Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5A

Orthogroup ID

OG0002529

Physical Location & Seq

Genomic Coordinates Forward (+)

1166860 .. 1172024

Gene Structure 5165 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5AG016200.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 972 bp

ATGCAGGGTGGCTCTAATGGCACTAATTCGATGGCGTTTGGAGATAACAGTACTAACACTAACGGCGGAGGAGGGCTGTTTCCGATGACGATGATGATGCCTCTGATGACTACTAACTCCCAGCACCATCATGGTCATCACTCGCTTCACTCGAATAACAGTCCATTTCTTCTGCTACCTCCAAACCAAAACAATCATCAGCAAGACCAAACCCGCAATAGCAGCGGCGGCAGCTCATCTTTTGCTCTTGATAACCATAGCAATAACCCTGCAGCGGCGGCAGGCTGTTATTTCATGGATCACAACAACAACAGTGGTCATGGAAGCTCTTCTTCCTCTTCGTCTTCTTATATCAAGTCAAAGATCATGGCTCATCCTCACTATCACCGTCTACTGGCCGCCTACATCAACTGTCAAAAGGTTGGGGCGCCACCGGAGGTGGTGGGGAGGCTGGAAGAAGCATGCGAGTCGGCGACAACGATAGGTCAGATGGTAAGTAGTAGTAGTGGAAGTGCACATGGACATGGTTCCCTTGGTGAAGATCCAGCTCTGGATCAGTTCATGGAGGCCTACTGTGAGATGCTGATCAAGTATGAGCAAGAGGTCTCCAAACCCTTCAAGGAAGCCATGCTTTTTTTAAAGAAGATCGAGTCCCAATTCAAAACCCTCACCGTTTCTTCTGCTTCCGATTCTGGTTGTGGAGAGGGAGGTATGGATAGGAACAATAATGGATCATCTGAAGAAGAGGTTGATGTGAATAACAGCTTGATAGATCCGCAAGCAGAAGATAGGGAGCTCAAAGGTCAGCTTCTGCGCAAGTACAGTGGATACTTGGGTAGCTTGAAGCAGGAGTTCATGAAGAAGAGGAAGAAAGGCAAGCTGCCTAAAGAGGCGAGGCAGCAGTTGCTCGATTGGTGGAGCCGACATTACAAATGGCCTTATCCATCAGTAAGTACTACTTCCACAGTTTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0003006 GO:0003674 GO:0003676 GO:0003700 GO:0003723 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005737 GO:0005856 GO:0005911 GO:0006355 GO:0006725 GO:0006807 GO:0006810 GO:0007275 GO:0008150 GO:0008152 GO:0009058 GO:0009308 GO:0009506 GO:0009690 GO:0009691 GO:0009791 GO:0009889 GO:0009908 GO:0009934 GO:0009987 GO:0010468 GO:0010496 GO:0010497 GO:0010556 GO:0010817 GO:0015630 GO:0019219 GO:0019222 GO:0019827 GO:0022414 GO:0022603 GO:0030054 GO:0031323 GO:0031326 GO:0032501 GO:0032502 GO:0034754 GO:0042445 GO:0042446 GO:0042802 GO:0042803 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0044237 GO:0044249 GO:0044424 GO:0044464 GO:0046483 GO:0046983 GO:0048367 GO:0048437 GO:0048438 GO:0048440 GO:0048467 GO:0048509 GO:0048608 GO:0048731 GO:0048827 GO:0048856 GO:0050789 GO:0050793 GO:0050794 GO:0051171 GO:0051179 GO:0051234 GO:0051252 GO:0055044 GO:0060255 GO:0061458 GO:0065007 GO:0065008 GO:0071704 GO:0080090 GO:0090567 GO:0097159 GO:0098727 GO:0099402 GO:0140110 GO:1901363 GO:1901564 GO:1903506 GO:2000112 GO:2001141

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

ELK Homeobox_KN KNOX1 KNOX2

Protein Analysis

323

Amino Acids

35.29

Weight (kDa)

6.59

Isoelectric Point (pI)

40.97

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
KNOX1	PF03790	118 - 156	6.6e-21	KNOX1 domain
KNOX2	PF03791	178 - 224	2.2e-21	KNOX2 domain
ELK	PF03789	265 - 286	3.7e-11	ELK domain

