Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000003

Orthogroup ID

OG0015425

Physical Location & Seq

Genomic Coordinates Forward (+)

50855646 .. 50859170

Gene Structure 3525 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_3G00256460.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 885 bp

ATGCAAGACAGTGGCTTGGGAATGATGGGTTCTGGCGGAGGTGGAGGTCTGAGTGGCGGTGGCGGCGGCGGTGGTGACGACCATACTCACCAACTCAAGTCTGAGATTGCCACACACCCTCTGTGCGAACAACTCCTGTCGGCACACGTGTCGTGTCTCCGGGTCGCCACTCCGATCGATCAATTGCCGTTGATCGATGCTCAGCTCTCACAGTCACACCATCTCCTCCGCTCCTACGCCTCGCACCAACAACAGCGCGGCCATTCTTTATCGCCCCATGAGCGCCAAGAGCTCGATAACTTCTTGTCGCAGTATTTGATAGTGTTGTGCTCGTTCAAAGAACAACTGCAGCAACATGTGAGAGTTCATGCCGTCGAGGCGGTCATGGCCTGCCGTGAAATTGAAAGCACCTTGCAGGCTCTTACTGGAGTGAGTCTGGGTGAAGGAACAGGTGCAACAATGTCAGATGATGAAGATGACATGCCAATGGATTTCTCTATGGATCAAGCTGGCTCTGATGCCCACGACATGATGGGATTTGGACTCCCTACTGAATCTGAAAGATCTCTCATGGAAAGAGTTCGTCAGGAATTGAAGATTGAGCTTAAGCAGGGTTTTAAGTCGAGAATTGAGGATGTAAGGGAGGAAATCTTAAGAAAAAGAAGGGCAGGGAAATTACCTGGAGACACAACTACAGTGCTGAAGAATTGGTGGCAGCAACACTCGAAGTGGCCATATCCAACTGAAGATGACAAGGCAAAACTTGTGGAAGAGACAGGGTTGCAGCTTAAGCAAATAAACAATTGGTTCATCAATCAAAGGAAGCGCAATTGGCACAGCAACTCTCAGTCAGTGACTTCTTTGAAGTCGAAGCGCAAAAGATGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0003700 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0006355 GO:0008150 GO:0008152 GO:0009058 GO:0009888 GO:0009889 GO:0009890 GO:0009892 GO:0009987 GO:0010087 GO:0010089 GO:0010191 GO:0010192 GO:0010468 GO:0010556 GO:0010558 GO:0010605 GO:0010629 GO:0019219 GO:0019222 GO:0031323 GO:0031324 GO:0031326 GO:0031327 GO:0032502 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044087 GO:0044237 GO:0044249 GO:0044424 GO:0044464 GO:0045892 GO:0045934 GO:0048519 GO:0048523 GO:0048856 GO:0050789 GO:0050794 GO:0051171 GO:0051172 GO:0051252 GO:0051253 GO:0060255 GO:0065007 GO:0080090 GO:0140110 GO:1902679 GO:1903338 GO:1903506 GO:1903507 GO:2000112 GO:2000113 GO:2000652 GO:2001141

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

ELK Homeobox_KN KNOX1 KNOX2

Protein Analysis

294

Amino Acids

32.92

Weight (kDa)

6.27

Isoelectric Point (pI)

60.45

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
KNOX1	PF03790	32 - 73	3.4e-18	KNOX1 domain
KNOX2	PF03791	92 - 142	6.5e-17	KNOX2 domain
Homeobox_KN	PF05920	237 - 276	3.8e-19	Homeobox KN domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0015425)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G62990
fragaria_vesca	FvH4_5g01260
malus_domestica	MD04G1069700.v1.1 MD06G1071100.v1.1
prunus_persica	Prupe.5G088100_v2.0.a1 Prupe.5G088100_v2.0.a1
pyrus_communis	pycom04g06340
rosa_chinensis	RchiOBHm_Chr7g0199751
rosa_laevigata	RLG00000003773
rosa_multiflora	Rmu_sc0002748.1_g000022
rosa_roxburghii	Rroxscaffold_3G00256460
rosa_rugosa	Rorug07G0056000 Rorug07G0056100
rosa_samantha	Rh7AG181500 Rh7BG184300
rosa_wichuraiana	Rw7G015910

