Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000003

Orthogroup ID

OG0002636

Physical Location & Seq

Genomic Coordinates Reverse (-)

56289568 .. 56295543

Gene Structure 5976 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_3G00262250.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1062 bp

ATGGAAGAACTCTGCGGTTTCAGTAGTGGTTCTGATCATTATTACTCTTCTTCTTCAATGGCTATGCCACAGGAAAACTCGCCACTCGCCGACTACTACAGGAGATTCGAGCCTCTAACGGCGGTTGTACCCGAGAGTAGCTCCGACCCGGTATATTATTACTCGGGTTCTAATTCATCCACCGTGTCCGATTGTGTTTCGGTGGCGGTAGCAGGAAATCAACGAGGAGGAGAAGAGGTGTCGTGTACTACCGTTAATGCTAAGATCGCTTCTCATCCTCTCTACCCTAATCTTGTTCAAGCTTACATCGATTGCCAAAAGGTGGGAGCGCCTACGCAAATAGCGCATGTTTTGGAGGAAATCCGGCGAGAAAGTGATCAGCTCAGTAGGATAACCGTCGGTTCGACTTGCATGGGTGTCGATCCTGAGCTCGATGAGTTCATGGAAACTTACTGTGATATATTGTTGAAGTACAAATCGGATCTGACAAAGCCGTTCAACGAAGCAATCACCTTCTTGAACAGCATGGAGACGCAGCTCAACAATCTCGCCAATACCATTTCCGCTGTTGAAACTACAGTACTACTAGTACTGGTTGAATCTGCGGTGGCTGTGCTTTTGCTCCCCTGGGGTTTCTGTTTGCTAGCTGATGCTCCAGCAGTTAATTCTTCTGATGACGAAGACTTGAGTGGAGGAGAGATCGAAGTACAGGACTCTGATCATCAGCGAACACATGAAGATCACGAATTGAAGGACAAGCTGTTGCGTAAATACAGTGGTTATATAAGCACTCTGAAGCATGAGTTTTCTAAGAAAAAGAAGAAGGGAAAGCTGCCTAAAGATGCTAAGCAAATCCTTACGGATTGGTGGAACCTTCACTATAAATGGCCATATCCAACGGAAGTAGACAAGATGACACTGGCCCAAGTGACGGGTTTGGATCCGAAACAAATAAACAACTGGTTTATAAATCAAAGGAAGCGCCATTGGAAACCATCGGAAAACATGCAGTTTGCTGTTATGGAAAGCCTCTATGGTCCTAGTACTTTTTCCAGAGACTGA

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:0009888 GO:0009889 GO:0010073 GO:0010468 GO:0010556 GO:0019219 GO:0019222 GO:0031323 GO:0031326 GO:0032501 GO:0032502 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044424 GO:0044464 GO:0048507 GO:0048856 GO:0050789 GO:0050794 GO:0051171 GO:0051252 GO:0060255 GO:0065007 GO:0080090 GO:0140110 GO:1903506 GO:2000112 GO:2001141

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

ELK Homeobox_KN KNOX1 KNOX2

Protein Analysis

353

Amino Acids

39.7

Weight (kDa)

5.03

Isoelectric Point (pI)

44.71

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
KNOX1	PF03790	86 - 126	1.4e-18	KNOX1 domain
KNOX2	PF03791	137 - 183	6.2e-24	KNOX2 domain
ELK	PF03789	249 - 270	1.9e-11	ELK domain
Homeobox_KN	PF05920	289 - 328	7.2e-18	Homeobox KN domain
Homeodomain	PF00046	297 - 329	7.4e-06	Homeodomain

