Basic Information

Type: gene

Biological Identity

Species

rosa_chinensis

Chromosome

Orthogroup ID

OG0000701

Physical Location & Seq

Genomic Coordinates Forward (+)

38100297 .. 38101872

Gene Structure 1576 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

PRQ57219

Sequence Viewer

CDS Protein Promoter (2k)

Length: 585 bp

ATGCAAATGCTGAAAGATCGGGACTATCTAATTGTTGATCATGATCTCAACATGACAATGTTGCAGTTTAAAAACAAACATGGAGAGAACATGAAAAGGGAGGACCGTACTATCAATAGAAGGAAGAGAGGTCGCGAGTCTGATCAGCTATTTGATGGGATTTGTATTTATGTGTTTTTCCCTGAGGAACCAAAAGTTGGGTTCAAGACAATGAAGAGTTACATTACACGCATGAATCAGGAGAATGTGATTAGAGCAATCTTAGTTGCTCAACAAAATCTGACTCCTTTTGCAAAGACCTCCATTAGTGTGATGGGTTCAAAGTACCGCTTGGAGATTTTCCAGGAGGCAGAATTGTTGGTAAATATTAAAGAGCATGTTCTAGTTCCTGAGCATCGGGTTCTTGCAAATAAGGAAAAAAAGACTTTGCTGGAGAGGTGTACCGTGAAAGAAACACAGCTTCCTCGTATTCAGCTGATTGATCCAATTGCAAGATATTACGAGCTTAAGCGTGGACAAGTTGTGAAGATAATCTGGCCGAGTGAGACTGCAGGACGATTTGTCACCTACCATTACGTTATCTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000418 GO:0000428 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005665 GO:0005666 GO:0005730 GO:0005736 GO:0006139 GO:0006351 GO:0006366 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009987 GO:0010467 GO:0016070 GO:0016591 GO:0018130 GO:0019438 GO:0030880 GO:0031974 GO:0031981 GO:0032774 GO:0032991 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044452 GO:0044464 GO:0046483 GO:0055029 GO:0061695 GO:0070013 GO:0071704 GO:0090304 GO:0097659 GO:1901360 GO:1901362 GO:1901576 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 ko04623 ko05016 ko05169 map00230 map00240 map01100 map03020 map04623 map05016 map05169

Pfam Domains

Protein Families

RNA_pol_Rpb5_C RNA_pol_Rpb5_N

Protein Analysis

194

Amino Acids

23.03

Weight (kDa)

9.54

Isoelectric Point (pI)

33.51

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb5_N	PF03871	1 - 78	7.1e-17	RNA polymerase Rpb5, N-terminal domain
RNA_pol_Rpb5_C	PF01191	121 - 193	8.3e-30	RNA polymerase Rpb5, C-terminal domain

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: OG0000701)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G22320
fragaria_vesca	FvH4_5g21560 FvH4_7g09301 FvH4_7g09301
malus_domestica	MD02G1080800.v1.1 MD02G1093900.v1.1 MD15G1208600.v1.1
prunus_persica	Prupe.2G121300_v2.0.a1 Prupe.2G121300_v2.0.a1 Prupe.2G121400_v2.0.a1 Prupe.2G121400_v2.0.a1
pyrus_communis	pycom02g06410 pycom02g07430 pycom15g18470
rosa_chinensis	RchiOBHm_Chr1g0332791 RchiOBHm_Chr1g0344101 RchiOBHm_Chr1g0344151 RchiOBHm_Chr1g0344171 RchiOBHm_Chr1g0345361 RchiOBHm_Chr1g0345421 RchiOBHm_Chr1g0345561 RchiOBHm_Chr1g0345591 RchiOBHm_Chr1g0345671 RchiOBHm_Chr1g0345701 RchiOBHm_Chr1g0345711 RchiOBHm_Chr1g0345721 RchiOBHm_Chr1g0345801 RchiOBHm_Chr1g0345851 RchiOBHm_Chr1g0345901 RchiOBHm_Chr1g0345921 RchiOBHm_Chr1g0345931 RchiOBHm_Chr1g0345951 RchiOBHm_Chr1g0345961 RchiOBHm_Chr7g0208981
rosa_laevigata	RLG00000003175 RLG00000029644
rosa_multiflora	Rmu_co8382943.1_g000001 Rmu_sc0000532.1_g000035 Rmu_sc0001292.1_g000003 Rmu_sc0001349.1_g000004 Rmu_sc0001692.1_g000006 Rmu_sc0001692.1_g000027 Rmu_sc0002329.1_g000024 Rmu_sc0002329.1_g000032 Rmu_sc0004239.1_g000023 Rmu_sc0008115.1_g000011
rosa_roxburghii	Rroxscaffold_3G00238160 Rroxscaffold_3G00249920 Rroxscaffold_4G00310020 Rroxscaffold_4G00317980 Rroxscaffold_5G00344600
rosa_rugosa	Rorug01G0103700 Rorug01G0103800 Rorug01G0103900 Rorug01G0171800 Rorug07G0107800
rosa_samantha	Rh1BG097500 Rh1BG161500 Rh1CG122000 Rh1CG173900 Rh1CG180700 Rh1CG181100 Rh1DG133900 Rh1DG191900 Rh7AG242600 Rh7BG237400 Rh7DG249500
rosa_wichuraiana	Rw1G010510 Rw1G016120 Rw1G016200 Rw1G016220 Rw1G016430 Rw1G016490 Rw7G020550