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccBSI	CCGCTC	1 cut(s)	231
AccII	CGCG	1 cut(s)	258
AciI	CCGC	8 cut(s)	36, 57, 63, 66, 69, 229, 258, 380
AclWI	GGATC	1 cut(s)	510
AcoI	YGGCCR	2 cut(s)	259, 731
AcuI	CTGAAG	2 cut(s)	722, 765
AcvI	CACGTG	1 cut(s)	148
AflII	CTTAAG	3 cut(s)	605, 652, 788
AflIII	ACRYGT	3 cut(s)	145, 147, 355
AgsI	TTSAA	4 cut(s)	337, 404, 595, 865
AjnI	CCWGG	1 cut(s)	679
AluBI	AGCT	5 cut(s)	205, 292, 509, 604, 787
AluI	AGCT	5 cut(s)	205, 292, 509, 604, 787
Alw21I	GWGCWC	2 cut(s)	294, 332
Alw26I	GTCTC	3 cut(s)	161, 678, 767
AlwI	GGATC	1 cut(s)	510
AoxI	GGCC	3 cut(s)	259, 387, 731
ApeKI	GCWGC	3 cut(s)	349, 715, 784
Asp700I	GAANNNNTTC	1 cut(s)	579
AspLEI	GCGC	4 cut(s)	258, 285, 828, 876
AsuC2I	CCSGG	1 cut(s)	161
AsuHPI	GGTGA	3 cut(s)	80, 86, 452
BalI	TGGCCA	1 cut(s)	733
BanII	GRGCYC	1 cut(s)	294
BbrPI	CACGTG	1 cut(s)	148
Bbv12I	GWGCWC	2 cut(s)	294, 332
BbvI	GCAGC	3 cut(s)	361, 727, 796
BccI	CCATC	3 cut(s)	19, 228, 526
BceAI	ACGGC	3 cut(s)	172, 356, 378
BcgI	CGANNNNNNTGC	2 cut(s)	132, 166
BciT130I	CCWGG	1 cut(s)	681
BcnI	CCSGG	1 cut(s)	161
BcoDI	GTCTC	3 cut(s)	161, 678, 767
BfmI	CTRYAG	2 cut(s)	347, 693
BfoI	RGCGCY	1 cut(s)	286
BfrI	CTTAAG	3 cut(s)	605, 652, 788
BglI	GCCNNNNNGGC	1 cut(s)	377
BglII	AGATCT	1 cut(s)	563
BisI	GCNGC	6 cut(s)	64, 67, 259, 350, 716, 785
BlpI	GCTNAGC	1 cut(s)	201
BlsI	GCNGC	6 cut(s)	65, 68, 260, 351, 717, 786
Bme1390I	CCNGG	2 cut(s)	161, 681
BmrFI	CCNGG	2 cut(s)	161, 681
BmsI	GCATC	2 cut(s)	187, 508
BpmI	CTGGAG	2 cut(s)	447, 702
Bpu1102I	GCTNAGC	1 cut(s)	201
BpuEI	CTTGAG	1 cut(s)	80
BpuMI	CCSGG	1 cut(s)	161
Bsa29I	ATCGAT	2 cut(s)	177, 195
BsaAI	YACGTR	1 cut(s)	148
BsaXI	ACNNNNNCTCC	2 cut(s)	207, 237
Bse1I	ACTGG	1 cut(s)	430
BseBI	CCWGG	1 cut(s)	681
BseCI	ATCGAT	2 cut(s)	177, 195
BseGI	GGATG	1 cut(s)	640
BseMII	CTCAG	4 cut(s)	41, 93, 215, 860
BseNI	ACTGG	1 cut(s)	430
BseRI	GAGGAG	1 cut(s)	215
BseXI	GCAGC	3 cut(s)	361, 727, 796
Bsh1236I	CGCG	1 cut(s)	258
Bsh1285I	CGRYCG	1 cut(s)	177
BshFI	GGCC	3 cut(s)	261, 389, 733
BshVI	ATCGAT	2 cut(s)	177, 195
BsiEI	CGRYCG	1 cut(s)	177
BsiHKAI	GWGCWC	2 cut(s)	294, 332
BsiSI	CCGG	1 cut(s)	160
