GCWGC	1 cut(s)	59
ApoI	RAATTY	2 cut(s)	560, 665
ArsI	GACNNNNNNTTYG	2 cut(s)	126, 158
Asp700I	GAANNNNTTC	1 cut(s)	629
AspLEI	GCGC	1 cut(s)	440
AspS9I	GGNCC	1 cut(s)	340
AsuHPI	GGTGA	2 cut(s)	136, 307
AsuII	TTCGAA	2 cut(s)	29, 637
AvaI	CYCGRG	1 cut(s)	752
AvaII	GGWCC	1 cut(s)	340
AxyI	CCTNAGG	1 cut(s)	404
BaeGI	GKGCMC	1 cut(s)	753
BanI	GGYRCC	1 cut(s)	100
BbvCI	CCTCAGC	1 cut(s)	329
BbvI	GCAGC	1 cut(s)	71
BccI	CCATC	2 cut(s)	301, 679
BcgI	CGANNNNNNTGC	2 cut(s)	121, 155
BcoDI	GTCTC	3 cut(s)	427, 724, 752
BfmI	CTRYAG	1 cut(s)	620
BfuAI	ACCTGC	2 cut(s)	115, 467
BisI	GCNGC	2 cut(s)	60, 496
BlsI	GCNGC	2 cut(s)	61, 497
Bme18I	GGWCC	1 cut(s)	340
BmeT110I	CYCGRG	1 cut(s)	752
BmgT120I	GGNCC	1 cut(s)	340
BmiI	GGNNCC	1 cut(s)	102
BmsI	GCATC	1 cut(s)	618
BpmI	CTGGAG	1 cut(s)	203
Bpu10I	CCTNAGC	1 cut(s)	329
Bpu14I	TTCGAA	2 cut(s)	29, 637
BsaBI	GATNNNNATC	1 cut(s)	231
BsaI	GGTCTC	2 cut(s)	724, 752
BsaJI	CCNNGG	1 cut(s)	753
Bse1I	ACTGG	1 cut(s)	474
Bse21I	CCTNAGG	1 cut(s)	404
Bse8I	GATNNNNATC	1 cut(s)	231
BseDI	CCNNGG	1 cut(s)	753
BseGI	GGATG	8 cut(s)	232, 274, 289, 312, 382, 414, 602, 715
BseJI	GATNNNNATC	1 cut(s)	231
BseMII	CTCAG	3 cut(s)	167, 320, 561
BseNI	ACTGG	1 cut(s)	474
BseSI	GKGCMC	1 cut(s)	753
BseXI	GCAGC	1 cut(s)	71
BseYI	CCCAGC	1 cut(s)	44
Bsh1236I	CGCG	1 cut(s)	438
BshFI	GGCC	1 cut(s)	5
BshNI	GGYRCC	1 cut(s)	100
BsiHKCI	CYCGRG	1 cut(s)	752
BsmAI	GTCTC	3 cut(s)	427, 724, 752
BsmBI	CGTCTC	1 cut(s)	427
BsnI	GGCC	1 cut(s)	5
Bso31I	GGTCTC	2 cut(s)	724, 752
BsoBI	CYCGRG	1 cut(s)	752
Bsp119I	TTCGAA	2 cut(s)	29, 637
Bsp1286I	GDGCHC	1 cut(s)	753
Bsp143I	GATC	5 cut(s)	214, 232, 249, 538, 670
BspACI	CCGC	2 cut(s)	22, 496
BspANI	GGCC	1 cut(s)	5
BspCNI	CTCAG	3 cut(s)	166, 321, 562
BspFNI	CGCG	1 cut(s)	438
BspHI	TCATGA	1 cut(s)	694
BspLI	GGNNCC	1 cut(s)	102
BspMAI	CTGCAG	1 cut(s)	624
BspMI	ACCTGC	2 cut(s)	115, 467
BspPI	GGATC	2 cut(s)	240, 244
BspT104I	TTCGAA	2 cut(s)	29, 637
BspT107I	GGYRCC	1 cut(s)	100
BspTNI	GGTCTC	2 cut(s)	724, 752
BsrI	ACTGG	1 cut(s)	474
BssECI	CCNNGG	1 cut(s)	753
BssMI	GATC	5 cut(s)	214, 232, 249, 538, 670
Bst6I	CTCTTC	1 cut(s)	116
BstBI	TTCGAA	2 cut(s)	29, 637
BstDEI	CTNAG	6 cut(s)	153, 162, 257, 329, 404, 570