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: OG0002529)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G62360
fragaria_vesca	FvH4_3g01400 FvH4_3g01400 FvH4_3g01400 FvH4_3g01400 FvH4_6g42570 FvH4_6g42570
malus_domestica	MD05G1352500.v1.1 MD09G1112500.v1.1 MD10G1276200.v1.1 MD10G1326500.v1.1 MD17G1102600.v1.1
prunus_persica	Prupe.3G212100_v2.0.a1 Prupe.4G015200_v2.0.a1 Prupe.4G015200_v2.0.a1
pyrus_communis	pycom05g31940 pycom09g03690 pycom10g27650 pycom17g09700
rosa_chinensis	RchiOBHm_Chr2g0158421 RchiOBHm_Chr5g0002121
rosa_laevigata	RLG00000021086 RLG00000030997
rosa_multiflora	Rmu_sc0004855.1_g000009 Rmu_ssc0000001.1_g000013
rosa_roxburghii	Rroxscaffold_1G00073790 Rroxscaffold_2G00091400
rosa_rugosa	Rorug02G0468500 Rorug02G0468600 Rorug04G0394500 Rorug04G0394500
rosa_samantha	Rh2AG534700 Rh2BG548100 Rh2CG518500 Rh2DG557700 Rh5AG016200 Rh5BG019600 Rh5CG017500 Rh5DG017700
rosa_wichuraiana	Rw2G044280 Rw5G001580

