Basic Information

Type: gene

Biological Identity

Species

rosa_laevigata

Chromosome

Chr3

Orthogroup ID

OG0001390

Physical Location & Seq

Genomic Coordinates Forward (+)

25261050 .. 25269761

Gene Structure 8712 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

RLM00000013035

Sequence Viewer

CDS Protein Promoter (2k)

Length: 714 bp

ATGAGATTCATCAACAAAGATTGGGTCCGGCATCGGCACCGTCGTGAACGAATTCCAATGTGGAATCAGAGCAGTGGTGCTTATGGCGGACCCGGAGATGAACTTCGAAGAAGAGGATTCTCCCGCACCCGGTTCTATTCAACCGCCGCAGCTGAACTGAGTCACCGCCGAACAGCGGGAACTCACCGTCCCGGCAATCCTGTCCTCGGTCTCTACTCTCTAGTTTGCGCTGCGAGCAAGACTGAACTACTAAAGGCTGATGTCGGAGCACTTGACAATTTTGAAGTGCTCGAATTCCTAAAATCTAAAGGGGCCTCAAAGAATGATCTATCACGGGTGGCAAGAGTTACGCAATCAGAGTATAAGGTTTTCGATTATTTGGTTGATACTCCTGCTGGTACTCACACAAGAGAGGGTGTTGAAGAGTTCAAGGAGAAGTGTAGACAATATGACCTTGGGAACGATAAGATCCTCAATATTATTAACACTAGGCCAGCTTCAGTGGTTGAAATATATGCGATCGTGGAGGATAATGCTGATGAGCTAGTAGAGCTGGTTGCAGAGGTCTTGACTCCTCCAACTGTACCATCCCCTAAACCTGAAGCCGATACTAATGAGATTGATGCAGAGACCATGAACGTGGAACAAATTGAACAAAATGATGGCAATAAAGAAAAACCTGAATTTGGGGAAGCACCAATGGAGACTAGTTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0003674 GO:0003824 GO:0003899 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005666 GO:0005737 GO:0005886 GO:0006139 GO:0006351 GO:0006352 GO:0006383 GO:0006384 GO:0006725 GO:0006807 GO:0007568 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009360 GO:0009987 GO:0010467 GO:0016020 GO:0016070 GO:0016740 GO:0016772 GO:0016779 GO:0018130 GO:0019438 GO:0030424 GO:0030425 GO:0030880 GO:0031974 GO:0031981 GO:0032502 GO:0032774 GO:0032991 GO:0034062 GO:0034641 GO:0034645 GO:0034654 GO:0036477 GO:0042575 GO:0042995 GO:0043005 GO:0043025 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044297 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044463 GO:0044464 GO:0046483 GO:0055029 GO:0061695 GO:0070013 GO:0071704 GO:0071944 GO:0090304 GO:0097447 GO:0097458 GO:0097659 GO:0097747 GO:0120025 GO:0120038 GO:0140098 GO:1901360 GO:1901362 GO:1901576 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

RNA_pol_Rpb4

Protein Analysis

238

Amino Acids

26.65

Weight (kDa)

5.41

Isoelectric Point (pI)

42.35

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb4	PF03874	91 - 180	1.9e-09	RNA polymerase Rpb4

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

Font Size (px)

Line Width

Align Labels (Cladogram)

