Basic Information

Type: gene

Biological Identity

Species

rosa_wichuraiana

Chromosome

Chr3

Orthogroup ID

OG0003009

Physical Location & Seq

Genomic Coordinates Reverse (-)

1992549 .. 1993504

Gene Structure 956 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rw3G002260.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 651 bp

ATGCCCGCCGAAACCGCCGTCGTCAAGGCCAAGAAGCCGCGATCGCCGCCCGCTCACCCTCCCTTCGTCGAGATGATCACGGAGGCGATTGTGGCCCTGAAGGAGAGGACTGGTTCGAGCCAGTACGCCATCGCCAAATTCGTGGAGGAGAAGCACAAGCAGTTGCCTCAGAGCTTCAAGAAGCTTCTGCTCCTCAACCTGAAGAAGCTCGTCGCCTCCGGCAAGCTCGTCAAGGTCAAAGCCTCCTTCAAGCTCCCTCCTCGCTCCGCCGCGGCGGCGGCATCTGCTCCGGCCAAGGAGAAGACCAAGCCGGAAGCTTCCAAGCCTAAGAAGTCCGCCGCTGCCAAGACTACTACTAAGCCCAAGGCCAAAACCGTCGCGAAGCCCAAGGCGGTGGCGAAGCCGAAGACCAAGGCTTTGGCGGTGGTTGCGAAGGCCAAGGCGGCGGCGGCGAAGCCCAAGGCCAAGGCCAAGGTGGCTAAACCTGCTGCCAAGGTGGCGAGGACGTCGTCGAGGACTTCGCCGGGGAAGAAGGTCGAGGCAAAAGCCAAGGCGGCGAAGAAGCCGGCGGCGACTAAGGTCGTGAAGAAGCCGAAGAGTGTGAAGTCTCCGGCGAAGAAGAAGGTTCAGCCAAAGAGGGGCAAGAAGTGA

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

216

Amino Acids

22.7

Weight (kDa)

10.96

Isoelectric Point (pI)

