Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3B

Orthogroup ID

OG0003009

Physical Location & Seq

Genomic Coordinates Reverse (-)

1978169 .. 1979597

Gene Structure 1429 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3BG029800.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 636 bp

ATGCCCGCCGAAACCGCCGTCGTCAAGGCCAAGAAGCCGCGATCGCCGCCCGCTCACCCTCCCTTCGTCGAGATGATCACGGAGGCGATTGTGGCCCTGAAGGAGAGGACTGGTTCGAGCCAGTACGCCATCGCCAAATTCGTGGAGGAGAAGCACAAGCAGTTGCCTCAGAGCTTCAAGAAGCTTCTGCTCCTCAACCTGAAGAAGCTCGTCGCCTCCGGCAAGCTCGTCAAGGTCAAAGCCTCCTTCAAGCTCCCTCCTCGCTCCGCCGCCGCCGCGGCTGCTCCGGTCAAGGAGAAGACCAAGCCGGAAGCTTCCAAGCCTAAGAAGTCCACCGCCAAGACTACTACTAAGCCCAAGGCCAAAACCGTCGCGAAGCCCAAGGCGGTGGCGAAGCCGAAGACCAAAGCTTTGGCGGTGGTTGCCAAGGCCAAGGCGGCGAAGCCGAAGGCCAAGGCTGCTAAGCCTGCTGCTGCCAAGGCGGCGAGGACGTCGTCGAGGACTTCGCCGGGGAAGAAGGTCGAGGCAAAAGCCAAGGCGGCGAAGAAGCCGGCGGCGACCAAGGTCGTGAAGAAGCCGAAGAGTGTGAAGTCTCCGGCGAAGAAGAAGGTTCAGCCAAAGAGGGGCAAGAAGTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005694 GO:0005730 GO:0005737 GO:0005739 GO:0031974 GO:0031981 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044422 GO:0044424 GO:0044428 GO:0044444 GO:0044446 GO:0044464 GO:0070013

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

Linker_histone

Protein Analysis

211

Amino Acids

22.28

Weight (kDa)

10.95

Isoelectric Point (pI)

36.2

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Linker_histone	PF00538	19 - 85	5.2e-20	linker histone H1 and H5 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)

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: OG0003009)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT2G30620 AT2G30620
fragaria_vesca	FvH4_2g02381 FvH4_2g22280 FvH4_6g02630 FvH4_7g09410
malus_domestica	MD01G1078700.v1.1 MD04G1226600.v1.1 MD05G1204100.v1.1 MD10G1191200.v1.1 MD12G1243700.v1.1
prunus_persica	Prupe.6G345300_v2.0.a1 Prupe.8G230400_v2.0.a1
pyrus_communis	pycom04g19980 pycom05g19050 pycom10g16480 pycom12g22270
rosa_chinensis	RchiOBHm_Chr3g0450571 RchiOBHm_Chr6g0289241
rosa_laevigata	RLG00000012318 RLG00000025721
rosa_multiflora	Rmu_co8346219.1_g000001 Rmu_sc0000078.1_g000047 Rmu_sc0001527.1_g000013 Rmu_sc0005951.1_g000008
rosa_roxburghii	Rroxscaffold_6G00428260 Rroxscaffold_7G00179420
rosa_rugosa	Rorug02G0628700 Rorug06G0202300
rosa_samantha	Rh3AG029400 Rh3BG029800 Rh3CG028700 Rh3DG029500 Rh6BG320600 Rh6CG326700 Rh6DG312600
rosa_wichuraiana	Rw3G002260 Rw6G027060

