Basic Information

Type: gene

Biological Identity

Species

rosa_wichuraiana

Chromosome

Chr1

Orthogroup ID

OG0000701

Physical Location & Seq

Genomic Coordinates Forward (+)

36634535 .. 36639990

Gene Structure 5456 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rw1G016490.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 663 bp

ATGGATATAACTGCAGAGGAAATTACGAGGCTTTATCAAGTTCAAAAAACAGTGATGCATATGCTGAAAGATCTGGACTACATAAGTTCGAAAGACAGTGAAATGCTGAAAGATCGGGACTATCTAACTGTTGATCATGATCTCAACATGACAATGTCGCAGTTTAAAAACAGACATGGAGAGAACATGAAGAGGGAGGACCTTACTATCAATAGAAGGAAGAGAGATGATGAATTTTATGTGTTTTTCCCTTACGAACCAAAATTTGGGGCCAAGACAATGAAGAGTTACATCACACGCATGAATCAGGAGAATCTAATTAGAGCAATCTTAGTTGTTCAACAAAATCTGACTCCTTTTGTAGAGACCTCCATTAGTGAGATGGGTTCAAAGTACCACTTGGAGATTTTCCAGGAGGCAGAATTGTTGGTGAATATTAAAGAGTATGTTCTAGTTCCTGAGCATCGGTTTCTTACAAATGAGGAAAAGAAGAGACTTGCTGGAGAGCTTCCTCTTATTCAGCTGATTGATCCAATTGCAAGATATTACGGGCTTAAGCGTGGACAAGTTGTGAAGATAATCCGGCCAAGTGAGACTGCAGGGCGATATGTCACCTACCGTTACGTTATCCAAGTACAGCAGCAGAAACCTGGATTGCATTAG

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

220

Amino Acids

26.16

Weight (kDa)

8.55

Isoelectric Point (pI)

39.75

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb5_N	PF03871	34 - 101	1.6e-15	RNA polymerase Rpb5, N-terminal domain
RNA_pol_Rpb5_C	PF01191	144 - 209	1.2e-22	RNA polymerase Rpb5, C-terminal domain