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)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0002636)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G23380 AT1G23380 AT1G70510 AT1G70510
fragaria_vesca	FvH4_4g26090 FvH4_4g26090 FvH4_4g26090 FvH4_4g26090 FvH4_5g05530 FvH4_5g05530
malus_domestica	MD06G1171700.v1.1 MD13G1095800.v1.1 MD14G1177200.v1.1 MD16G1097200.v1.1
prunus_persica	Prupe.1G249600_v2.0.a1 Prupe.5G171100_v2.0.a1
pyrus_communis	pycom06g15280 pycom13g08340 pycom14g14800 pycom16g08280
rosa_chinensis	RchiOBHm_Chr4g0433571 RchiOBHm_Chr7g0193251
rosa_laevigata	RLG00000004283 RLG00000006743
rosa_multiflora	Rmu_sc0017266.1_g000003
rosa_roxburghii	Rroxscaffold_3G00262250 Rroxscaffold_5G00375060
rosa_rugosa	Rorug04G0269800 Rorug07G0008500 Rorug07G0008600
rosa_samantha	Rh4AG324700 Rh4BG332400 Rh4CG347700 Rh4DG328800 Rh7AG134100 Rh7BG135100 Rh7CG138100 Rh7DG136100
rosa_wichuraiana	Rw4G028100 Rw7G011470

