Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4D

Orthogroup ID

OG0002636

Physical Location & Seq

Genomic Coordinates Reverse (-)

55217915 .. 55224678

Gene Structure 6764 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4DG328800.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 849 bp

ATGGAGGAAATGTACGGATTGCAATCAGCGGTGGACTACGGGGATAAGTCGACGGACTACGCCGACAAGGCCCTTATGACGCCGGAGAACCTGATCCTTCCTATGGATTACCAGAGCCTGCTCTCCTCCGTAGCTTTCCGCGACCATCGGGTCCCGATGATGTTCGGATCCGACGCCGGCGACTTGTACTCGGCCATATCCTCCGTGCCGGAGTTTCGGCGCGGGGAGGAAGATGTTTTTGGACCCATCAAAGCCAAAATTGCTTCCCATCCAAGCTACCCTAGACTTATTGAGGCCTACATCGATTGCCAGAAGGTAGGAGCGCCTCCGGAAATAGCGAGCTTCTTGGAGGAAATCCGCCGAGAAAATGACCTTTATAAACGAGAAAGAGACGCTGCTATGTCCACGTGTTTAGGAGCCGATCCCGAGCTCGACGAGTTCATGGAAACCTACTGCGATATGCTGGTCAAGTACAAATCAGATCTAGCAAGGCCTTTTGATGAAGCCACCACGTTCTTGAACAAGATTGAAACGCAACTCAGCAATCTCTGCATTCGAACTCTCTCCGATGAAGGTGCTGTGTCATCAGAGGAGGAGTTCAGCGGAGGCGAATTAGAGGTACAAGAAGCTCAAGCTCGGGGAGAAGATCGAGATCTCAAAAATAGGCTTTTCCGTAAGTTTGGCAGTCATATTGGCACCTTGAAGCTGGAATTCTCCAAGAAGAAGAAGAAGGGAAAGCTTCCGAAGGAAGCAAGACAAGCGTTACTTCATTGGTGGAGTGTTCACTATAAATGGCCATACCCGACGGTACTACTTCATTATCTCGAACGGTCTTATATACAACGATAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0003002 GO:0003006 GO:0003674 GO:0003700 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0006355 GO:0007154 GO:0007165 GO:0007275 GO:0007389 GO:0008150 GO:0009653 GO:0009719 GO:0009725 GO:0009735 GO:0009736 GO:0009755 GO:0009791 GO:0009888 GO:0009889 GO:0009908 GO:0009987 GO:0010033 GO:0010073 GO:0010093 GO:0010094 GO:0010468 GO:0010556 GO:0019219 GO:0019222 GO:0022414 GO:0023052 GO:0031323 GO:0031326 GO:0032501 GO:0032502 GO:0032870 GO:0042221 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044424 GO:0044464 GO:0048367 GO:0048437 GO:0048438 GO:0048440 GO:0048444 GO:0048445 GO:0048449 GO:0048462 GO:0048467 GO:0048507 GO:0048608 GO:0048646 GO:0048731 GO:0048827 GO:0048856 GO:0050789 GO:0050794 GO:0050896 GO:0051171 GO:0051252 GO:0051716 GO:0060255 GO:0061458 GO:0065007 GO:0070887 GO:0071310 GO:0071368 GO:0071495 GO:0080090 GO:0090567 GO:0090696 GO:0090697 GO:0090698 GO:0090701 GO:0099402 GO:0140110 GO:1903506 GO:1905392 GO:1905393 GO:2000112 GO:2001141

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

ELK Homeobox_KN KNOX1 KNOX2

Protein Analysis

282

Amino Acids

32.38

Weight (kDa)

5.26

Isoelectric Point (pI)

47.97

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
KNOX1	PF03790	83 - 124	3.5e-21	KNOX1 domain
KNOX2	PF03791	137 - 184	1.2e-26	KNOX2 domain
ELK	PF03789	218 - 239	4.5e-06	ELK 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

iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

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)	378
AasI	GACNNNNNNGTC	1 cut(s)	149
AccB1I	GGYRCC	1 cut(s)	695
AccI	GTMKAC	1 cut(s)	50
AccII	CGCG	2 cut(s)	141, 222
AccIII	TCCGGA	1 cut(s)	328
AciI	CCGC	5 cut(s)	29, 139, 222, 358, 603
AclWI	GGATC	4 cut(s)	88, 162, 175, 416
AcoI	YGGCCR	2 cut(s)	192, 794
AcsI	RAATTY	1 cut(s)	710
AcvI	CACGTG	1 cut(s)	408
AcyI	GRCGYC	2 cut(s)	80, 174
AfaI	GTAC	5 cut(s)	14, 188, 473, 621, 810
AfiI	CCNNNNNNNGG	1 cut(s)	103
AflIII	ACRYGT	1 cut(s)	407
AgsI	TTSAA	3 cut(s)	520, 530, 703
AjuI	GAANNNNNNNTTGG	2 cut(s)	222, 254
AluBI	AGCT	8 cut(s)	134, 276, 342, 430, 629, 635, 706, 739
AluI	AGCT	8 cut(s)	134, 276, 342, 430, 629, 635, 706, 739
Alw21I	GWGCWC	1 cut(s)	432
Alw26I	GTCTC	1 cut(s)	384
AlwI	GGATC	4 cut(s)	88, 162, 175, 416
AlwNI	CAGNNNCTG	1 cut(s)	118
Ama87I	CYCGRG	2 cut(s)	425, 636
Aor13HI	TCCGGA	1 cut(s)	328
AoxI	GGCC	5 cut(s)	69, 192, 294, 491, 794
ApeKI	GCWGC	1 cut(s)	395
ApoI	RAATTY	1 cut(s)	710
AspLEI	GCGC	2 cut(s)	222, 325
AspS9I	GGNCC	3 cut(s)	70, 151, 242
AsuII	TTCGAA	1 cut(s)	556
AvaI	CYCGRG	2 cut(s)	425, 636
AvaII	GGWCC	2 cut(s)	151, 242
BalI	TGGCCA	1 cut(s)	796
BamHI	GGATCC	1 cut(s)	167
BanI	GGYRCC	1 cut(s)	695
BanII	GRGCYC	1 cut(s)	432
BbrPI	CACGTG	1 cut(s)	408
Bbv12I	GWGCWC	1 cut(s)	432
BbvI	GCAGC	1 cut(s)	382
BccI	CCATC	3 cut(s)	153, 254, 276
BcgI	CGANNNNNNTGC	2 cut(s)	557, 591
BcoDI	GTCTC	1 cut(s)	384
BfaI	CTAG	2 cut(s)	282, 485
BfoI	RGCGCY	1 cut(s)	326
BglI	GCCNNNNNGGC	1 cut(s)	68
BglII	AGATCT	2 cut(s)	481, 652
BisI	GCNGC	1 cut(s)	396
BlsI	GCNGC	1 cut(s)	397
Bme18I	GGWCC	2 cut(s)	151, 242
BmeT110I	CYCGRG	2 cut(s)	425, 636
BmgT120I	GGNCC	3 cut(s)	70, 151, 242
BmiI	GGNNCC	6 cut(s)	152, 153, 169, 244, 418, 697
Bpu14I	TTCGAA	1 cut(s)	556
BpuEI	CTTGAG	1 cut(s)	615
Bsa29I	ATCGAT	1 cut(s)	303
BsaAI	YACGTR	1 cut(s)	408
BsaBI	GATNNNNATC	2 cut(s)	22, 651
BsaHI	GRCGYC	2 cut(s)	80, 174
BsaWI	WCCGGW	1 cut(s)	328
BsaXI	ACNNNNNCTCC	1 cut(s)	26
Bsc4I	CCNNNNNNNGG	1 cut(s)	103
Bse118I	RCCGGY	1 cut(s)	176
Bse8I	GATNNNNATC	2 cut(s)	22, 651
BseAI	TCCGGA	1 cut(s)	328
BseCI	ATCGAT	1 cut(s)	303
BseGI	GGATG	1 cut(s)	268
BseJI	GATNNNNATC	2 cut(s)	22, 651
BseLI	CCNNNNNNNGG	1 cut(s)	103
BseMII	CTCAG	1 cut(s)	553
BseRI	GAGGAG	3 cut(s)	115, 605, 608