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AatII	GACGTC	1 cut(s)	494
AccBSI	CCGCTC	1 cut(s)	53
AccII	CGCG	3 cut(s)	40, 278, 374
AcsI	RAATTY	1 cut(s)	137
AcuI	CTGAAG	2 cut(s)	119, 221
AcyI	GRCGYC	1 cut(s)	491
AfaI	GTAC	1 cut(s)	125
AfiI	CCNNNNNNNGG	1 cut(s)	623
AgsI	TTSAA	2 cut(s)	178, 250
AluBI	AGCT	7 cut(s)	174, 184, 208, 226, 253, 314, 410
AluI	AGCT	7 cut(s)	174, 184, 208, 226, 253, 314, 410
Alw26I	GTCTC	1 cut(s)	597
AoxI	GGCC	5 cut(s)	27, 93, 360, 429, 450
ApeKI	GCWGC	4 cut(s)	281, 458, 470, 473
ApoI	RAATTY	1 cut(s)	137
ArsI	GACNNNNNNTTYG	3 cut(s)	35, 394, 426
AsiSI	GCGATCGC	1 cut(s)	44
AspS9I	GGNCC	1 cut(s)	94
AsuC2I	CCSGG	1 cut(s)	510
AsuHPI	GGTGA	1 cut(s)	47
BbsI	GAAGAC	2 cut(s)	305, 407
BbvI	GCAGC	4 cut(s)	268, 445, 457, 460
BccI	CCATC	1 cut(s)	137
BceAI	ACGGC	1 cut(s)	2
BclI	TGATCA	1 cut(s)	75
BcnI	CCSGG	1 cut(s)	510
BcoDI	GTCTC	1 cut(s)	597
BglI	GCCNNNNNGGC	4 cut(s)	278, 437, 482, 539
BlpI	GCTNAGC	1 cut(s)	462
Bme1390I	CCNGG	1 cut(s)	510
BmgT120I	GGNCC	1 cut(s)	94
BmrFI	CCNGG	1 cut(s)	510
BoxI	GACNNNNGTC	1 cut(s)	563
BpiI	GAAGAC	2 cut(s)	305, 407
Bpu1102I	GCTNAGC	1 cut(s)	462
BpuMI	CCSGG	1 cut(s)	510
BsaHI	GRCGYC	1 cut(s)	491
BsaWI	WCCGGW	1 cut(s)	286
Bsc4I	CCNNNNNNNGG	1 cut(s)	623
Bse118I	RCCGGY	1 cut(s)	550
Bse1I	ACTGG	2 cut(s)	115, 121
BseLI	CCNNNNNNNGG	1 cut(s)	623
BseMII	CTCAG	1 cut(s)	182
BseNI	ACTGG	2 cut(s)	115, 121
BseRI	GAGGAG	3 cut(s)	161, 182, 249
BseXI	GCAGC	4 cut(s)	268, 445, 457, 460
Bsh1236I	CGCG	3 cut(s)	40, 278, 374
Bsh1285I	CGRYCG	1 cut(s)	44
BshFI	GGCC	5 cut(s)	29, 95, 362, 431, 452
BsiEI	CGRYCG	1 cut(s)	44
BsiSI	CCGG	6 cut(s)	219, 287, 308, 509, 551, 596
BslI	CCNNNNNNNGG	1 cut(s)	623
BsmAI	GTCTC	1 cut(s)	597
BsnI	GGCC	5 cut(s)	29, 95, 362, 431, 452
Bsp143I	GATC	2 cut(s)	41, 75
Bsp1720I	GCTNAGC	1 cut(s)	462
Bsp68I	TCGCGA	1 cut(s)	374
BspANI	GGCC	5 cut(s)	29, 95, 362, 431, 452
BspCNI	CTCAG	1 cut(s)	181
BspFNI	CGCG	3 cut(s)	40, 278, 374
BsrBI	CCGCTC	1 cut(s)	53
BsrFI	RCCGGY	1 cut(s)	550
BsrI	ACTGG	2 cut(s)	115, 121
BssAI	RCCGGY	1 cut(s)	550
BssMI	GATC	2 cut(s)	41, 75
BssNI	GRCGYC	1 cut(s)	491
BssT1I	CCWWGG	8 cut(s)	357, 381, 426, 432, 453, 477, 534, 561
Bst4CI	ACNGT	1 cut(s)	370
Bst6I	CTCTTC	1 cut(s)	575
BstACI	GRCGYC	1 cut(s)	491
BstC8I	GCNNGC	5 cut(s)	6, 51, 224, 468, 552
BstDEI	CTNAG	4 cut(s)	168, 324, 351, 462
BstDSI	CCRYGG	1 cut(s)	276
BstFNI	CGCG	3 cut(s)	40, 278, 374
BstKTI	GATC	2 cut(s)	44, 78
BstMAI	GTCTC	1 cut(s)	597
BstMBI	GATC	2 cut(s)	41, 75
BstMCI	CGRYCG	1 cut(s)	44
BstPAI	GACNNNNGTC	1 cut(s)	563
BstSCI	CCNGG	1 cut(s)	508
BstUI	CGCG	3 cut(s)	40, 278, 374
BstV1I	GCAGC	4 cut(s)	268, 445, 457, 460
BstV2I	GAAGAC	2 cut(s)	305, 407
BstXI	CCANNNNNNTGG	3 cut(s)	142, 388, 412
BsuRI	GGCC	5 cut(s)	29, 95, 362, 431, 452
BtgI	CCRYGG	1 cut(s)	276
BtgZI	GCGATG	1 cut(s)	115
BtuMI	TCGCGA	1 cut(s)	374
Cac8I	GCNNGC	5 cut(s)	6, 51, 224, 468, 552