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

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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)	266
AclWI	GGATC	1 cut(s)	524
AcoI	YGGCCR	1 cut(s)	584
AcsI	RAATTY	2 cut(s)	233, 263
AfaI	GTAC	2 cut(s)	395, 636
AfiI	CCNNNNNNNGG	1 cut(s)	266
AflII	CTTAAG	1 cut(s)	554
AgsI	TTSAA	3 cut(s)	44, 341, 390
AjnI	CCWGG	2 cut(s)	411, 649
AjuI	GAANNNNNNNTTGG	2 cut(s)	249, 281
AluBI	AGCT	2 cut(s)	508, 523
AluI	AGCT	2 cut(s)	508, 523
Alw26I	GTCTC	3 cut(s)	359, 487, 587
AlwI	GGATC	1 cut(s)	524
AoxI	GGCC	2 cut(s)	270, 584
ApeKI	GCWGC	1 cut(s)	640
ApoI	RAATTY	2 cut(s)	233, 263
AspS9I	GGNCC	2 cut(s)	199, 270
AsuHPI	GGTGA	2 cut(s)	442, 604
AsuII	TTCGAA	1 cut(s)	89
AvaII	GGWCC	1 cut(s)	199
BbvI	GCAGC	1 cut(s)	652
BccI	CCATC	1 cut(s)	376
BciT130I	CCWGG	2 cut(s)	413, 651
BclI	TGATCA	1 cut(s)	133
BcoDI	GTCTC	3 cut(s)	359, 487, 587
BfaI	CTAG	1 cut(s)	452
BfmI	CTRYAG	2 cut(s)	12, 597
BfrI	CTTAAG	1 cut(s)	554
BglII	AGATCT	1 cut(s)	70
BisI	GCNGC	1 cut(s)	641
BlsI	GCNGC	1 cut(s)	642
Bme1390I	CCNGG	2 cut(s)	413, 651
Bme18I	GGWCC	1 cut(s)	199
BmgT120I	GGNCC	2 cut(s)	199, 270
BmiI	GGNNCC	1 cut(s)	271
BmrFI	CCNGG	2 cut(s)	413, 651
BmsI	GCATC	2 cut(s)	45, 472
BpmI	CTGGAG	1 cut(s)	522
Bpu10I	CCTNAGC	1 cut(s)	459
Bpu14I	TTCGAA	1 cut(s)	89
BsaBI	GATNNNNATC	1 cut(s)	138
BsaI	GGTCTC	1 cut(s)	359
Bsc4I	CCNNNNNNNGG	1 cut(s)	266
Bse8I	GATNNNNATC	1 cut(s)	138
BseBI	CCWGG	2 cut(s)	413, 651
BseJI	GATNNNNATC	1 cut(s)	138
BseLI	CCNNNNNNNGG	1 cut(s)	266
BseMII	CTCAG	1 cut(s)	450
BseXI	GCAGC	1 cut(s)	652
BshFI	GGCC	2 cut(s)	272, 586
BsiSI	CCGG	1 cut(s)	583
BslFI	GGGAC	1 cut(s)	131
BslI	CCNNNNNNNGG	1 cut(s)	266
BsmAI	GTCTC	3 cut(s)	359, 487, 587
BsmFI	GGGAC	1 cut(s)	131
BsnI	GGCC	2 cut(s)	272, 586
Bso31I	GGTCTC	1 cut(s)	359
Bsp119I	TTCGAA	1 cut(s)	89
Bsp143I	GATC	5 cut(s)	70, 112, 133, 139, 529
BspANI	GGCC	2 cut(s)	272, 586
BspCNI	CTCAG	1 cut(s)	451
BspHI	TCATGA	1 cut(s)	136
BspLI	GGNNCC	1 cut(s)	271
BspMAI	CTGCAG	2 cut(s)	16, 601
BspPI	GGATC	1 cut(s)	524
BspT104I	TTCGAA	1 cut(s)	89
BspTI	CTTAAG	1 cut(s)	554
BspTNI	GGTCTC	1 cut(s)	359
BssMI	GATC	5 cut(s)	70, 112, 133, 139, 529
Bst2UI	CCWGG	2 cut(s)	413, 651
Bst4CI	ACNGT	4 cut(s)	52, 98, 130, 620
Bst6I	CTCTTC	4 cut(s)	185, 215, 278, 485
BstAFI	CTTAAG	1 cut(s)	554
BstBI	TTCGAA	1 cut(s)	89
BstDEI	CTNAG	2 cut(s)	331, 459
BstKTI	GATC	5 cut(s)	73, 115, 136, 142, 532