BsmAI	GTCTC	3 cut(s)	161, 678, 767
BsnI	GGCC	3 cut(s)	261, 389, 733
Bsp1286I	GDGCHC	2 cut(s)	294, 332
Bsp143I	GATC	5 cut(s)	174, 178, 192, 502, 563
Bsp1720I	GCTNAGC	1 cut(s)	201
BspACI	CCGC	8 cut(s)	36, 57, 63, 66, 69, 229, 258, 380
BspANI	GGCC	3 cut(s)	261, 389, 733
BspCNI	CTCAG	4 cut(s)	42, 94, 214, 859
BspDI	ATCGAT	2 cut(s)	177, 195
BspFNI	CGCG	1 cut(s)	258
BspMAI	CTGCAG	1 cut(s)	351
BspPI	GGATC	1 cut(s)	510
BspTI	CTTAAG	3 cut(s)	605, 652, 788
BsrBI	CCGCTC	1 cut(s)	231
BsrI	ACTGG	1 cut(s)	430
BssMI	GATC	5 cut(s)	174, 178, 192, 502, 563
Bst2UI	CCWGG	1 cut(s)	681
Bst4CI	ACNGT	3 cut(s)	11, 213, 697
Bst6I	CTCTTC	1 cut(s)	765
BstAFI	CTTAAG	3 cut(s)	605, 652, 788
BstBAI	YACGTR	1 cut(s)	148
BstC8I	GCNNGC	3 cut(s)	391, 417, 511
BstDEI	CTNAG	4 cut(s)	50, 102, 201, 846
BstF5I	GGATG	1 cut(s)	640
BstFNI	CGCG	1 cut(s)	258
BstH2I	RGCGCY	1 cut(s)	286
BstHHI	GCGC	4 cut(s)	258, 285, 828, 876
BstKTI	GATC	5 cut(s)	177, 181, 195, 505, 566
BstMAI	GTCTC	3 cut(s)	161, 678, 767
BstMBI	GATC	5 cut(s)	174, 178, 192, 502, 563
BstMCI	CGRYCG	1 cut(s)	177
BstMWI	GCNNNNNNNGC	7 cut(s)	63, 280, 289, 377, 386, 790, 832
BstNI	CCWGG	1 cut(s)	681
BstNSI	RCATGY	2 cut(s)	359, 484
BstSCI	CCNGG	2 cut(s)	159, 679
BstSFI	CTRYAG	2 cut(s)	347, 693
BstUI	CGCG	1 cut(s)	258
BstV1I	GCAGC	3 cut(s)	361, 727, 796
BstX2I	RGATCY	1 cut(s)	563
BstYI	RGATCY	1 cut(s)	563
Bsu15I	ATCGAT	2 cut(s)	177, 195
BsuRI	GGCC	3 cut(s)	261, 389, 733
BsuTUI	ATCGAT	2 cut(s)	177, 195
BtsCI	GGATG	1 cut(s)	640
BtsIMutI	CAGTG	3 cut(s)	16, 702, 858
Cac8I	GCNNGC	3 cut(s)	391, 417, 511
CfoI	GCGC	4 cut(s)	258, 285, 828, 876
ClaI	ATCGAT	2 cut(s)	177, 195
CspCI	CAANNNNNGTGG	2 cut(s)	747, 782
CviAII	CATG	7 cut(s)	278, 356, 368, 385, 481, 529, 571
DdeI	CTNAG	4 cut(s)	50, 102, 201, 846
DpnI	GATC	5 cut(s)	176, 180, 194, 504, 565
DpnII	GATC	5 cut(s)	174, 178, 192, 502, 563
EaeI	YGGCCR	2 cut(s)	259, 731
Eam1104I	CTCTTC	1 cut(s)	765
EarI	CTCTTC	1 cut(s)	765
EciI	GGCGGA	1 cut(s)	51
Ecl136II	GAGCTC	1 cut(s)	292
Eco24I	GRGCYC	1 cut(s)	294
Eco53kI	GAGCTC	1 cut(s)	292
Eco57I	CTGAAG	2 cut(s)	722, 765
Eco72I	CACGTG	1 cut(s)	148
EcoICRI	GAGCTC	1 cut(s)	292
EcoRII	CCWGG	1 cut(s)	679