BstF5I	GGATG	8 cut(s)	232, 274, 289, 312, 382, 414, 602, 715
BstFNI	CGCG	1 cut(s)	438
BstHHI	GCGC	1 cut(s)	440
BstKTI	GATC	5 cut(s)	217, 235, 252, 541, 673
BstMAI	GTCTC	3 cut(s)	427, 724, 752
BstMBI	GATC	5 cut(s)	214, 232, 249, 538, 670
BstSFI	CTRYAG	1 cut(s)	620
BstSLI	GKGCMC	1 cut(s)	753
BstUI	CGCG	1 cut(s)	438
BstV1I	GCAGC	1 cut(s)	71
BstX2I	RGATCY	1 cut(s)	249
BstYI	RGATCY	1 cut(s)	249
Bsu36I	CCTNAGG	1 cut(s)	404
BsuRI	GGCC	1 cut(s)	5
BtsCI	GGATG	8 cut(s)	232, 274, 289, 312, 382, 414, 602, 715
BtsI	GCAGTG	1 cut(s)	617
BtsIMutI	CAGTG	3 cut(s)	318, 356, 617
BveI	ACCTGC	2 cut(s)	115, 467
CaiI	CAGNNNCTG	1 cut(s)	358
CciI	TCATGA	1 cut(s)	694
CfoI	GCGC	1 cut(s)	440
Cfr13I	GGNCC	1 cut(s)	340
CseI	GACGC	1 cut(s)	444
Csp6I	GTAC	2 cut(s)	287, 456
CviAII	CATG	4 cut(s)	116, 236, 371, 695
CviQI	GTAC	2 cut(s)	287, 456
DdeI	CTNAG	6 cut(s)	153, 162, 257, 329, 404, 570
DpnI	GATC	5 cut(s)	216, 234, 251, 540, 672
DpnII	GATC	5 cut(s)	214, 232, 249, 538, 670
EaeI	YGGCCR	1 cut(s)	3
Eam1104I	CTCTTC	1 cut(s)	116
EarI	CTCTTC	1 cut(s)	116
Eco31I	GGTCTC	2 cut(s)	724, 752
Eco32I	GATATC	1 cut(s)	94
Eco47I	GGWCC	1 cut(s)	340
Eco57I	CTGAAG	4 cut(s)	195, 513, 563, 759
Eco81I	CCTNAGG	1 cut(s)	404
Eco88I	CYCGRG	1 cut(s)	752
EcoRV	GATATC	1 cut(s)	94
Esp3I	CGTCTC	1 cut(s)	427
FaeI	CATG	4 cut(s)	119, 239, 374, 698
FaiI	YATR	8 cut(s)	90, 117, 237, 372, 399, 465, 515, 696
FatI	CATG	4 cut(s)	115, 235, 370, 694
Fnu4HI	GCNGC	2 cut(s)	60, 496
FokI	GGATG	8 cut(s)	239, 281, 296, 319, 389, 421, 589, 722
Fsp4HI	GCNGC	2 cut(s)	60, 496
GlaI	GCGC	1 cut(s)	439
GluI	GCNGC	2 cut(s)	60, 496
GsaI	CCCAGC	1 cut(s)	48
GsuI	CTGGAG	1 cut(s)	203
HaeIII	GGCC	1 cut(s)	5
HgaI	GACGC	1 cut(s)	444
HhaI	GCGC	1 cut(s)	440
Hin1II	CATG	4 cut(s)	119, 239, 374, 698
Hin6I	GCGC	1 cut(s)	438
HinP1I	GCGC	1 cut(s)	438
HindIII	AAGCTT	1 cut(s)	525
HinfI	GANTC	3 cut(s)	180, 481, 490
HphI	GGTGA	2 cut(s)	136, 307
Hpy166II	GTNNAC	1 cut(s)	520
Hpy188I	TCNGA	5 cut(s)	175, 344, 480, 489, 543
Hpy188III	TCNNGA	4 cut(s)	220, 569, 652, 695
Hpy8I	GTNNAC	1 cut(s)	520
Hpy99I	CGWCG	1 cut(s)	11
HpyAV	CCTTC	8 cut(s)	25, 34, 49, 73, 170, 217, 274, 538
HpyCH4V	TGCA	3 cut(s)	274, 556, 622