Image

Tree File

Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready

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

Orthologous Genes (Group: OG0001390)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT5G62950 AT5G62950 AT5G62950 AT5G62950 AT5G62950 AT5G62950 AT5G62950
fragaria_vesca	FvH4_4g01070 FvH4_4g01070 FvH4_5g27570
malus_domestica	MD13G1198900.v1.1
prunus_persica	Prupe.1G020700_v2.0.a1 Prupe.1G020700_v2.0.a1 Prupe.1G020700_v2.0.a1 Prupe.1G020700_v2.0.a1
pyrus_communis	pycom13g17270
rosa_chinensis	RchiOBHm_Chr4g0387641 RchiOBHm_Chr6g0280701
rosa_laevigata	RLG00000010104 RLG00000013035
rosa_multiflora	Rmu_sc0000976.1_g000021 Rmu_sc0003953.1_g000006
rosa_roxburghii	Rroxscaffold_7G00187720
rosa_rugosa	Rorug03G0311800 Rorug03G0311900 Rorug03G0312000 Rorug03G0312100 Rorug06G0133900 Rorug06G0133900 Rorug06G0133900 Rorug06G0134000
rosa_samantha	Rh4AG017400 Rh4BG012200 Rh4CG018600 Rh4DG013200 Rh6AG246600 Rh6BG248900 Rh6CG250000 Rh6DG241500
rosa_wichuraiana	Rw4G001120 Rw6G021350