EcoT38I	GRGCYC	1 cut(s)	294
FaeI	CATG	7 cut(s)	281, 359, 371, 388, 484, 532, 574
FatI	CATG	7 cut(s)	277, 355, 367, 384, 480, 528, 570
Fnu4HI	GCNGC	6 cut(s)	64, 67, 259, 350, 716, 785
FokI	GGATG	1 cut(s)	647
FriOI	GRGCYC	1 cut(s)	294
Fsp4HI	GCNGC	6 cut(s)	64, 67, 259, 350, 716, 785
GlaI	GCGC	4 cut(s)	257, 284, 827, 875
GluI	GCNGC	6 cut(s)	64, 67, 259, 350, 716, 785
GsuI	CTGGAG	2 cut(s)	447, 702
HaeII	RGCGCY	1 cut(s)	286
HaeIII	GGCC	3 cut(s)	261, 389, 733
HapII	CCGG	1 cut(s)	160
HhaI	GCGC	4 cut(s)	258, 285, 828, 876
Hin1II	CATG	7 cut(s)	281, 359, 371, 388, 484, 532, 574
Hin6I	GCGC	4 cut(s)	256, 283, 826, 874
HinP1I	GCGC	4 cut(s)	256, 283, 826, 874
HinfI	GANTC	3 cut(s)	433, 543, 554
HpaII	CCGG	1 cut(s)	160
HphI	GGTGA	3 cut(s)	80, 86, 452
Hpy188I	TCNGA	6 cut(s)	51, 103, 174, 466, 517, 559
Hpy188III	TCNNGA	2 cut(s)	587, 624
Hpy99I	CGWCG	1 cut(s)	377
HpyAV	CCTTC	2 cut(s)	437, 657
HpyCH4III	ACNGT	3 cut(s)	11, 213, 697
HpyCH4IV	ACGT	1 cut(s)	147
HpyCH4V	TGCA	5 cut(s)	4, 349, 415, 455, 784
HpyF10VI	GCNNNNNNNGC	7 cut(s)	63, 280, 289, 377, 386, 790, 832
HpyF3I	CTNAG	4 cut(s)	50, 102, 201, 846
HpySE526I	ACGT	1 cut(s)	147
Hsp92II	CATG	7 cut(s)	281, 359, 371, 388, 484, 532, 574
HspAI	GCGC	4 cut(s)	256, 283, 826, 874
Kzo9I	GATC	5 cut(s)	174, 178, 192, 502, 563
LmnI	GCTCC	1 cut(s)	236
Lsp1109I	GCAGC	3 cut(s)	361, 727, 796
LweI	GCATC	2 cut(s)	187, 508
MaeII	ACGT	1 cut(s)	147
MaeIII	GTNAC	3 cut(s)	74, 213, 853
MalI	GATC	5 cut(s)	176, 180, 194, 504, 565
MbiI	CCGCTC	1 cut(s)	231
MboI	GATC	5 cut(s)	174, 178, 192, 502, 563
MboII	GAAGA	5 cut(s)	485, 607, 715, 758, 782
MfeI	CAATTG	3 cut(s)	182, 802, 829
MflI	RGATCY	1 cut(s)	563
MhlI	GDGCHC	2 cut(s)	294, 332
MlsI	TGGCCA	1 cut(s)	733
MluCI	AATT	8 cut(s)	182, 399, 590, 627, 674, 706, 802, 829
MluNI	TGGCCA	1 cut(s)	733
MlyI	GAGTC	2 cut(s)	442, 537
MmeI	TCCRAC	1 cut(s)	764
MnlI	CCTC	8 cut(s)	32, 38, 129, 236, 250, 370, 625, 637
Mox20I	TGGCCA	1 cut(s)	733
MroXI	GAANNNNTTC	1 cut(s)	579
MscI	TGGCCA	1 cut(s)	733
MseI	TTAA	4 cut(s)	606, 618, 653, 789
MslI	CAYNNNNRTG	1 cut(s)	485
Msp20I	TGGCCA	1 cut(s)	733
MspCI	CTTAAG	3 cut(s)	605, 652, 788
MspI	CCGG	1 cut(s)	160