HpyF3I	CTNAG	6 cut(s)	153, 162, 257, 329, 404, 570
Hsp92II	CATG	4 cut(s)	119, 239, 374, 698
HspAI	GCGC	1 cut(s)	438
Kzo9I	GATC	5 cut(s)	214, 232, 249, 538, 670
LmnI	GCTCC	1 cut(s)	664
Lsp1109I	GCAGC	1 cut(s)	71
LweI	GCATC	1 cut(s)	618
MaeIII	GTNAC	1 cut(s)	142
MalI	GATC	5 cut(s)	216, 234, 251, 540, 672
MboI	GATC	5 cut(s)	214, 232, 249, 538, 670
MboII	GAAGA	4 cut(s)	49, 88, 103, 752
MflI	RGATCY	1 cut(s)	249
MhlI	GDGCHC	1 cut(s)	753
MluCI	AATT	5 cut(s)	510, 560, 665, 723, 744
MlyI	GAGTC	1 cut(s)	174
MnlI	CCTC	9 cut(s)	149, 193, 223, 259, 324, 358, 682, 700, 748
MroXI	GAANNNNTTC	1 cut(s)	629
MslI	CAYNNNNRTG	1 cut(s)	375
MspA1I	CMGCKG	2 cut(s)	62, 737
MvnI	CGCG	1 cut(s)	438
NdeII	GATC	5 cut(s)	214, 232, 249, 538, 670
NlaIII	CATG	4 cut(s)	119, 239, 374, 698
NlaIV	GGNNCC	1 cut(s)	102
NmuCI	GTSAC	1 cut(s)	142
NspV	TTCGAA	2 cut(s)	29, 637
PagI	TCATGA	1 cut(s)	694
PdmI	GAANNNNTTC	1 cut(s)	629
PfeI	GAWTC	2 cut(s)	481, 490
PkrI	GCNGC	2 cut(s)	61, 497
PleI	GAGTC	1 cut(s)	174
PpsI	GAGTC	1 cut(s)	174
PspFI	CCCAGC	1 cut(s)	44
PspN4I	GGNNCC	1 cut(s)	102
PspPI	GGNCC	1 cut(s)	340
PstI	CTGCAG	1 cut(s)	624
PstNI	CAGNNNCTG	1 cut(s)	358
PsuI	RGATCY	1 cut(s)	249
PvuII	CAGCTG	2 cut(s)	62, 737
RsaI	GTAC	2 cut(s)	288, 457
RsaNI	GTAC	2 cut(s)	287, 456
RseI	CAYNNNNRTG	1 cut(s)	375
SatI	GCNGC	2 cut(s)	60, 496
Sau3AI	GATC	5 cut(s)	214, 232, 249, 538, 670
Sau96I	GGNCC	1 cut(s)	340
SchI	GAGTC	1 cut(s)	174
SduI	GDGCHC	1 cut(s)	753
SfaNI	GCATC	1 cut(s)	618
SfcI	CTRYAG	1 cut(s)	620
SfuI	TTCGAA	2 cut(s)	29, 637
SinI	GGWCC	1 cut(s)	340
SmiMI	CAYNNNNRTG	1 cut(s)	375
Sse9I	AATT	5 cut(s)	510, 560, 665, 723, 744
SsiI	CCGC	2 cut(s)	22, 496
TaqI	TCGA	5 cut(s)	29, 190, 198, 637, 669
TasI	AATT	5 cut(s)	510, 560, 665, 723, 744
TatI	WGTACW	1 cut(s)	286
TauI	GCSGC	1 cut(s)	498
TfiI	GAWTC	2 cut(s)	481, 490
TscAI	CASTG	3 cut(s)	325, 363, 624
TseFI	GTSAC	1 cut(s)	142
TseI	GCWGC	1 cut(s)	59
Tsp45I	GTSAC	1 cut(s)	142
TspDTI	ATGAA	3 cut(s)	553, 622, 683
TspGWI	ACGGA	1 cut(s)	242
TspRI	CASTG	3 cut(s)	325, 363, 624
VpaK11BI	GGWCC	1 cut(s)	340
XapI	RAATTY	2 cut(s)	560, 665
XmnI	GAANNNNTTC	1 cut(s)	629

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