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB7I	CCANNNNNTGG	1 cut(s)	197
AccII	CGCG	1 cut(s)	135
AciI	CCGC	1 cut(s)	328
AclWI	GGATC	1 cut(s)	476
AcoI	YGGCCR	1 cut(s)	536
AfaI	GTAC	3 cut(s)	109, 326, 442
AfiI	CCNNNNNNNGG	1 cut(s)	197
AflII	CTTAAG	1 cut(s)	506
AgsI	TTSAA	2 cut(s)	205, 321
AhdI	GACNNNNNGTC	1 cut(s)	560
AjnI	CCWGG	1 cut(s)	342
AjuI	GAANNNNNNNTTGG	2 cut(s)	180, 212
AluBI	AGCT	4 cut(s)	148, 460, 475, 505
AluI	AGCT	4 cut(s)	148, 460, 475, 505
Alw26I	GTCTC	1 cut(s)	539
AlwI	GGATC	1 cut(s)	476
AoxI	GGCC	1 cut(s)	536
AspS9I	GGNCC	1 cut(s)	103
AsuHPI	GGTGA	1 cut(s)	556
AvaII	GGWCC	1 cut(s)	103
AxyI	CCTNAGG	1 cut(s)	183
BccI	CCATC	2 cut(s)	149, 307
BciT130I	CCWGG	1 cut(s)	344
BclI	TGATCA	2 cut(s)	37, 142
BcoDI	GTCTC	1 cut(s)	539
BfaI	CTAG	1 cut(s)	383
BfmI	CTRYAG	1 cut(s)	549
BfrI	CTTAAG	1 cut(s)	506
Bme1390I	CCNGG	1 cut(s)	344
Bme18I	GGWCC	1 cut(s)	103
BmeRI	GACNNNNNGTC	1 cut(s)	560
BmgT120I	GGNCC	1 cut(s)	103
BmiI	GGNNCC	1 cut(s)	189
BmrFI	CCNGG	1 cut(s)	344
BmsI	GCATC	1 cut(s)	403
BpmI	CTGGAG	1 cut(s)	452
Bpu10I	CCTNAGC	1 cut(s)	390
BsaBI	GATNNNNATC	1 cut(s)	42
Bsc4I	CCNNNNNNNGG	1 cut(s)	197
Bse21I	CCTNAGG	1 cut(s)	183
Bse8I	GATNNNNATC	1 cut(s)	42
BseBI	CCWGG	1 cut(s)	344
BseJI	GATNNNNATC	1 cut(s)	42
BseLI	CCNNNNNNNGG	1 cut(s)	197
BseMII	CTCAG	2 cut(s)	174, 381
Bsh1236I	CGCG	1 cut(s)	135
BshFI	GGCC	1 cut(s)	538
BslFI	GGGAC	1 cut(s)	35
BslI	CCNNNNNNNGG	1 cut(s)	197
BsmAI	GTCTC	1 cut(s)	539
BsmFI	GGGAC	1 cut(s)	35
BsnI	GGCC	1 cut(s)	538
Bsp143I	GATC	5 cut(s)	16, 37, 43, 142, 481
Bsp68I	TCGCGA	1 cut(s)	135
BspACI	CCGC	1 cut(s)	328
BspANI	GGCC	1 cut(s)	538
BspCNI	CTCAG	2 cut(s)	175, 382
BspFNI	CGCG	1 cut(s)	135
BspHI	TCATGA	1 cut(s)	40
BspLI	GGNNCC	1 cut(s)	189
BspMAI	CTGCAG	1 cut(s)	553
BspPI	GGATC	1 cut(s)	476
BspTI	CTTAAG	1 cut(s)	506
BssMI	GATC	5 cut(s)	16, 37, 43, 142, 481
Bst2UI	CCWGG	1 cut(s)	344
Bst4CI	ACNGT	2 cut(s)	107, 445
Bst6I	CTCTTC	2 cut(s)	119, 209
BstAFI	CTTAAG	1 cut(s)	506
BstDEI	CTNAG	3 cut(s)	183, 262, 390
BstFNI	CGCG	1 cut(s)	135
BstKTI	GATC	5 cut(s)	19, 40, 46, 145, 484