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	968
AccB7I	CCANNNNNTGG	1 cut(s)	322
AccI	GTMKAC	1 cut(s)	906
AciI	CCGC	5 cut(s)	15, 122, 206, 564, 605
AclWI	GGATC	4 cut(s)	416, 489, 935, 948
AcoI	YGGCCR	1 cut(s)	887
AcuI	CTGAAG	1 cut(s)	815
AfaI	GTAC	7 cut(s)	129, 247, 473, 582, 591, 708, 1045
AfiI	CCNNNNNNNGG	2 cut(s)	322, 931
AgsI	TTSAA	8 cut(s)	57, 299, 469, 499, 520, 572, 599, 751
AhlI	ACTAGT	1 cut(s)	586
AjnI	CCWGG	1 cut(s)	626
AluBI	AGCT	8 cut(s)	141, 302, 382, 430, 538, 647, 760, 832
AluI	AGCT	8 cut(s)	141, 302, 382, 430, 538, 647, 760, 832
Alw21I	GWGCWC	1 cut(s)	432
Alw26I	GTCTC	2 cut(s)	524, 1050
AlwI	GGATC	4 cut(s)	416, 489, 935, 948
AlwNI	CAGNNNCTG	1 cut(s)	1059
Ama87I	CYCGRG	2 cut(s)	131, 163
AoxI	GGCC	2 cut(s)	887, 921
ApeKI	GCWGC	2 cut(s)	535, 832
AspLEI	GCGC	3 cut(s)	331, 346, 984
AspS9I	GGNCC	2 cut(s)	922, 1037
AsuC2I	CCSGG	1 cut(s)	149
AsuHPI	GGTGA	1 cut(s)	502
AsuNHI	GCTAGC	1 cut(s)	643
AvaI	CYCGRG	2 cut(s)	131, 163
AvaII	GGWCC	1 cut(s)	1037
BalI	TGGCCA	1 cut(s)	889
BamHI	GGATCC	1 cut(s)	940
BanII	GRGCYC	1 cut(s)	432
BbsI	GAAGAC	1 cut(s)	687
Bbv12I	GWGCWC	1 cut(s)	432
BbvI	GCAGC	2 cut(s)	547, 819
BccI	CCATC	1 cut(s)	1003
BceAI	ACGGC	2 cut(s)	135, 478
BcgI	CGANNNNNNTGC	2 cut(s)	400, 434
BciT130I	CCWGG	1 cut(s)	628
BclI	TGATCA	3 cut(s)	34, 376, 718
BcnI	CCSGG	1 cut(s)	149
BcoDI	GTCTC	2 cut(s)	524, 1050
BcuI	ACTAGT	1 cut(s)	586
BfaI	CTAG	3 cut(s)	587, 644, 1041
BfmI	CTRYAG	2 cut(s)	97, 576
BfoI	RGCGCY	2 cut(s)	332, 985
BisI	GCNGC	2 cut(s)	536, 833
BlpI	GCTNAGC	1 cut(s)	846
BlsI	GCNGC	2 cut(s)	537, 834
BmcAI	AGTACT	3 cut(s)	582, 591, 1045
Bme1390I	CCNGG	2 cut(s)	149, 628
Bme18I	GGWCC	1 cut(s)	1037
BmeT110I	CYCGRG	2 cut(s)	131, 163
BmgT120I	GGNCC	2 cut(s)	922, 1037
BmiI	GGNNCC	2 cut(s)	872, 942
BmrFI	CCNGG	2 cut(s)	149, 628
BmsI	GCATC	2 cut(s)	640, 832
BmtI	GCTAGC	1 cut(s)	647
BpiI	GAAGAC	1 cut(s)	687
BplI	GAGNNNNNCTC	2 cut(s)	125, 157
BpmI	CTGGAG	1 cut(s)	639
Bpu10I	CCTNAGC	1 cut(s)	426
Bpu1102I	GCTNAGC	1 cut(s)	846
BpuEI	CTTGAG	1 cut(s)	706
BpuMI	CCSGG	1 cut(s)	149
Bsa29I	ATCGAT	1 cut(s)	309
BsaJI	CCNNGG	2 cut(s)	626, 627
BsaXI	ACNNNNNCTCC	2 cut(s)	222, 252
Bsc4I	CCNNNNNNNGG	2 cut(s)	322, 931
Bse1I	ACTGG	3 cut(s)	597, 924, 965
BseBI	CCWGG	1 cut(s)	628
BseCI	ATCGAT	1 cut(s)	309
BseDI	CCNNGG	2 cut(s)	626, 627
BseGI	GGATG	2 cut(s)	176, 274