MspR9I	CCNGG	2 cut(s)	161, 681
MunI	CAATTG	3 cut(s)	182, 802, 829
MvaI	CCWGG	1 cut(s)	681
MvnI	CGCG	1 cut(s)	258
MwoI	GCNNNNNNNGC	7 cut(s)	63, 280, 289, 377, 386, 790, 832
NciI	CCSGG	1 cut(s)	161
NdeII	GATC	5 cut(s)	174, 178, 192, 502, 563
NlaIII	CATG	7 cut(s)	281, 359, 371, 388, 484, 532, 574
NmuCI	GTSAC	3 cut(s)	74, 213, 853
NspI	RCATGY	2 cut(s)	359, 484
PciI	ACATGT	1 cut(s)	355
PdmI	GAANNNNTTC	1 cut(s)	579
PfeI	GAWTC	1 cut(s)	554
PkrI	GCNGC	6 cut(s)	65, 68, 260, 351, 717, 786
Ple19I	CGATCG	1 cut(s)	177
PleI	GAGTC	2 cut(s)	441, 537
PmaCI	CACGTG	1 cut(s)	148
PmlI	CACGTG	1 cut(s)	148
PpsI	GAGTC	2 cut(s)	441, 537
Ppu21I	YACGTR	1 cut(s)	148
PscI	ACATGT	1 cut(s)	355
Psp124BI	GAGCTC	1 cut(s)	294
Psp6I	CCWGG	1 cut(s)	679
PspCI	CACGTG	1 cut(s)	148
PspGI	CCWGG	1 cut(s)	679
PstI	CTGCAG	1 cut(s)	351
PsuI	RGATCY	1 cut(s)	563
PvuI	CGATCG	1 cut(s)	177
RseI	CAYNNNNRTG	1 cut(s)	485
SacI	GAGCTC	1 cut(s)	294
SaqAI	TTAA	4 cut(s)	606, 618, 653, 789
SatI	GCNGC	6 cut(s)	64, 67, 259, 350, 716, 785
Sau3AI	GATC	5 cut(s)	174, 178, 192, 502, 563
SchI	GAGTC	2 cut(s)	442, 537
ScrFI	CCNGG	2 cut(s)	161, 681
SduI	GDGCHC	2 cut(s)	294, 332
SfaNI	GCATC	2 cut(s)	187, 508
SfcI	CTRYAG	2 cut(s)	347, 693
SmiMI	CAYNNNNRTG	1 cut(s)	485
SmlI	CTYRAG	4 cut(s)	95, 605, 652, 788
SmoI	CTYRAG	4 cut(s)	95, 605, 652, 788
Sse9I	AATT	8 cut(s)	182, 399, 590, 627, 674, 706, 802, 829
SsiI	CCGC	8 cut(s)	36, 57, 63, 66, 69, 229, 258, 380
SstI	GAGCTC	1 cut(s)	294
StyD4I	CCNGG	2 cut(s)	159, 679
TaaI	ACNGT	3 cut(s)	11, 213, 697
TaiI	ACGT	1 cut(s)	150
TaqI	TCGA	7 cut(s)	177, 195, 294, 375, 623, 725, 869
TasI	AATT	8 cut(s)	182, 399, 590, 627, 674, 706, 802, 829
TauI	GCSGC	3 cut(s)	66, 69, 261
TfiI	GAWTC	1 cut(s)	554
Tru1I	TTAA	4 cut(s)	606, 618, 653, 789
Tru9I	TTAA	4 cut(s)	606, 618, 653, 789
TscAI	CASTG	3 cut(s)	16, 702, 858
TseFI	GTSAC	3 cut(s)	74, 213, 853
TseI	GCWGC	3 cut(s)	349, 715, 784
Tsp45I	GTSAC	3 cut(s)	74, 213, 853
TspDTI	ATGAA	3 cut(s)	356, 486, 799
TspRI	CASTG	3 cut(s)	16, 702, 858
Vha464I	CTTAAG	3 cut(s)	605, 652, 788
XceI	RCATGY	2 cut(s)	359, 484
XmnI	GAANNNNTTC	1 cut(s)	579

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