BstMAI	GTCTC	1 cut(s)	539
BstMBI	GATC	5 cut(s)	16, 37, 43, 142, 481
BstNI	CCWGG	1 cut(s)	344
BstNSI	RCATGY	1 cut(s)	380
BstSCI	CCNGG	1 cut(s)	342
BstSFI	CTRYAG	1 cut(s)	549
BstUI	CGCG	1 cut(s)	135
Bsu36I	CCTNAGG	1 cut(s)	183
BsuRI	GGCC	1 cut(s)	538
BtuMI	TCGCGA	1 cut(s)	135
CciI	TCATGA	1 cut(s)	40
Cfr13I	GGNCC	1 cut(s)	103
Csp6I	GTAC	3 cut(s)	108, 325, 441
CviAII	CATG	6 cut(s)	41, 52, 80, 91, 232, 377
CviJI	RGCY	5 cut(s)	148, 460, 475, 505, 538
CviKI_1	RGCY	5 cut(s)	148, 460, 475, 505, 538
CviQI	GTAC	3 cut(s)	108, 325, 441
DdeI	CTNAG	3 cut(s)	183, 262, 390
DpnI	GATC	5 cut(s)	18, 39, 45, 144, 483
DpnII	GATC	5 cut(s)	16, 37, 43, 142, 481
DraI	TTTAAA	1 cut(s)	70
DriI	GACNNNNNGTC	1 cut(s)	560
EaeI	YGGCCR	1 cut(s)	536
Eam1104I	CTCTTC	2 cut(s)	119, 209
Eam1105I	GACNNNNNGTC	1 cut(s)	560
EarI	CTCTTC	2 cut(s)	119, 209
Eco47I	GGWCC	1 cut(s)	103
Eco81I	CCTNAGG	1 cut(s)	183
EcoRII	CCWGG	1 cut(s)	342
FaeI	CATG	6 cut(s)	44, 55, 83, 94, 235, 380
FaiI	YATR	7 cut(s)	42, 53, 81, 92, 171, 233, 378
FalI	AAGNNNNNCTT	2 cut(s)	314, 346
FaqI	GGGAC	1 cut(s)	35
FatI	CATG	6 cut(s)	40, 51, 79, 90, 231, 376
FbaI	TGATCA	2 cut(s)	37, 142
FspBI	CTAG	1 cut(s)	383
GsuI	CTGGAG	1 cut(s)	452
HaeIII	GGCC	1 cut(s)	538
Hin1II	CATG	6 cut(s)	44, 55, 83, 94, 235, 380
HinfI	GANTC	3 cut(s)	137, 235, 283
HphI	GGTGA	1 cut(s)	556
Hpy166II	GTNNAC	2 cut(s)	441, 515
Hpy188I	TCNGA	2 cut(s)	142, 282
Hpy188III	TCNNGA	6 cut(s)	20, 41, 134, 205, 239, 389
Hpy8I	GTNNAC	2 cut(s)	441, 515
HpyAV	CCTTC	1 cut(s)	114
HpyCH4III	ACNGT	2 cut(s)	107, 445
HpyCH4IV	ACGT	1 cut(s)	576
HpyCH4V	TGCA	6 cut(s)	4, 64, 293, 407, 491, 551
HpyF3I	CTNAG	3 cut(s)	183, 262, 390
HpySE526I	ACGT	1 cut(s)	576
Hsp92II	CATG	6 cut(s)	44, 55, 83, 94, 235, 380
Ksp22I	TGATCA	2 cut(s)	37, 142
Kzo9I	GATC	5 cut(s)	16, 37, 43, 142, 481
LpnPI	CCDG	8 cut(s)	195, 224, 329, 356, 402, 416, 520, 537
LweI	GCATC	1 cut(s)	403
MaeI	CTAG	1 cut(s)	383
MaeII	ACGT	1 cut(s)	576
MaeIII	GTNAC	2 cut(s)	218, 562
MalI	GATC	5 cut(s)	18, 39, 45, 144, 483
MboI	GATC	5 cut(s)	16, 37, 43, 142, 481