BseLI	CCNNNNNNNGG	2 cut(s)	322, 931
BseMII	CTCAG	2 cut(s)	397, 417
BseNI	ACTGG	3 cut(s)	597, 924, 965
BseRI	GAGGAG	3 cut(s)	240, 243, 708
BseXI	GCAGC	2 cut(s)	547, 819
BshFI	GGCC	2 cut(s)	889, 923
BshVI	ATCGAT	1 cut(s)	309
BsiHKAI	GWGCWC	1 cut(s)	432
BsiHKCI	CYCGRG	2 cut(s)	131, 163
BsiSI	CCGG	2 cut(s)	149, 364
BslI	CCNNNNNNNGG	2 cut(s)	322, 931
BsmAI	GTCTC	2 cut(s)	524, 1050
BsmBI	CGTCTC	1 cut(s)	524
BsnI	GGCC	2 cut(s)	889, 923
BsoBI	CYCGRG	2 cut(s)	131, 163
Bsp1286I	GDGCHC	1 cut(s)	432
Bsp143I	GATC	9 cut(s)	34, 264, 376, 421, 481, 699, 718, 739, 940
Bsp1720I	GCTNAGC	1 cut(s)	846
BspACI	CCGC	5 cut(s)	15, 122, 206, 564, 605
BspANI	GGCC	2 cut(s)	889, 923
BspCNI	CTCAG	2 cut(s)	396, 418
BspDI	ATCGAT	1 cut(s)	309
BspLI	GGNNCC	2 cut(s)	872, 942
BspOI	GCTAGC	1 cut(s)	647
BspPI	GGATC	4 cut(s)	416, 489, 935, 948
BsrI	ACTGG	3 cut(s)	597, 924, 965
BssECI	CCNNGG	2 cut(s)	626, 627
BssMI	GATC	9 cut(s)	34, 264, 376, 421, 481, 699, 718, 739, 940
Bst2UI	CCWGG	1 cut(s)	628
Bst4CI	ACNGT	6 cut(s)	184, 253, 397, 455, 580, 776
Bst6I	CTCTTC	2 cut(s)	52, 228
BstC8I	GCNNGC	1 cut(s)	645
BstDEI	CTNAG	5 cut(s)	261, 383, 426, 810, 846
BstF5I	GGATG	2 cut(s)	176, 274
BstH2I	RGCGCY	2 cut(s)	332, 985
BstHHI	GCGC	3 cut(s)	331, 346, 984
BstKTI	GATC	9 cut(s)	37, 267, 379, 424, 484, 702, 721, 742, 943
BstMAI	GTCTC	2 cut(s)	524, 1050
BstMBI	GATC	9 cut(s)	34, 264, 376, 421, 481, 699, 718, 739, 940
BstMWI	GCNNNNNNNGC	2 cut(s)	266, 343
BstNI	CCWGG	1 cut(s)	628
BstNSI	RCATGY	2 cut(s)	350, 1009
BstSCI	CCNGG	2 cut(s)	147, 626
BstSFI	CTRYAG	2 cut(s)	97, 576
BstV1I	GCAGC	2 cut(s)	547, 819
BstV2I	GAAGAC	1 cut(s)	687
BstX2I	RGATCY	2 cut(s)	481, 940
BstYI	RGATCY	2 cut(s)	481, 940
Bsu15I	ATCGAT	1 cut(s)	309
BsuRI	GGCC	2 cut(s)	889, 923
BsuTUI	ATCGAT	1 cut(s)	309
BtsCI	GGATG	2 cut(s)	176, 274
BtsIMutI	CAGTG	2 cut(s)	781, 917
Cac8I	GCNNGC	1 cut(s)	645
CaiI	CAGNNNCTG	1 cut(s)	1059
CfoI	GCGC	3 cut(s)	331, 346, 984
Cfr13I	GGNCC	2 cut(s)	922, 1037
ClaI	ATCGAT	1 cut(s)	309
CseI	GACGC	1 cut(s)	541
Csp6I	GTAC	7 cut(s)	128, 246, 472, 581, 590, 707, 1044
CviAII	CATG	7 cut(s)	347, 412, 442, 526, 734, 800, 1006
CviQI	GTAC	7 cut(s)	128, 246, 472, 581, 590, 707, 1044
DdeI	CTNAG	5 cut(s)	261, 383, 426, 810, 846
DpnI	GATC	9 cut(s)	36, 266, 378, 423, 483, 701, 720, 741, 942
DpnII	GATC	9 cut(s)	34, 264, 376, 421, 481, 699, 718, 739, 940
EaeI	YGGCCR	1 cut(s)	887