BseXI	GCAGC	1 cut(s)	382
Bsh1236I	CGCG	2 cut(s)	141, 222
BshFI	GGCC	5 cut(s)	71, 194, 296, 493, 796
BshNI	GGYRCC	1 cut(s)	695
BshVI	ATCGAT	1 cut(s)	303
BsiHKAI	GWGCWC	1 cut(s)	432
BsiHKCI	CYCGRG	2 cut(s)	425, 636
BsiSI	CCGG	4 cut(s)	83, 177, 209, 329
BslFI	GGGAC	1 cut(s)	137
BslI	CCNNNNNNNGG	1 cut(s)	103
BsmAI	GTCTC	1 cut(s)	384
BsmBI	CGTCTC	1 cut(s)	384
BsmFI	GGGAC	1 cut(s)	137
BsmI	GAATGC	1 cut(s)	552
BsnI	GGCC	5 cut(s)	71, 194, 296, 493, 796
BsoBI	CYCGRG	2 cut(s)	425, 636
Bsp119I	TTCGAA	1 cut(s)	556
Bsp1286I	GDGCHC	1 cut(s)	432
Bsp13I	TCCGGA	1 cut(s)	328
Bsp143I	GATC	6 cut(s)	93, 167, 421, 481, 646, 652
BspACI	CCGC	5 cut(s)	29, 139, 222, 358, 603
BspANI	GGCC	5 cut(s)	71, 194, 296, 493, 796
BspCNI	CTCAG	1 cut(s)	552
BspDI	ATCGAT	1 cut(s)	303
BspEI	TCCGGA	1 cut(s)	328
BspFNI	CGCG	2 cut(s)	141, 222
BspLI	GGNNCC	6 cut(s)	152, 153, 169, 244, 418, 697
BspPI	GGATC	4 cut(s)	88, 162, 175, 416
BspT104I	TTCGAA	1 cut(s)	556
BspT107I	GGYRCC	1 cut(s)	695
BsrFI	RCCGGY	1 cut(s)	176
BssAI	RCCGGY	1 cut(s)	176
BssMI	GATC	6 cut(s)	93, 167, 421, 481, 646, 652
BssNI	GRCGYC	2 cut(s)	80, 174
Bst4CI	ACNGT	2 cut(s)	808, 831
BstACI	GRCGYC	2 cut(s)	80, 174
BstAPI	GCANNNNNTGC	1 cut(s)	549
BstBAI	YACGTR	1 cut(s)	408
BstBI	TTCGAA	1 cut(s)	556
BstC8I	GCNNGC	3 cut(s)	119, 178, 340
BstDEI	CTNAG	1 cut(s)	539
BstF5I	GGATG	1 cut(s)	268
BstFNI	CGCG	2 cut(s)	141, 222
BstH2I	RGCGCY	1 cut(s)	326
BstHHI	GCGC	2 cut(s)	222, 325
BstKTI	GATC	6 cut(s)	96, 170, 424, 484, 649, 655
BstMAI	GTCTC	1 cut(s)	384
BstMBI	GATC	6 cut(s)	93, 167, 421, 481, 646, 652
BstMWI	GCNNNNNNNGC	4 cut(s)	68, 260, 549, 758
BstUI	CGCG	2 cut(s)	141, 222
BstV1I	GCAGC	1 cut(s)	382
BstX2I	RGATCY	3 cut(s)	167, 481, 652
BstYI	RGATCY	3 cut(s)	167, 481, 652
Bsu15I	ATCGAT	1 cut(s)	303
BsuRI	GGCC	5 cut(s)	71, 194, 296, 493, 796
BsuTUI	ATCGAT	1 cut(s)	303
BtsCI	GGATG	1 cut(s)	268
Cac8I	GCNNGC	3 cut(s)	119, 178, 340
CaiI	CAGNNNCTG	1 cut(s)	118
CfoI	GCGC	2 cut(s)	222, 325
Cfr10I	RCCGGY	1 cut(s)	176
Cfr13I	GGNCC	3 cut(s)	70, 151, 242
ClaI	ATCGAT	1 cut(s)	303
CseI	GACGC	3 cut(s)	88, 182, 401
Csp6I	GTAC	5 cut(s)	13, 187, 472, 620, 809
CviAII	CATG	1 cut(s)	442
CviQI	GTAC	5 cut(s)	13, 187, 472, 620, 809
DdeI	CTNAG	1 cut(s)	539
DpnI	GATC	6 cut(s)	95, 169, 423, 483, 648, 654