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc16I	TGCGCA	1 cut(s)	815
AccB1I	GGYRCC	1 cut(s)	427
AccI	GTMKAC	1 cut(s)	391
AciI	CCGC	8 cut(s)	66, 214, 225, 228, 275, 278, 399, 776
AclWI	GGATC	5 cut(s)	306, 536, 561, 739, 767
AcoI	YGGCCR	1 cut(s)	396
AcuI	CTGAAG	1 cut(s)	759
AcyI	GRCGYC	1 cut(s)	428
AfaI	GTAC	3 cut(s)	52, 821, 955
AfiI	CCNNNNNNNGG	2 cut(s)	274, 394
AgsI	TTSAA	3 cut(s)	619, 661, 844
AluBI	AGCT	8 cut(s)	234, 327, 548, 765, 796, 808, 840, 880
AluI	AGCT	8 cut(s)	234, 327, 548, 765, 796, 808, 840, 880
Alw21I	GWGCWC	2 cut(s)	517, 798
Alw26I	GTCTC	1 cut(s)	610
Alw44I	GTGCAC	1 cut(s)	513
AlwI	GGATC	5 cut(s)	306, 536, 561, 739, 767
AlwNI	CAGNNNCTG	1 cut(s)	811
AoxI	GGCC	3 cut(s)	396, 567, 935
ApaLI	GTGCAC	1 cut(s)	513
ApeKI	GCWGC	5 cut(s)	222, 231, 272, 880, 898
Asp700I	GAANNNNTTC	1 cut(s)	328
AspLEI	GCGC	2 cut(s)	430, 816
AsuHPI	GGTGA	3 cut(s)	377, 548, 661
BaeGI	GKGCMC	1 cut(s)	517
BaeI	ACNNNNGTAYC	2 cut(s)	820, 853
BanI	GGYRCC	1 cut(s)	427
BanII	GRGCYC	1 cut(s)	798
BbsI	GAAGAC	1 cut(s)	336
Bbv12I	GWGCWC	2 cut(s)	517, 798
BbvI	GCAGC	5 cut(s)	234, 243, 284, 867, 910
BccI	CCATC	4 cut(s)	25, 135, 484, 952
BceAI	ACGGC	1 cut(s)	79
BcgI	CGANNNNNNTGC	4 cut(s)	79, 113, 450, 484
BciVI	GTATCC	1 cut(s)	821
BclI	TGATCA	1 cut(s)	585
BcoDI	GTCTC	1 cut(s)	610
BfmI	CTRYAG	1 cut(s)	270
BfoI	RGCGCY	1 cut(s)	431
BfuI	GTATCC	1 cut(s)	821
BmcAI	AGTACT	2 cut(s)	52, 955
BmiI	GGNNCC	3 cut(s)	429, 529, 920
BmsI	GCATC	2 cut(s)	87, 570
BpiI	GAAGAC	1 cut(s)	336
BsaBI	GATNNNNATC	1 cut(s)	584
BsaHI	GRCGYC	1 cut(s)	428
BsaI	GGTCTC	1 cut(s)	610
BsaJI	CCNNGG	1 cut(s)	532
BsaWI	WCCGGW	1 cut(s)	433
Bsc4I	CCNNNNNNNGG	2 cut(s)	274, 394
Bse1I	ACTGG	1 cut(s)	399
Bse8I	GATNNNNATC	1 cut(s)	584
BseDI	CCNNGG	1 cut(s)	532
BseGI	GGATG	1 cut(s)	373
BseJI	GATNNNNATC	1 cut(s)	584
BseLI	CCNNNNNNNGG	2 cut(s)	274, 394
BseNI	ACTGG	1 cut(s)	399
BseRI	GAGGAG	1 cut(s)	84
BseSI	GKGCMC	1 cut(s)	517
BseXI	GCAGC	5 cut(s)	234, 243, 284, 867, 910
BseYI	CCCAGC	1 cut(s)	120
BshFI	GGCC	3 cut(s)	398, 569, 937
BshNI	GGYRCC	1 cut(s)	427
BsiHKAI	GWGCWC	2 cut(s)	517, 798
BsiSI	CCGG	1 cut(s)	434
BslFI	GGGAC	1 cut(s)	637
BslI	CCNNNNNNNGG	2 cut(s)	274, 394
BsmAI	GTCTC	1 cut(s)	610
BsmFI	GGGAC	1 cut(s)	637
BsnI	GGCC	3 cut(s)	398, 569, 937
Bso31I	GGTCTC	1 cut(s)	610
Bsp1286I	GDGCHC	2 cut(s)	517, 798
Bsp143I	GATC	8 cut(s)	298, 363, 541, 553, 585, 645, 731, 772
BspACI	CCGC	8 cut(s)	66, 214, 225, 228, 275, 278, 399, 776
BspANI	GGCC	3 cut(s)	398, 569, 937
BspHI	TCATGA	1 cut(s)	855
BspLI	GGNNCC	3 cut(s)	429, 529, 920
BspMAI	CTGCAG	1 cut(s)	274
BspPI	GGATC	5 cut(s)	306, 536, 561, 739, 767
BspQI	GCTCTTC	1 cut(s)	334
BspT107I	GGYRCC	1 cut(s)	427
BspTNI	GGTCTC	1 cut(s)	610
BsrI	ACTGG	1 cut(s)	399
BssECI	CCNNGG	1 cut(s)	532