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	1 cut(s)	36
AccI	GTMKAC	1 cut(s)	442
AciI	CCGC	6 cut(s)	87, 124, 144, 147, 166, 176
AclWI	GGATC	1 cut(s)	463
AcsI	RAATTY	3 cut(s)	51, 293, 683
AcuI	CTGAAG	2 cut(s)	483, 621
AfaI	GTAC	2 cut(s)	400, 585
AfiI	CCNNNNNNNGG	4 cut(s)	129, 175, 206, 686
AgsI	TTSAA	6 cut(s)	141, 284, 422, 430, 509, 653
AhlI	ACTAGT	1 cut(s)	707
AleI	CACNNNNGTG	1 cut(s)	42
AloI	GAACNNNNNNTCC	2 cut(s)	172, 204
AluBI	AGCT	4 cut(s)	152, 497, 544, 553
AluI	AGCT	4 cut(s)	152, 497, 544, 553
Alw21I	GWGCWC	2 cut(s)	271, 291
Alw26I	GTCTC	3 cut(s)	215, 623, 698
AlwI	GGATC	1 cut(s)	463
AoxI	GGCC	2 cut(s)	312, 491
ApeKI	GCWGC	2 cut(s)	149, 230
ApoI	RAATTY	3 cut(s)	51, 293, 683
ArsI	GACNNNNNNTTYG	2 cut(s)	9, 41
Asp700I	GAANNNNTTC	1 cut(s)	51
AspLEI	GCGC	1 cut(s)	230
AspS9I	GGNCC	3 cut(s)	25, 89, 312
AsuC2I	CCSGG	3 cut(s)	93, 130, 192
AsuHPI	GGTGA	2 cut(s)	155, 176
AsuII	TTCGAA	1 cut(s)	106
AvaII	GGWCC	2 cut(s)	25, 89
BanI	GGYRCC	1 cut(s)	36
Bbv12I	GWGCWC	2 cut(s)	271, 291
BbvI	GCAGC	2 cut(s)	161, 217
BccI	CCATC	2 cut(s)	595, 656
BcnI	CCSGG	3 cut(s)	93, 130, 192
BcoDI	GTCTC	3 cut(s)	215, 623, 698
BcuI	ACTAGT	1 cut(s)	707
BfaI	CTAG	4 cut(s)	221, 489, 545, 708
BisI	GCNGC	3 cut(s)	147, 150, 231
BlsI	GCNGC	3 cut(s)	148, 151, 232
Bme1390I	CCNGG	3 cut(s)	93, 130, 192
Bme18I	GGWCC	2 cut(s)	25, 89
BmgT120I	GGNCC	3 cut(s)	25, 89, 312
BmiI	GGNNCC	4 cut(s)	26, 38, 91, 313
BmrFI	CCNGG	3 cut(s)	93, 130, 192
BmsI	GCATC	2 cut(s)	40, 613
Bpu14I	TTCGAA	1 cut(s)	106
BpuMI	CCSGG	3 cut(s)	93, 130, 192
BsaI	GGTCTC	2 cut(s)	215, 623
BsaJI	CCNNGG	2 cut(s)	205, 454
Bsc4I	CCNNNNNNNGG	4 cut(s)	129, 175, 206, 686
BseDI	CCNNGG	2 cut(s)	205, 454
BseGI	GGATG	1 cut(s)	587
BseLI	CCNNNNNNNGG	4 cut(s)	129, 175, 206, 686
BseMII	CTCAG	1 cut(s)	149
BseRI	GAGGAG	1 cut(s)	564
BseXI	GCAGC	2 cut(s)	161, 217
Bsh1285I	CGRYCG	1 cut(s)	522
BshFI	GGCC	2 cut(s)	314, 493
BshNI	GGYRCC	1 cut(s)	36
BsiEI	CGRYCG	1 cut(s)	522
BsiHKAI	GWGCWC	2 cut(s)	271, 291
BsiSI	CCGG	4 cut(s)	28, 93, 130, 192
BslFI	GGGAC	1 cut(s)	174
BslI	CCNNNNNNNGG	4 cut(s)	129, 175, 206, 686
BsmAI	GTCTC	3 cut(s)	215, 623, 698
BsmFI	GGGAC	1 cut(s)	174
BsnI	GGCC	2 cut(s)	314, 493
Bso31I	GGTCTC	2 cut(s)	215, 623
Bsp119I	TTCGAA	1 cut(s)	106
Bsp1286I	GDGCHC	2 cut(s)	271, 291
Bsp143I	GATC	3 cut(s)	325, 468, 519
BspACI	CCGC	6 cut(s)	87, 124, 144, 147, 166, 176
BspANI	GGCC	2 cut(s)	314, 493
BspCNI	CTCAG	1 cut(s)	150
BspLI	GGNNCC	4 cut(s)	26, 38, 91, 313
BspPI	GGATC	1 cut(s)	463
BspT104I	TTCGAA	1 cut(s)	106
BspT107I	GGYRCC	1 cut(s)	36
BspTNI	GGTCTC	2 cut(s)	215, 623