34.94

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Linker_histone	PF00538	19 - 85	5.4e-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)	509
Acc36I	ACCTGC	1 cut(s)	493
AccBSI	CCGCTC	1 cut(s)	53
AccII	CGCG	3 cut(s)	40, 272, 380
AcoI	YGGCCR	1 cut(s)	291
AcsI	RAATTY	1 cut(s)	137
AcuI	CTGAAG	2 cut(s)	119, 221
AcyI	GRCGYC	1 cut(s)	506
AfaI	GTAC	1 cut(s)	125
AfiI	CCNNNNNNNGG	1 cut(s)	638
AgsI	TTSAA	2 cut(s)	178, 250
AluBI	AGCT	6 cut(s)	174, 184, 208, 226, 253, 317
AluI	AGCT	6 cut(s)	174, 184, 208, 226, 253, 317
Alw26I	GTCTC	1 cut(s)	612
AoxI	GGCC	7 cut(s)	27, 93, 291, 366, 435, 462, 468
ApeKI	GCWGC	2 cut(s)	341, 488
ApoI	RAATTY	1 cut(s)	137
ArsI	GACNNNNNNTTYG	3 cut(s)	35, 400, 432
AsiSI	GCGATCGC	1 cut(s)	44
AspS9I	GGNCC	1 cut(s)	94
AsuC2I	CCSGG	1 cut(s)	525
AsuHPI	GGTGA	1 cut(s)	47
BbsI	GAAGAC	2 cut(s)	308, 413
BbvI	GCAGC	2 cut(s)	328, 475
BccI	CCATC	1 cut(s)	137
BceAI	ACGGC	1 cut(s)	2
BclI	TGATCA	1 cut(s)	75
BcnI	CCSGG	1 cut(s)	525
BcoDI	GTCTC	1 cut(s)	612
BfuAI	ACCTGC	1 cut(s)	493
BglI	GCCNNNNNGGC	5 cut(s)	275, 443, 476, 497, 554
Bme1390I	CCNGG	1 cut(s)	525
BmgT120I	GGNCC	1 cut(s)	94
BmrFI	CCNGG	1 cut(s)	525
BmsI	GCATC	1 cut(s)	290
BoxI	GACNNNNGTC	1 cut(s)	578
BpiI	GAAGAC	2 cut(s)	308, 413
BpuMI	CCSGG	1 cut(s)	525
BsaHI	GRCGYC	1 cut(s)	506
Bsc4I	CCNNNNNNNGG	1 cut(s)	638
Bse118I	RCCGGY	1 cut(s)	565
Bse1I	ACTGG	2 cut(s)	115, 121
BseLI	CCNNNNNNNGG	1 cut(s)	638
BseMII	CTCAG	1 cut(s)	182
BseNI	ACTGG	2 cut(s)	115, 121
BseRI	GAGGAG	3 cut(s)	161, 182, 249
BseXI	GCAGC	2 cut(s)	328, 475
Bsh1236I	CGCG	3 cut(s)	40, 272, 380
Bsh1285I	CGRYCG	1 cut(s)	44
BshFI	GGCC	7 cut(s)	29, 95, 293, 368, 437, 464, 470
BsiEI	CGRYCG	1 cut(s)	44
BsiSI	CCGG	6 cut(s)	219, 290, 311, 524, 566, 611
BslI	CCNNNNNNNGG	1 cut(s)	638
BsmAI	GTCTC	1 cut(s)	612
BsnI	GGCC	7 cut(s)	29, 95, 293, 368, 437, 464, 470
Bsp143I	GATC	2 cut(s)	41, 75
Bsp68I	TCGCGA	1 cut(s)	380
BspANI	GGCC	7 cut(s)	29, 95, 293, 368, 437, 464, 470
BspCNI	CTCAG	1 cut(s)	181
BspFNI	CGCG	3 cut(s)	40, 272, 380
BspMI	ACCTGC	1 cut(s)	493
BsrBI	CCGCTC	1 cut(s)	53
BsrFI	RCCGGY	1 cut(s)	565
BsrI	ACTGG	2 cut(s)	115, 121
BssAI	RCCGGY	1 cut(s)	565
BssMI	GATC	2 cut(s)	41, 75
BssNI	GRCGYC	1 cut(s)	506
Bst4CI	ACNGT	1 cut(s)	376
Bst6I	CTCTTC	1 cut(s)	590
BstACI	GRCGYC	1 cut(s)	506
BstC8I	GCNNGC	4 cut(s)	6, 51, 224, 567
BstDEI	CTNAG	4 cut(s)	168, 327, 357, 576
BstDSI	CCRYGG	1 cut(s)	270
BstFNI	CGCG	3 cut(s)	40, 272, 380
BstKTI	GATC	2 cut(s)	44, 78
BstMAI	GTCTC	1 cut(s)	612
BstMBI	GATC	2 cut(s)	41, 75
BstMCI	CGRYCG	1 cut(s)	44
BstPAI	GACNNNNGTC	1 cut(s)	578
BstSCI	CCNGG	1 cut(s)	523
BstUI	CGCG	3 cut(s)	40, 272, 380
BstV1I	GCAGC	2 cut(s)	328, 475
BstV2I	GAAGAC	2 cut(s)	308, 413
BstXI	CCANNNNNNTGG	3 cut(s)	142, 394, 418
BsuRI	GGCC	7 cut(s)	29, 95, 293, 368, 437, 464, 470