BssMI	GATC	8 cut(s)	298, 363, 541, 553, 585, 645, 731, 772
BssNI	GRCGYC	1 cut(s)	428
BssT1I	CCWWGG	1 cut(s)	532
Bst4CI	ACNGT	9 cut(s)	50, 161, 314, 389, 413, 575, 673, 824, 967
Bst6I	CTCTTC	4 cut(s)	334, 343, 738, 857
BstACI	GRCGYC	1 cut(s)	428
BstAPI	GCANNNNNTGC	1 cut(s)	904
BstC8I	GCNNGC	4 cut(s)	283, 463, 780, 878
BstF5I	GGATG	1 cut(s)	373
BstH2I	RGCGCY	1 cut(s)	431
BstHHI	GCGC	2 cut(s)	430, 816
BstKTI	GATC	8 cut(s)	301, 366, 544, 556, 588, 648, 734, 775
BstMAI	GTCTC	1 cut(s)	610
BstMBI	GATC	8 cut(s)	298, 363, 541, 553, 585, 645, 731, 772
BstMWI	GCNNNNNNNGC	6 cut(s)	18, 222, 228, 231, 278, 904
BstNSI	RCATGY	1 cut(s)	465
BstSFI	CTRYAG	1 cut(s)	270
BstSLI	GKGCMC	1 cut(s)	517
BstV1I	GCAGC	5 cut(s)	234, 243, 284, 867, 910
BstV2I	GAAGAC	1 cut(s)	336
BstX2I	RGATCY	2 cut(s)	541, 772
BstYI	RGATCY	2 cut(s)	541, 772
BsuI	GTATCC	1 cut(s)	821
BsuRI	GGCC	3 cut(s)	398, 569, 937
BtsCI	GGATG	1 cut(s)	373
BtsIMutI	CAGTG	2 cut(s)	319, 829
Cac8I	GCNNGC	4 cut(s)	283, 463, 780, 878
CaiI	CAGNNNCTG	1 cut(s)	811
CciI	TCATGA	1 cut(s)	855
CfoI	GCGC	2 cut(s)	430, 816
Csp6I	GTAC	3 cut(s)	51, 820, 954
CspCI	CAANNNNNGTGG	4 cut(s)	295, 330, 805, 840
CviQI	GTAC	3 cut(s)	51, 820, 954
DinI	GGCGCC	1 cut(s)	429
DpnI	GATC	8 cut(s)	300, 365, 543, 555, 587, 647, 733, 774
DpnII	GATC	8 cut(s)	298, 363, 541, 553, 585, 645, 731, 772
DraI	TTTAAA	1 cut(s)	639
EaeI	YGGCCR	1 cut(s)	396
Eam1104I	CTCTTC	4 cut(s)	334, 343, 738, 857
EarI	CTCTTC	4 cut(s)	334, 343, 738, 857
EciI	GGCGGA	1 cut(s)	81
Ecl136II	GAGCTC	1 cut(s)	796
Eco130I	CCWWGG	1 cut(s)	532
Eco147I	AGGCCT	1 cut(s)	569
Eco24I	GRGCYC	1 cut(s)	798
Eco31I	GGTCTC	1 cut(s)	610
Eco53kI	GAGCTC	1 cut(s)	796
Eco57I	CTGAAG	1 cut(s)	759
EcoICRI	GAGCTC	1 cut(s)	796
EcoT14I	CCWWGG	1 cut(s)	532
EcoT38I	GRGCYC	1 cut(s)	798
EgeI	GGCGCC	1 cut(s)	429
EheI	GGCGCC	1 cut(s)	429
ErhI	CCWWGG	1 cut(s)	532
FalI	AAGNNNNNCTT	7 cut(s)	316, 348, 615, 647, 792, 824, 943
FaqI	GGGAC	1 cut(s)	637
FauI	CCCGC	1 cut(s)	221
FbaI	TGATCA	1 cut(s)	585
FblI	GTMKAC	1 cut(s)	391
FokI	GGATG	1 cut(s)	360
FriOI	GRGCYC	1 cut(s)	798
FspI	TGCGCA	1 cut(s)	815
GlaI	GCGC	2 cut(s)	429, 815
GsaI	CCCAGC	1 cut(s)	124
HaeII	RGCGCY	1 cut(s)	431
HaeIII	GGCC	3 cut(s)	398, 569, 937
HapII	CCGG	1 cut(s)	434
HhaI	GCGC	2 cut(s)	430, 816
Hin1I	GRCGYC	1 cut(s)	428
Hin6I	GCGC	2 cut(s)	428, 814
HinP1I	GCGC	2 cut(s)	428, 814
HinfI	GANTC	3 cut(s)	467, 650, 689
HpaII	CCGG	1 cut(s)	434
HphI	GGTGA	3 cut(s)	377, 548, 661
Hpy166II	GTNNAC	2 cut(s)	392, 515
Hpy188I	TCNGA	5 cut(s)	84, 105, 489, 688, 739
Hpy188III	TCNNGA	3 cut(s)	248, 551, 856
Hpy8I	GTNNAC	2 cut(s)	392, 515
HpyAV	CCTTC	1 cut(s)	625
HpyCH4III	ACNGT	9 cut(s)	50, 161, 314, 389, 413, 575, 673, 824, 967
HpyCH4V	TGCA	3 cut(s)	4, 272, 515
HpyF10VI	GCNNNNNNNGC	6 cut(s)	18, 222, 228, 231, 278, 904