BstMAI	GTCTC	3 cut(s)	359, 487, 587
BstMBI	GATC	5 cut(s)	70, 112, 133, 139, 529
BstNI	CCWGG	2 cut(s)	413, 651
BstSCI	CCNGG	2 cut(s)	411, 649
BstSFI	CTRYAG	2 cut(s)	12, 597
BstV1I	GCAGC	1 cut(s)	652
BstX2I	RGATCY	1 cut(s)	70
BstYI	RGATCY	1 cut(s)	70
BsuRI	GGCC	2 cut(s)	272, 586
BtsIMutI	CAGTG	2 cut(s)	57, 103
CciI	TCATGA	1 cut(s)	136
Cfr13I	GGNCC	2 cut(s)	199, 270
Csp6I	GTAC	2 cut(s)	394, 635
CviAII	CATG	5 cut(s)	137, 148, 176, 187, 301
CviJI	RGCY	6 cut(s)	31, 272, 508, 523, 553, 586
CviKI_1	RGCY	6 cut(s)	31, 272, 508, 523, 553, 586
CviQI	GTAC	2 cut(s)	394, 635
DdeI	CTNAG	2 cut(s)	331, 459
DpnI	GATC	5 cut(s)	72, 114, 135, 141, 531
DpnII	GATC	5 cut(s)	70, 112, 133, 139, 529
DraI	TTTAAA	1 cut(s)	166
EaeI	YGGCCR	1 cut(s)	584
Eam1104I	CTCTTC	4 cut(s)	185, 215, 278, 485
EarI	CTCTTC	4 cut(s)	185, 215, 278, 485
Eco31I	GGTCTC	1 cut(s)	359
Eco47I	GGWCC	1 cut(s)	199
EcoO109I	RGGNCCY	1 cut(s)	199
EcoRII	CCWGG	2 cut(s)	411, 649
EcoT22I	ATGCAT	1 cut(s)	60
FaeI	CATG	5 cut(s)	140, 151, 179, 190, 304
FalI	AAGNNNNNCTT	2 cut(s)	383, 415
FaqI	GGGAC	1 cut(s)	131
FatI	CATG	5 cut(s)	136, 147, 175, 186, 300
FauNDI	CATATG	1 cut(s)	60
FbaI	TGATCA	1 cut(s)	133
Fnu4HI	GCNGC	1 cut(s)	641
Fsp4HI	GCNGC	1 cut(s)	641
FspBI	CTAG	1 cut(s)	452
GluI	GCNGC	1 cut(s)	641
GsuI	CTGGAG	1 cut(s)	522
HaeIII	GGCC	2 cut(s)	272, 586
HapII	CCGG	1 cut(s)	583
Hin1II	CATG	5 cut(s)	140, 151, 179, 190, 304
HinfI	GANTC	3 cut(s)	304, 313, 352
HpaII	CCGG	1 cut(s)	583
HphI	GGTGA	2 cut(s)	442, 604
Hpy166II	GTNNAC	1 cut(s)	563
Hpy188I	TCNGA	1 cut(s)	351
Hpy188III	TCNNGA	5 cut(s)	74, 116, 137, 308, 458
Hpy8I	GTNNAC	1 cut(s)	563
HpyAV	CCTTC	1 cut(s)	210
HpyCH4III	ACNGT	4 cut(s)	52, 98, 130, 620
HpyCH4IV	ACGT	1 cut(s)	624
HpyCH4V	TGCA	5 cut(s)	14, 58, 539, 599, 658
HpyF3I	CTNAG	2 cut(s)	331, 459
HpySE526I	ACGT	1 cut(s)	624
Hsp92II	CATG	5 cut(s)	140, 151, 179, 190, 304
Ksp22I	TGATCA	1 cut(s)	133
Kzo9I	GATC	5 cut(s)	70, 112, 133, 139, 529
LpnPI	CCDG	9 cut(s)	59, 293, 398, 425, 471, 486, 585, 596, 636
Lsp1109I	GCAGC	1 cut(s)	652
LweI	GCATC	2 cut(s)	45, 472
MaeI	CTAG	1 cut(s)	452
MaeII	ACGT	1 cut(s)	624
MaeIII	GTNAC	3 cut(s)	287, 610, 620
MalI	GATC	5 cut(s)	72, 114, 135, 141, 531
MboI	GATC	5 cut(s)	70, 112, 133, 139, 529
MboII	GAAGA	5 cut(s)	202, 232, 295, 502, 586
MfeI	CAATTG	1 cut(s)	534
MflI	RGATCY	1 cut(s)	70
MluCI	AATT	6 cut(s)	21, 233, 263, 318, 422, 534
MlyI	GAGTC	1 cut(s)	346