Eam1104I	CTCTTC	2 cut(s)	52, 228
EarI	CTCTTC	2 cut(s)	52, 228
Ecl136II	GAGCTC	1 cut(s)	430
Eco24I	GRGCYC	1 cut(s)	432
Eco47I	GGWCC	1 cut(s)	1037
Eco53kI	GAGCTC	1 cut(s)	430
Eco57I	CTGAAG	1 cut(s)	815
Eco88I	CYCGRG	2 cut(s)	131, 163
EcoICRI	GAGCTC	1 cut(s)	430
EcoRII	CCWGG	1 cut(s)	626
EcoT38I	GRGCYC	1 cut(s)	432
Esp3I	CGTCTC	1 cut(s)	524
FaeI	CATG	7 cut(s)	350, 415, 445, 529, 737, 803, 1009
FatI	CATG	7 cut(s)	346, 411, 441, 525, 733, 799, 1005
FbaI	TGATCA	3 cut(s)	34, 376, 718
FblI	GTMKAC	1 cut(s)	906
Fnu4HI	GCNGC	2 cut(s)	536, 833
FokI	GGATG	2 cut(s)	163, 261
FriOI	GRGCYC	1 cut(s)	432
Fsp4HI	GCNGC	2 cut(s)	536, 833
FspBI	CTAG	3 cut(s)	587, 644, 1041
GlaI	GCGC	3 cut(s)	330, 345, 983
GluI	GCNGC	2 cut(s)	536, 833
GsuI	CTGGAG	1 cut(s)	639
HaeII	RGCGCY	2 cut(s)	332, 985
HaeIII	GGCC	2 cut(s)	889, 923
HapII	CCGG	2 cut(s)	149, 364
HgaI	GACGC	1 cut(s)	541
HhaI	GCGC	3 cut(s)	331, 346, 984
Hin1II	CATG	7 cut(s)	350, 415, 445, 529, 737, 803, 1009
Hin6I	GCGC	3 cut(s)	329, 344, 982
HinP1I	GCGC	3 cut(s)	329, 344, 982
HindIII	AAGCTT	1 cut(s)	300
HinfI	GANTC	3 cut(s)	105, 599, 713
HpaII	CCGG	2 cut(s)	149, 364
HphI	GGTGA	1 cut(s)	502
Hpy166II	GTNNAC	2 cut(s)	246, 907
Hpy188III	TCNNGA	4 cut(s)	425, 517, 743, 1053
Hpy8I	GTNNAC	2 cut(s)	246, 907
Hpy99I	CGWCG	1 cut(s)	401
HpyAV	CCTTC	4 cut(s)	523, 745, 817, 884
HpyCH4III	ACNGT	6 cut(s)	184, 253, 397, 455, 580, 776
HpyCH4V	TGCA	2 cut(s)	411, 1009
HpyF10VI	GCNNNNNNNGC	2 cut(s)	266, 343
HpyF3I	CTNAG	5 cut(s)	261, 383, 426, 810, 846
Hsp92II	CATG	7 cut(s)	350, 415, 445, 529, 737, 803, 1009
HspAI	GCGC	3 cut(s)	329, 344, 982
Ksp22I	TGATCA	3 cut(s)	34, 376, 718
Kzo9I	GATC	9 cut(s)	34, 264, 376, 421, 481, 699, 718, 739, 940
LmnI	GCTCC	4 cut(s)	146, 326, 627, 658
Lsp1109I	GCAGC	2 cut(s)	547, 819
LweI	GCATC	2 cut(s)	640, 832
MaeI	CTAG	3 cut(s)	587, 644, 1041
MaeIII	GTNAC	1 cut(s)	928
MalI	GATC	9 cut(s)	36, 266, 378, 423, 483, 701, 720, 741, 942
MboI	GATC	9 cut(s)	34, 264, 376, 421, 481, 699, 718, 739, 940
MboII	GAAGA	9 cut(s)	17, 39, 42, 45, 245, 660, 692, 749, 832
MflI	RGATCY	2 cut(s)	481, 940
MhlI	GDGCHC	1 cut(s)	432
MlsI	TGGCCA	1 cut(s)	889
MluCI	AATT	3 cut(s)	172, 664, 746
MluNI	TGGCCA	1 cut(s)	889
MlyI	GAGTC	1 cut(s)	707
MmeI	TCCRAC	2 cut(s)	168, 920
MnlI	CCTC	8 cut(s)	123, 218, 221, 229, 288, 349, 686, 1040
Mox20I	TGGCCA	1 cut(s)	889