MboII	GAAGA	3 cut(s)	136, 226, 538
MfeI	CAATTG	1 cut(s)	486
MluCI	AATT	3 cut(s)	30, 353, 486
MlyI	GAGTC	2 cut(s)	146, 277
MnlI	CCTC	7 cut(s)	94, 122, 178, 310, 340, 429, 474
MseI	TTAA	3 cut(s)	69, 369, 507
MslI	CAYNNNNRTG	2 cut(s)	56, 308
MspA1I	CMGCKG	1 cut(s)	475
MspCI	CTTAAG	1 cut(s)	506
MspR9I	CCNGG	1 cut(s)	344
MunI	CAATTG	1 cut(s)	486
MvaI	CCWGG	1 cut(s)	344
MvnI	CGCG	1 cut(s)	135
NdeII	GATC	5 cut(s)	16, 37, 43, 142, 481
NlaIII	CATG	6 cut(s)	44, 55, 83, 94, 235, 380
NlaIV	GGNNCC	1 cut(s)	189
NmeAIII	GCCGAG	1 cut(s)	564
NmuCI	GTSAC	1 cut(s)	562
NruI	TCGCGA	1 cut(s)	135
NspI	RCATGY	1 cut(s)	380
PagI	TCATGA	1 cut(s)	40
PfeI	GAWTC	1 cut(s)	235
PflMI	CCANNNNNTGG	1 cut(s)	197
PfoI	TCCNGGA	1 cut(s)	342
PleI	GAGTC	2 cut(s)	145, 277
PpsI	GAGTC	2 cut(s)	145, 277
Psp6I	CCWGG	1 cut(s)	342
PspGI	CCWGG	1 cut(s)	342
PspN4I	GGNNCC	1 cut(s)	189
PspPI	GGNCC	1 cut(s)	103
PstI	CTGCAG	1 cut(s)	553
PvuII	CAGCTG	1 cut(s)	475
RruI	TCGCGA	1 cut(s)	135
RsaI	GTAC	3 cut(s)	109, 326, 442
RsaNI	GTAC	3 cut(s)	108, 325, 441
RseI	CAYNNNNRTG	2 cut(s)	56, 308
SaqAI	TTAA	3 cut(s)	69, 369, 507
Sau3AI	GATC	5 cut(s)	16, 37, 43, 142, 481
Sau96I	GGNCC	1 cut(s)	103
SchI	GAGTC	2 cut(s)	146, 277
ScrFI	CCNGG	1 cut(s)	344
SetI	ASST	9 cut(s)	133, 150, 302, 440, 462, 477, 507, 569, 579
SfaNI	GCATC	1 cut(s)	403
SfcI	CTRYAG	1 cut(s)	549
SinI	GGWCC	1 cut(s)	103
SmiMI	CAYNNNNRTG	2 cut(s)	56, 308
SmlI	CTYRAG	1 cut(s)	506
SmoI	CTYRAG	1 cut(s)	506
Sse9I	AATT	3 cut(s)	30, 353, 486
SsiI	CCGC	1 cut(s)	328
SspI	AATATT	1 cut(s)	367
SspMI	CTAG	1 cut(s)	383
StyD4I	CCNGG	1 cut(s)	342
TaaI	ACNGT	2 cut(s)	107, 445
TaiI	ACGT	1 cut(s)	579
TasI	AATT	3 cut(s)	30, 353, 486
TfiI	GAWTC	1 cut(s)	235
Tru1I	TTAA	3 cut(s)	69, 369, 507
Tru9I	TTAA	3 cut(s)	69, 369, 507
TseFI	GTSAC	1 cut(s)	562
Tsp45I	GTSAC	1 cut(s)	562
TspDTI	ATGAA	3 cut(s)	107, 227, 248
Van91I	CCANNNNNTGG	1 cut(s)	197
Vha464I	CTTAAG	1 cut(s)	506
VpaK11BI	GGWCC	1 cut(s)	103
XceI	RCATGY	1 cut(s)	380
XcmI	CCANNNNNNNNNTGG	1 cut(s)	310
XspI	CTAG	1 cut(s)	383

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