DpnII	GATC	6 cut(s)	93, 167, 421, 481, 646, 652
DrdI	GACNNNNNNGTC	1 cut(s)	149
DseDI	GACNNNNNNGTC	1 cut(s)	149
EaeI	YGGCCR	2 cut(s)	192, 794
EciI	GGCGGA	1 cut(s)	347
Ecl136II	GAGCTC	1 cut(s)	430
Eco147I	AGGCCT	2 cut(s)	296, 493
Eco24I	GRGCYC	1 cut(s)	432
Eco47I	GGWCC	2 cut(s)	151, 242
Eco53kI	GAGCTC	1 cut(s)	430
Eco72I	CACGTG	1 cut(s)	408
Eco88I	CYCGRG	2 cut(s)	425, 636
EcoICRI	GAGCTC	1 cut(s)	430
EcoO109I	RGGNCCY	2 cut(s)	70, 151
EcoRI	GAATTC	1 cut(s)	710
EcoT38I	GRGCYC	1 cut(s)	432
Esp3I	CGTCTC	1 cut(s)	384
FaeI	CATG	1 cut(s)	445
FalI	AAGNNNNNCTT	2 cut(s)	750, 782
FaqI	GGGAC	1 cut(s)	137
FatI	CATG	1 cut(s)	441
FauI	CCCGC	1 cut(s)	215
FblI	GTMKAC	1 cut(s)	50
Fnu4HI	GCNGC	1 cut(s)	396
FokI	GGATG	1 cut(s)	255
FriOI	GRGCYC	1 cut(s)	432
Fsp4HI	GCNGC	1 cut(s)	396
FspBI	CTAG	2 cut(s)	282, 485
GlaI	GCGC	2 cut(s)	221, 324
GluI	GCNGC	1 cut(s)	396
HaeII	RGCGCY	1 cut(s)	326
HaeIII	GGCC	5 cut(s)	71, 194, 296, 493, 796
HapII	CCGG	4 cut(s)	83, 177, 209, 329
HgaI	GACGC	3 cut(s)	88, 182, 401
HhaI	GCGC	2 cut(s)	222, 325
Hin1I	GRCGYC	2 cut(s)	80, 174
Hin1II	CATG	1 cut(s)	445
Hin6I	GCGC	2 cut(s)	220, 323
HinP1I	GCGC	2 cut(s)	220, 323
HincII	GTYRAC	1 cut(s)	51
HindII	GTYRAC	1 cut(s)	51
HindIII	AAGCTT	1 cut(s)	737
HpaII	CCGG	4 cut(s)	83, 177, 209, 329
Hpy166II	GTNNAC	4 cut(s)	34, 51, 405, 784
Hpy188I	TCNGA	6 cut(s)	167, 172, 481, 568, 589, 744
Hpy188III	TCNNGA	6 cut(s)	154, 329, 425, 517, 650, 824
Hpy8I	GTNNAC	4 cut(s)	34, 51, 405, 784
Hpy99I	CGWCG	4 cut(s)	55, 176, 437, 808
HpyAV	CCTTC	5 cut(s)	107, 307, 566, 724, 739
HpyCH4III	ACNGT	2 cut(s)	808, 831
HpyCH4IV	ACGT	2 cut(s)	407, 512
HpyCH4V	TGCA	2 cut(s)	22, 552
HpyF10VI	GCNNNNNNNGC	4 cut(s)	68, 260, 549, 758
HpyF3I	CTNAG	1 cut(s)	539
HpySE526I	ACGT	2 cut(s)	407, 512
Hsp92I	GRCGYC	2 cut(s)	80, 174
Hsp92II	CATG	1 cut(s)	445
HspAI	GCGC	2 cut(s)	220, 323
KflI	GGGWCCC	1 cut(s)	151
Kpn2I	TCCGGA	1 cut(s)	328
KroI	GCCGGC	1 cut(s)	176
KroNI	GCCGGC	1 cut(s)	178
Kzo9I	GATC	6 cut(s)	93, 167, 421, 481, 646, 652
LmnI	GCTCC	2 cut(s)	320, 416
Lsp1109I	GCAGC	1 cut(s)	382
MaeI	CTAG	2 cut(s)	282, 485
MaeII	ACGT	2 cut(s)	407, 512
MaeIII	GTNAC	1 cut(s)	762
MalI	GATC	6 cut(s)	95, 169, 423, 483, 648, 654
MboI	GATC	6 cut(s)	93, 167, 421, 481, 646, 652
MboII	GAAGA	5 cut(s)	242, 656, 733, 736, 739