Cfr10I	RCCGGY	1 cut(s)	550
Cfr13I	GGNCC	1 cut(s)	94
Cfr42I	CCGCGG	1 cut(s)	279
Csp6I	GTAC	1 cut(s)	124
CviQI	GTAC	1 cut(s)	124
DdeI	CTNAG	4 cut(s)	168, 324, 351, 462
DpnI	GATC	2 cut(s)	43, 77
DpnII	GATC	2 cut(s)	41, 75
Eam1104I	CTCTTC	1 cut(s)	575
EarI	CTCTTC	1 cut(s)	575
EciI	GGCGGA	1 cut(s)	256
Eco130I	CCWWGG	8 cut(s)	357, 381, 426, 432, 453, 477, 534, 561
Eco57I	CTGAAG	2 cut(s)	119, 221
EcoT14I	CCWWGG	8 cut(s)	357, 381, 426, 432, 453, 477, 534, 561
ErhI	CCWWGG	8 cut(s)	357, 381, 426, 432, 453, 477, 534, 561
FauI	CCCGC	2 cut(s)	13, 58
FbaI	TGATCA	1 cut(s)	75
HaeIII	GGCC	5 cut(s)	29, 95, 362, 431, 452
HapII	CCGG	6 cut(s)	219, 287, 308, 509, 551, 596
Hin1I	GRCGYC	1 cut(s)	491
HindIII	AAGCTT	3 cut(s)	182, 312, 408
HpaII	CCGG	6 cut(s)	219, 287, 308, 509, 551, 596
HphI	GGTGA	1 cut(s)	47
Hpy166II	GTNNAC	1 cut(s)	333
Hpy188I	TCNGA	1 cut(s)	171
Hpy188III	TCNNGA	4 cut(s)	70, 178, 373, 568
Hpy8I	GTNNAC	1 cut(s)	333
Hpy99I	CGWCG	6 cut(s)	23, 71, 215, 374, 496, 499
HpyAV	CCTTC	6 cut(s)	73, 94, 256, 442, 511, 601
HpyCH4III	ACNGT	1 cut(s)	370
HpyCH4IV	ACGT	1 cut(s)	491
HpyF3I	CTNAG	4 cut(s)	168, 324, 351, 462
HpySE526I	ACGT	1 cut(s)	491
Hsp92I	GRCGYC	1 cut(s)	491
KroI	GCCGGC	1 cut(s)	550
KroNI	GCCGGC	1 cut(s)	552
Ksp22I	TGATCA	1 cut(s)	75
KspI	CCGCGG	1 cut(s)	279
Kzo9I	GATC	2 cut(s)	41, 75
LmnI	GCTCC	4 cut(s)	195, 258, 269, 289
Lsp1109I	GCAGC	4 cut(s)	268, 445, 457, 460
MaeII	ACGT	1 cut(s)	491
MalI	GATC	2 cut(s)	43, 77
MbiI	CCGCTC	1 cut(s)	53
MboI	GATC	2 cut(s)	41, 75
MboII	GAAGA	9 cut(s)	214, 310, 412, 526, 556, 583, 592, 613, 616
MluCI	AATT	1 cut(s)	137
MroNI	GCCGGC	1 cut(s)	550
MspA1I	CMGCKG	1 cut(s)	278
MspI	CCGG	6 cut(s)	219, 287, 308, 509, 551, 596
MspR9I	CCNGG	1 cut(s)	510
MvnI	CGCG	3 cut(s)	40, 278, 374
NaeI	GCCGGC	1 cut(s)	552
NciI	CCSGG	1 cut(s)	510
NdeII	GATC	2 cut(s)	41, 75
NgoMIV	GCCGGC	1 cut(s)	550
NruI	TCGCGA	1 cut(s)	374
PcsI	WCGNNNNNNNCGW	1 cut(s)	138
PdiI	GCCGGC	1 cut(s)	552
PflFI	GACNNNGTC	1 cut(s)	493
Ple19I	CGATCG	1 cut(s)	44
PshAI	GACNNNNGTC	1 cut(s)	563
PspPI	GGNCC	1 cut(s)	94
PsyI	GACNNNGTC	1 cut(s)	493
PvuI	CGATCG	1 cut(s)	44
RgaI	GCGATCGC	1 cut(s)	44
RruI	TCGCGA	1 cut(s)	374
RsaI	GTAC	1 cut(s)	125
RsaNI	GTAC	1 cut(s)	124
SacII	CCGCGG	1 cut(s)	279
Sau3AI	GATC	2 cut(s)	41, 75
Sau96I	GGNCC	1 cut(s)	94
ScrFI	CCNGG	1 cut(s)	510
SfaAI	GCGATCGC	1 cut(s)	44
Sfr303I	CCGCGG	1 cut(s)	279
SgfI	GCGATCGC	1 cut(s)	44
SgrBI	CCGCGG	1 cut(s)	279
Sse9I	AATT	1 cut(s)	137
StyD4I	CCNGG	1 cut(s)	508
StyI	CCWWGG	8 cut(s)	357, 381, 426, 432, 453, 477, 534, 561
TaaI	ACNGT	1 cut(s)	370
TaiI	ACGT	1 cut(s)	494
TaqI	TCGA	4 cut(s)	69, 116, 497, 522
TasI	AATT	1 cut(s)	137
TseI	GCWGC	4 cut(s)	281, 458, 470, 473
TspGWI	ACGGA	1 cut(s)	95
Tth111I	GACNNNGTC	1 cut(s)	493
XapI	RAATTY	1 cut(s)	137
ZraI	GACGTC	1 cut(s)	492

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