BssECI	CCNNGG	2 cut(s)	205, 454
BssMI	GATC	3 cut(s)	325, 468, 519
BssT1I	CCWWGG	1 cut(s)	454
Bst4CI	ACNGT	3 cut(s)	41, 188, 583
Bst6I	CTCTTC	2 cut(s)	106, 417
BstBI	TTCGAA	1 cut(s)	106
BstC8I	GCNNGC	2 cut(s)	235, 495
BstDEI	CTNAG	1 cut(s)	158
BstF5I	GGATG	1 cut(s)	587
BstHHI	GCGC	1 cut(s)	230
BstKTI	GATC	3 cut(s)	328, 471, 522
BstMAI	GTCTC	3 cut(s)	215, 623, 698
BstMBI	GATC	3 cut(s)	325, 468, 519
BstMCI	CGRYCG	1 cut(s)	522
BstMWI	GCNNNNNNNGC	2 cut(s)	234, 550
BstSCI	CCNGG	3 cut(s)	91, 128, 190
BstV1I	GCAGC	2 cut(s)	161, 217
BstX2I	RGATCY	1 cut(s)	468
BstXI	CCANNNNNNTGG	1 cut(s)	640
BstYI	RGATCY	1 cut(s)	468
BsuRI	GGCC	2 cut(s)	314, 493
BtsCI	GGATG	1 cut(s)	587
BtsI	GCAGTG	1 cut(s)	79
BtsIMutI	CAGTG	2 cut(s)	79, 507
Cac8I	GCNNGC	2 cut(s)	235, 495
CfoI	GCGC	1 cut(s)	230
Cfr13I	GGNCC	3 cut(s)	25, 89, 312
Csp6I	GTAC	2 cut(s)	399, 584
CviAII	CATG	1 cut(s)	634
CviJI	RGCY	8 cut(s)	152, 257, 314, 493, 497, 544, 553, 605
CviKI_1	RGCY	8 cut(s)	152, 257, 314, 493, 497, 544, 553, 605
CviQI	GTAC	2 cut(s)	399, 584
DdeI	CTNAG	1 cut(s)	158
DpnI	GATC	3 cut(s)	327, 470, 521
DpnII	GATC	3 cut(s)	325, 468, 519
Eam1104I	CTCTTC	2 cut(s)	106, 417
EarI	CTCTTC	2 cut(s)	106, 417
EciI	GGCGGA	1 cut(s)	102
Eco130I	CCWWGG	1 cut(s)	454
Eco31I	GGTCTC	2 cut(s)	215, 623
Eco47I	GGWCC	2 cut(s)	25, 89
Eco57I	CTGAAG	2 cut(s)	483, 621
EcoO109I	RGGNCCY	1 cut(s)	312
EcoRI	GAATTC	2 cut(s)	51, 293
EcoT14I	CCWWGG	1 cut(s)	454
ErhI	CCWWGG	1 cut(s)	454
FaeI	CATG	1 cut(s)	637
FaiI	YATR	6 cut(s)	84, 363, 450, 514, 516, 635
FaqI	GGGAC	1 cut(s)	174
FatI	CATG	1 cut(s)	633
FauI	CCCGC	2 cut(s)	131, 169
FblI	GTMKAC	1 cut(s)	442
Fnu4HI	GCNGC	3 cut(s)	147, 150, 231
FokI	GGATG	1 cut(s)	574
Fsp4HI	GCNGC	3 cut(s)	147, 150, 231
FspBI	CTAG	4 cut(s)	221, 489, 545, 708
GlaI	GCGC	1 cut(s)	229
GluI	GCNGC	3 cut(s)	147, 150, 231
HaeIII	GGCC	2 cut(s)	314, 493
HapII	CCGG	4 cut(s)	28, 93, 130, 192
HhaI	GCGC	1 cut(s)	230
Hin1II	CATG	1 cut(s)	637
Hin6I	GCGC	1 cut(s)	228
HinP1I	GCGC	1 cut(s)	228
HinfI	GANTC	5 cut(s)	6, 64, 117, 160, 571
HpaII	CCGG	4 cut(s)	28, 93, 130, 192
HphI	GGTGA	2 cut(s)	155, 176
Hpy166II	GTNNAC	2 cut(s)	47, 443
Hpy188I	TCNGA	3 cut(s)	69, 266, 358
Hpy188III	TCNNGA	2 cut(s)	44, 568
Hpy8I	GTNNAC	2 cut(s)	47, 443
Hpy99I	CGWCG	1 cut(s)	45
HpyCH4III	ACNGT	3 cut(s)	41, 188, 583
HpyCH4IV	ACGT	1 cut(s)	639
HpyCH4V	TGCA	2 cut(s)	560, 626
HpyF10VI	GCNNNNNNNGC	2 cut(s)	234, 550
HpyF3I	CTNAG	1 cut(s)	158
HpySE526I	ACGT	1 cut(s)	639
Hsp92II	CATG	1 cut(s)	637
HspAI	GCGC	1 cut(s)	228
Kzo9I	GATC	3 cut(s)	325, 468, 519
LmnI	GCTCC	1 cut(s)	266
Lsp1109I	GCAGC	2 cut(s)	161, 217