MflI	RGATCY	3 cut(s)	167, 481, 652
MhlI	GDGCHC	1 cut(s)	432
MlsI	TGGCCA	1 cut(s)	796
MluCI	AATT	3 cut(s)	258, 611, 710
MluNI	TGGCCA	1 cut(s)	796
MmeI	TCCRAC	1 cut(s)	195
Mox20I	TGGCCA	1 cut(s)	796
MreI	CGCCGGCG	1 cut(s)	176
MroI	TCCGGA	1 cut(s)	328
MroNI	GCCGGC	1 cut(s)	176
MscI	TGGCCA	1 cut(s)	796
Msp20I	TGGCCA	1 cut(s)	796
MspA1I	CMGCKG	2 cut(s)	29, 603
MspI	CCGG	4 cut(s)	83, 177, 209, 329
Mva1269I	GAATGC	1 cut(s)	552
MvnI	CGCG	2 cut(s)	141, 222
MwoI	GCNNNNNNNGC	4 cut(s)	68, 260, 549, 758
NaeI	GCCGGC	1 cut(s)	178
NdeII	GATC	6 cut(s)	93, 167, 421, 481, 646, 652
NgoMIV	GCCGGC	1 cut(s)	176
NlaIII	CATG	1 cut(s)	445
NlaIV	GGNNCC	6 cut(s)	152, 153, 169, 244, 418, 697
NmeAIII	GCCGAG	2 cut(s)	170, 386
NspV	TTCGAA	1 cut(s)	556
PceI	AGGCCT	2 cut(s)	296, 493
PctI	GAATGC	1 cut(s)	552
PdiI	GCCGGC	1 cut(s)	178
PkrI	GCNGC	1 cut(s)	397
PmaCI	CACGTG	1 cut(s)	408
PmlI	CACGTG	1 cut(s)	408
Ppu21I	YACGTR	1 cut(s)	408
PpuMI	RGGWCCY	1 cut(s)	151
PsiI	TTATAA	1 cut(s)	378
Psp124BI	GAGCTC	1 cut(s)	432
Psp5II	RGGWCCY	1 cut(s)	151
PspCI	CACGTG	1 cut(s)	408
PspN4I	GGNNCC	6 cut(s)	152, 153, 169, 244, 418, 697
PspPI	GGNCC	3 cut(s)	70, 151, 242
PspPPI	RGGWCCY	1 cut(s)	151
PstNI	CAGNNNCTG	1 cut(s)	118
PsuI	RGATCY	3 cut(s)	167, 481, 652
RsaI	GTAC	5 cut(s)	14, 188, 473, 621, 810
RsaNI	GTAC	5 cut(s)	13, 187, 472, 620, 809
SacI	GAGCTC	1 cut(s)	432
SalI	GTCGAC	1 cut(s)	49
SatI	GCNGC	1 cut(s)	396
Sau3AI	GATC	6 cut(s)	93, 167, 421, 481, 646, 652
Sau96I	GGNCC	3 cut(s)	70, 151, 242
SduI	GDGCHC	1 cut(s)	432
SfuI	TTCGAA	1 cut(s)	556
SgrAI	CRCCGGYG	1 cut(s)	176
SinI	GGWCC	2 cut(s)	151, 242
SmlI	CTYRAG	1 cut(s)	630
SmoI	CTYRAG	1 cut(s)	630
Sse9I	AATT	3 cut(s)	258, 611, 710
SseBI	AGGCCT	2 cut(s)	296, 493
SsiI	CCGC	5 cut(s)	29, 139, 222, 358, 603
SspMI	CTAG	2 cut(s)	282, 485
SstI	GAGCTC	1 cut(s)	432
StuI	AGGCCT	2 cut(s)	296, 493
TaaI	ACNGT	2 cut(s)	808, 831
TaiI	ACGT	2 cut(s)	410, 515
TaqI	TCGA	6 cut(s)	50, 303, 432, 556, 649, 825
TasI	AATT	3 cut(s)	258, 611, 710
TatI	WGTACW	2 cut(s)	186, 471
TseI	GCWGC	1 cut(s)	395
TspDTI	ATGAA	5 cut(s)	430, 516, 585, 758, 806
TspGWI	ACGGA	5 cut(s)	30, 68, 118, 193, 662
VpaK11BI	GGWCC	2 cut(s)	151, 242
XapI	RAATTY	1 cut(s)	710
XmiI	GTMKAC	1 cut(s)	50
XspI	CTAG	2 cut(s)	282, 485

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