Hsp92I	GRCGYC	1 cut(s)	428
HspAI	GCGC	2 cut(s)	428, 814
KasI	GGCGCC	1 cut(s)	427
Ksp22I	TGATCA	1 cut(s)	585
Kzo9I	GATC	8 cut(s)	298, 363, 541, 553, 585, 645, 731, 772
LguI	GCTCTTC	1 cut(s)	334
LmnI	GCTCC	2 cut(s)	793, 918
Lsp1109I	GCAGC	5 cut(s)	234, 243, 284, 867, 910
LweI	GCATC	2 cut(s)	87, 570
MalI	GATC	8 cut(s)	300, 365, 543, 555, 587, 647, 733, 774
MboI	GATC	8 cut(s)	298, 363, 541, 553, 585, 645, 731, 772
MflI	RGATCY	2 cut(s)	541, 772
MhlI	GDGCHC	2 cut(s)	517, 798
MluCI	AATT	2 cut(s)	25, 656
Mly113I	GGCGCC	1 cut(s)	428
MlyI	GAGTC	2 cut(s)	476, 659
MroXI	GAANNNNTTC	1 cut(s)	328
MseI	TTAA	2 cut(s)	638, 970
MslI	CAYNNNNRTG	2 cut(s)	129, 522
MspA1I	CMGCKG	2 cut(s)	225, 275
MspI	CCGG	1 cut(s)	434
MwoI	GCNNNNNNNGC	6 cut(s)	18, 222, 228, 231, 278, 904
NarI	GGCGCC	1 cut(s)	428
NdeII	GATC	8 cut(s)	298, 363, 541, 553, 585, 645, 731, 772
NlaIV	GGNNCC	3 cut(s)	429, 529, 920
NsbI	TGCGCA	1 cut(s)	815
NspI	RCATGY	1 cut(s)	465
PaeI	GCATGC	1 cut(s)	465
PagI	TCATGA	1 cut(s)	855
PceI	AGGCCT	1 cut(s)	569
PciSI	GCTCTTC	1 cut(s)	334
PcsI	WCGNNNNNNNCGW	2 cut(s)	149, 476
PdmI	GAANNNNTTC	1 cut(s)	328
PfeI	GAWTC	1 cut(s)	689
PleI	GAGTC	2 cut(s)	475, 658
PluTI	GGCGCC	1 cut(s)	431
PpsI	GAGTC	2 cut(s)	475, 658
Psp124BI	GAGCTC	1 cut(s)	798
PspFI	CCCAGC	1 cut(s)	120
PspN4I	GGNNCC	3 cut(s)	429, 529, 920
PstI	CTGCAG	1 cut(s)	274
PstNI	CAGNNNCTG	1 cut(s)	811
PsuI	RGATCY	2 cut(s)	541, 772
RsaI	GTAC	3 cut(s)	52, 821, 955
RsaNI	GTAC	3 cut(s)	51, 820, 954
RseI	CAYNNNNRTG	2 cut(s)	129, 522
SacI	GAGCTC	1 cut(s)	798
SapI	GCTCTTC	1 cut(s)	334
SaqAI	TTAA	2 cut(s)	638, 970
Sau3AI	GATC	8 cut(s)	298, 363, 541, 553, 585, 645, 731, 772
ScaI	AGTACT	2 cut(s)	52, 955
SchI	GAGTC	2 cut(s)	476, 659
SduI	GDGCHC	2 cut(s)	517, 798
SfaNI	GCATC	2 cut(s)	87, 570
SfcI	CTRYAG	1 cut(s)	270
SfoI	GGCGCC	1 cut(s)	429
SmiMI	CAYNNNNRTG	2 cut(s)	129, 522
SphI	GCATGC	1 cut(s)	465
Sse9I	AATT	2 cut(s)	25, 656
SseBI	AGGCCT	1 cut(s)	569
SsiI	CCGC	8 cut(s)	66, 214, 225, 228, 275, 278, 399, 776
SspDI	GGCGCC	1 cut(s)	427
SstI	GAGCTC	1 cut(s)	798
StuI	AGGCCT	1 cut(s)	569
StyI	CCWWGG	1 cut(s)	532
TaaI	ACNGT	9 cut(s)	50, 161, 314, 389, 413, 575, 673, 824, 967
TaqI	TCGA	4 cut(s)	29, 152, 648, 909
TasI	AATT	2 cut(s)	25, 656
TatI	WGTACW	3 cut(s)	50, 819, 953
TauI	GCSGC	5 cut(s)	228, 231, 278, 281, 401
TfiI	GAWTC	1 cut(s)	689
Tru1I	TTAA	2 cut(s)	638, 970
Tru9I	TTAA	2 cut(s)	638, 970
TscAI	CASTG	2 cut(s)	319, 829
TseI	GCWGC	5 cut(s)	222, 231, 272, 880, 898
TspDTI	ATGAA	4 cut(s)	283, 550, 844, 872
TspRI	CASTG	2 cut(s)	319, 829
VneI	GTGCAC	1 cut(s)	513
XceI	RCATGY	1 cut(s)	465
XcmI	CCANNNNNNNNNTGG	1 cut(s)	128
XmiI	GTMKAC	1 cut(s)	391
XmnI	GAANNNNTTC	1 cut(s)	328
ZrmI	AGTACT	2 cut(s)	52, 955

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