LweI	GCATC	2 cut(s)	40, 613
MaeI	CTAG	4 cut(s)	221, 489, 545, 708
MaeII	ACGT	1 cut(s)	639
MaeIII	GTNAC	2 cut(s)	161, 346
MalI	GATC	3 cut(s)	327, 470, 521
MboI	GATC	3 cut(s)	325, 468, 519
MboII	GAAGA	3 cut(s)	120, 123, 434
MflI	RGATCY	1 cut(s)	468
MhlI	GDGCHC	2 cut(s)	271, 291
MluCI	AATT	5 cut(s)	51, 277, 293, 648, 683
MlyI	GAGTC	2 cut(s)	169, 565
MmeI	TCCRAC	2 cut(s)	244, 602
MnlI	CCTC	8 cut(s)	107, 215, 325, 406, 482, 520, 556, 585
MroXI	GAANNNNTTC	1 cut(s)	51
MseI	TTAA	1 cut(s)	483
MslI	CAYNNNNRTG	2 cut(s)	42, 638
MspA1I	CMGCKG	2 cut(s)	152, 176
MspI	CCGG	4 cut(s)	28, 93, 130, 192
MspR9I	CCNGG	3 cut(s)	93, 130, 192
MwoI	GCNNNNNNNGC	2 cut(s)	234, 550
NciI	CCSGG	3 cut(s)	93, 130, 192
NdeII	GATC	3 cut(s)	325, 468, 519
NlaIII	CATG	1 cut(s)	637
NlaIV	GGNNCC	4 cut(s)	26, 38, 91, 313
NmuCI	GTSAC	1 cut(s)	161
NspV	TTCGAA	1 cut(s)	106
OliI	CACNNNNGTG	1 cut(s)	42
PcsI	WCGNNNNNNNCGW	1 cut(s)	40
PdmI	GAANNNNTTC	1 cut(s)	51
PfeI	GAWTC	3 cut(s)	6, 64, 117
PkrI	GCNGC	3 cut(s)	148, 151, 232
Ple19I	CGATCG	1 cut(s)	522
PleI	GAGTC	2 cut(s)	168, 565
PpsI	GAGTC	2 cut(s)	168, 565
PspN4I	GGNNCC	4 cut(s)	26, 38, 91, 313
PspPI	GGNCC	3 cut(s)	25, 89, 312
PsuI	RGATCY	1 cut(s)	468
PvuI	CGATCG	1 cut(s)	522
PvuII	CAGCTG	1 cut(s)	152
RsaI	GTAC	2 cut(s)	400, 585
RsaNI	GTAC	2 cut(s)	399, 584
RseI	CAYNNNNRTG	2 cut(s)	42, 638
SaqAI	TTAA	1 cut(s)	483
SatI	GCNGC	3 cut(s)	147, 150, 231
Sau3AI	GATC	3 cut(s)	325, 468, 519
Sau96I	GGNCC	3 cut(s)	25, 89, 312
SchI	GAGTC	2 cut(s)	169, 565
ScrFI	CCNGG	3 cut(s)	93, 130, 192
SduI	GDGCHC	2 cut(s)	271, 291
SfaNI	GCATC	2 cut(s)	40, 613
SfuI	TTCGAA	1 cut(s)	106
SinI	GGWCC	2 cut(s)	25, 89
SmiMI	CAYNNNNRTG	2 cut(s)	42, 638
SpeI	ACTAGT	1 cut(s)	707
Sse9I	AATT	5 cut(s)	51, 277, 293, 648, 683
SsiI	CCGC	6 cut(s)	87, 124, 144, 147, 166, 176
SspI	AATATT	1 cut(s)	478
SspMI	CTAG	4 cut(s)	221, 489, 545, 708
StyD4I	CCNGG	3 cut(s)	91, 128, 190
StyI	CCWWGG	1 cut(s)	454
TaaI	ACNGT	3 cut(s)	41, 188, 583
TaiI	ACGT	1 cut(s)	642
TaqI	TCGA	3 cut(s)	106, 291, 372
TaqII	GACCGA	1 cut(s)	197
TasI	AATT	5 cut(s)	51, 277, 293, 648, 683
TauI	GCSGC	1 cut(s)	149
TfiI	GAWTC	3 cut(s)	6, 64, 117
Tru1I	TTAA	1 cut(s)	483
Tru9I	TTAA	1 cut(s)	483
TscAI	CASTG	2 cut(s)	79, 507
TseFI	GTSAC	1 cut(s)	161
TseI	GCWGC	2 cut(s)	149, 230
Tsp45I	GTSAC	1 cut(s)	161
TspDTI	ATGAA	2 cut(s)	114, 650
TspRI	CASTG	2 cut(s)	79, 507
VpaK11BI	GGWCC	2 cut(s)	25, 89
XapI	RAATTY	3 cut(s)	51, 293, 683
XmiI	GTMKAC	1 cut(s)	442
XmnI	GAANNNNTTC	1 cut(s)	51
XspI	CTAG	4 cut(s)	221, 489, 545, 708

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