MnlI	CCTC	8 cut(s)	10, 21, 186, 190, 379, 409, 475, 522
Mph1103I	ATGCAT	1 cut(s)	60
MseI	TTAA	3 cut(s)	165, 438, 555
MslI	CAYNNNNRTG	2 cut(s)	152, 299
MspA1I	CMGCKG	1 cut(s)	523
MspCI	CTTAAG	1 cut(s)	554
MspI	CCGG	1 cut(s)	583
MspR9I	CCNGG	2 cut(s)	413, 651
MunI	CAATTG	1 cut(s)	534
MvaI	CCWGG	2 cut(s)	413, 651
NdeI	CATATG	1 cut(s)	60
NdeII	GATC	5 cut(s)	70, 112, 133, 139, 529
NlaIII	CATG	5 cut(s)	140, 151, 179, 190, 304
NlaIV	GGNNCC	1 cut(s)	271
NmuCI	GTSAC	1 cut(s)	610
NsiI	ATGCAT	1 cut(s)	60
NspV	TTCGAA	1 cut(s)	89
PagI	TCATGA	1 cut(s)	136
PfeI	GAWTC	2 cut(s)	304, 313
PflFI	GACNNNGTC	1 cut(s)	154
PflMI	CCANNNNNTGG	1 cut(s)	266
PfoI	TCCNGGA	1 cut(s)	411
PkrI	GCNGC	1 cut(s)	642
PleI	GAGTC	1 cut(s)	346
PpsI	GAGTC	1 cut(s)	346
PpuMI	RGGWCCY	1 cut(s)	199
Psp5II	RGGWCCY	1 cut(s)	199
Psp6I	CCWGG	2 cut(s)	411, 649
PspGI	CCWGG	2 cut(s)	411, 649
PspN4I	GGNNCC	1 cut(s)	271
PspPI	GGNCC	2 cut(s)	199, 270
PspPPI	RGGWCCY	1 cut(s)	199
PstI	CTGCAG	2 cut(s)	16, 601
PsuI	RGATCY	1 cut(s)	70
PsyI	GACNNNGTC	1 cut(s)	154
PvuII	CAGCTG	1 cut(s)	523
RsaI	GTAC	2 cut(s)	395, 636
RsaNI	GTAC	2 cut(s)	394, 635
RseI	CAYNNNNRTG	2 cut(s)	152, 299
SaqAI	TTAA	3 cut(s)	165, 438, 555
SatI	GCNGC	1 cut(s)	641
Sau3AI	GATC	5 cut(s)	70, 112, 133, 139, 529
Sau96I	GGNCC	2 cut(s)	199, 270
SchI	GAGTC	1 cut(s)	346
ScrFI	CCNGG	2 cut(s)	413, 651
SetI	ASST	7 cut(s)	204, 371, 510, 525, 617, 627, 652
SfaNI	GCATC	2 cut(s)	45, 472
SfcI	CTRYAG	2 cut(s)	12, 597
SfuI	TTCGAA	1 cut(s)	89
SinI	GGWCC	1 cut(s)	199
SmiMI	CAYNNNNRTG	2 cut(s)	152, 299
SmlI	CTYRAG	1 cut(s)	554
SmoI	CTYRAG	1 cut(s)	554
Sse9I	AATT	6 cut(s)	21, 233, 263, 318, 422, 534
SspI	AATATT	1 cut(s)	436
SspMI	CTAG	1 cut(s)	452
StyD4I	CCNGG	2 cut(s)	411, 649
TaaI	ACNGT	4 cut(s)	52, 98, 130, 620
TaiI	ACGT	1 cut(s)	627
TaqI	TCGA	1 cut(s)	89
TasI	AATT	6 cut(s)	21, 233, 263, 318, 422, 534
TatI	WGTACW	1 cut(s)	634
TfiI	GAWTC	2 cut(s)	304, 313
Tru1I	TTAA	3 cut(s)	165, 438, 555
Tru9I	TTAA	3 cut(s)	165, 438, 555
TscAI	CASTG	2 cut(s)	57, 103
TseFI	GTSAC	1 cut(s)	610
TseI	GCWGC	1 cut(s)	640
Tsp45I	GTSAC	1 cut(s)	610
TspDTI	ATGAA	4 cut(s)	203, 246, 296, 317
TspRI	CASTG	2 cut(s)	57, 103
Tth111I	GACNNNGTC	1 cut(s)	154
Van91I	CCANNNNNTGG	1 cut(s)	266
Vha464I	CTTAAG	1 cut(s)	554
VpaK11BI	GGWCC	1 cut(s)	199
XapI	RAATTY	2 cut(s)	233, 263
XcmI	CCANNNNNNNNNTGG	1 cut(s)	379
XspI	CTAG	1 cut(s)	452
Zsp2I	ATGCAT	1 cut(s)	60

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