MscI	TGGCCA	1 cut(s)	889
MseI	TTAA	2 cut(s)	255, 663
Msp20I	TGGCCA	1 cut(s)	889
MspA1I	CMGCKG	1 cut(s)	566
MspI	CCGG	2 cut(s)	149, 364
MspR9I	CCNGG	2 cut(s)	149, 628
MvaI	CCWGG	1 cut(s)	628
MwoI	GCNNNNNNNGC	2 cut(s)	266, 343
NciI	CCSGG	1 cut(s)	149
NdeII	GATC	9 cut(s)	34, 264, 376, 421, 481, 699, 718, 739, 940
NheI	GCTAGC	1 cut(s)	643
NlaIII	CATG	7 cut(s)	350, 415, 445, 529, 737, 803, 1009
NlaIV	GGNNCC	2 cut(s)	872, 942
NmuCI	GTSAC	1 cut(s)	928
NspI	RCATGY	2 cut(s)	350, 1009
PasI	CCCWGGG	1 cut(s)	627
PfeI	GAWTC	2 cut(s)	105, 599
PflMI	CCANNNNNTGG	1 cut(s)	322
PkrI	GCNGC	2 cut(s)	537, 834
PleI	GAGTC	1 cut(s)	707
PpsI	GAGTC	1 cut(s)	707
PsiI	TTATAA	1 cut(s)	968
Psp124BI	GAGCTC	1 cut(s)	432
Psp6I	CCWGG	1 cut(s)	626
PspGI	CCWGG	1 cut(s)	626
PspN4I	GGNNCC	2 cut(s)	872, 942
PspPI	GGNCC	2 cut(s)	922, 1037
PstNI	CAGNNNCTG	1 cut(s)	1059
PsuI	RGATCY	2 cut(s)	481, 940
RsaI	GTAC	7 cut(s)	129, 247, 473, 582, 591, 708, 1045
RsaNI	GTAC	7 cut(s)	128, 246, 472, 581, 590, 707, 1044
SacI	GAGCTC	1 cut(s)	432
SaqAI	TTAA	2 cut(s)	255, 663
SatI	GCNGC	2 cut(s)	536, 833
Sau3AI	GATC	9 cut(s)	34, 264, 376, 421, 481, 699, 718, 739, 940
Sau96I	GGNCC	2 cut(s)	922, 1037
ScaI	AGTACT	3 cut(s)	582, 591, 1045
SchI	GAGTC	1 cut(s)	707
ScrFI	CCNGG	2 cut(s)	149, 628
SduI	GDGCHC	1 cut(s)	432
SfaNI	GCATC	2 cut(s)	640, 832
SfcI	CTRYAG	2 cut(s)	97, 576
SinI	GGWCC	1 cut(s)	1037
SmlI	CTYRAG	1 cut(s)	685
SmoI	CTYRAG	1 cut(s)	685
SpeI	ACTAGT	1 cut(s)	586
Sse9I	AATT	3 cut(s)	172, 664, 746
SsiI	CCGC	5 cut(s)	15, 122, 206, 564, 605
SspMI	CTAG	3 cut(s)	587, 644, 1041
SstI	GAGCTC	1 cut(s)	432
StyD4I	CCNGG	2 cut(s)	147, 626
TaaI	ACNGT	6 cut(s)	184, 253, 397, 455, 580, 776
TaqI	TCGA	6 cut(s)	108, 309, 404, 420, 432, 702
TasI	AATT	3 cut(s)	172, 664, 746
TatI	WGTACW	6 cut(s)	245, 471, 580, 589, 706, 1043
TfiI	GAWTC	2 cut(s)	105, 599
Tru1I	TTAA	2 cut(s)	255, 663
Tru9I	TTAA	2 cut(s)	255, 663
TscAI	CASTG	2 cut(s)	781, 924
TseFI	GTSAC	1 cut(s)	928
TseI	GCWGC	2 cut(s)	535, 832
Tsp45I	GTSAC	1 cut(s)	928
TspDTI	ATGAA	3 cut(s)	165, 430, 750
TspGWI	ACGGA	2 cut(s)	875, 914
TspRI	CASTG	2 cut(s)	781, 924
Van91I	CCANNNNNTGG	1 cut(s)	322
VpaK11BI	GGWCC	1 cut(s)	1037
XceI	RCATGY	2 cut(s)	350, 1009
XmiI	GTMKAC	1 cut(s)	906
XspI	CTAG	3 cut(s)	587, 644, 1041
ZrmI	AGTACT	3 cut(s)	582, 591, 1045

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