BtgI	CCRYGG	1 cut(s)	270
BtgZI	GCGATG	1 cut(s)	115
BtuMI	TCGCGA	1 cut(s)	380
BveI	ACCTGC	1 cut(s)	493
Cac8I	GCNNGC	4 cut(s)	6, 51, 224, 567
Cfr10I	RCCGGY	1 cut(s)	565
Cfr13I	GGNCC	1 cut(s)	94
Cfr42I	CCGCGG	1 cut(s)	273
Csp6I	GTAC	1 cut(s)	124
CviQI	GTAC	1 cut(s)	124
DdeI	CTNAG	4 cut(s)	168, 327, 357, 576
DpnI	GATC	2 cut(s)	43, 77
DpnII	GATC	2 cut(s)	41, 75
EaeI	YGGCCR	1 cut(s)	291
Eam1104I	CTCTTC	1 cut(s)	590
EarI	CTCTTC	1 cut(s)	590
EciI	GGCGGA	2 cut(s)	256, 325
Eco57I	CTGAAG	2 cut(s)	119, 221
FauI	CCCGC	2 cut(s)	13, 58
FbaI	TGATCA	1 cut(s)	75
HaeIII	GGCC	7 cut(s)	29, 95, 293, 368, 437, 464, 470
HapII	CCGG	6 cut(s)	219, 290, 311, 524, 566, 611
Hin1I	GRCGYC	1 cut(s)	506
HindIII	AAGCTT	2 cut(s)	182, 315
HpaII	CCGG	6 cut(s)	219, 290, 311, 524, 566, 611
HphI	GGTGA	1 cut(s)	47
Hpy188I	TCNGA	1 cut(s)	171
Hpy188III	TCNNGA	4 cut(s)	70, 178, 379, 583
Hpy99I	CGWCG	6 cut(s)	23, 71, 215, 380, 511, 514
HpyAV	CCTTC	6 cut(s)	73, 94, 256, 427, 526, 616
HpyCH4III	ACNGT	1 cut(s)	376
HpyCH4IV	ACGT	1 cut(s)	506
HpyF3I	CTNAG	4 cut(s)	168, 327, 357, 576
HpySE526I	ACGT	1 cut(s)	506
Hsp92I	GRCGYC	1 cut(s)	506
KroI	GCCGGC	1 cut(s)	565
KroNI	GCCGGC	1 cut(s)	567
Ksp22I	TGATCA	1 cut(s)	75
KspI	CCGCGG	1 cut(s)	273
Kzo9I	GATC	2 cut(s)	41, 75
LmnI	GCTCC	4 cut(s)	195, 258, 269, 292
Lsp1109I	GCAGC	2 cut(s)	328, 475
LweI	GCATC	1 cut(s)	290
MaeII	ACGT	1 cut(s)	506
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, 313, 418, 541, 571, 598, 607, 628, 631
MluCI	AATT	1 cut(s)	137
MroNI	GCCGGC	1 cut(s)	565
MspA1I	CMGCKG	2 cut(s)	272, 341
MspI	CCGG	6 cut(s)	219, 290, 311, 524, 566, 611
MspR9I	CCNGG	1 cut(s)	525
MvnI	CGCG	3 cut(s)	40, 272, 380
NaeI	GCCGGC	1 cut(s)	567
NciI	CCSGG	1 cut(s)	525
NdeII	GATC	2 cut(s)	41, 75
NgoMIV	GCCGGC	1 cut(s)	565
NruI	TCGCGA	1 cut(s)	380
PcsI	WCGNNNNNNNCGW	1 cut(s)	138
PdiI	GCCGGC	1 cut(s)	567
PflFI	GACNNNGTC	1 cut(s)	508
Ple19I	CGATCG	1 cut(s)	44
PshAI	GACNNNNGTC	1 cut(s)	578
PspPI	GGNCC	1 cut(s)	94
PsyI	GACNNNGTC	1 cut(s)	508
PvuI	CGATCG	1 cut(s)	44
RgaI	GCGATCGC	1 cut(s)	44
RruI	TCGCGA	1 cut(s)	380
RsaI	GTAC	1 cut(s)	125
RsaNI	GTAC	1 cut(s)	124
SacII	CCGCGG	1 cut(s)	273
Sau3AI	GATC	2 cut(s)	41, 75
Sau96I	GGNCC	1 cut(s)	94
ScrFI	CCNGG	1 cut(s)	525
SfaAI	GCGATCGC	1 cut(s)	44
SfaNI	GCATC	1 cut(s)	290
Sfr303I	CCGCGG	1 cut(s)	273
SgfI	GCGATCGC	1 cut(s)	44
SgrBI	CCGCGG	1 cut(s)	273
Sse9I	AATT	1 cut(s)	137
StyD4I	CCNGG	1 cut(s)	523
TaaI	ACNGT	1 cut(s)	376
TaiI	ACGT	1 cut(s)	509
TaqI	TCGA	4 cut(s)	69, 116, 512, 537
TasI	AATT	1 cut(s)	137
TseI	GCWGC	2 cut(s)	341, 488
TspGWI	ACGGA	1 cut(s)	95
Tth111I	GACNNNGTC	1 cut(s)	508
XapI	RAATTY	1 cut(s)	137
XcmI	CCANNNNNNNNNTGG	1 cut(s)	472
ZraI	GACGTC	1 cut(s)	507

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