Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000004

Orthogroup ID

OG0000701

Physical Location & Seq

Genomic Coordinates Forward (+)

43643989 .. 43646300

Gene Structure 2312 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_4G00317980.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 621 bp

ATGGTTTTGACAGAAGAAGAAATCACGAGGCTGTATAGGGTTCGAAAGACAGTGATGCAAATGCTGAAAGATCGGGACTATCTAATTGTTGATCATGATCTCAACATGACAATGTCGCAGTTTAAGAACAAATATGGAGAGAACATGAAAAGGGAGGACCTTACTATCAATAGAAGGAAGAGAGGTGACGAGTCTGATCAGATTTATGTGTTTTTCCCTGACGAACCAAAAGTTGGGGTCAAGACGATGAAGAGTTACATTGCACGTATGACTCAGGAGAATGTGATTAGAGCAATCTTAGTTGCTCAACAAAATCTGACCCCTTTTGCAAAGACCTCCATTAGTGAGATAGGTTCCAAGTACCACTTGGAGATCTTCCAGGAGGCAGAATTGTTGGTGAATATTAAAGAGCATGTTCTAGTTCCTGAGCATCGGGTTCTTACAAATGAGGAAAAGAAGACTTTGCTGGAGAGGTACACTGTGAAAGAAACACAGCTTCCTCGTATTCAGCTGATTGATCCAATTGCAAGATATTACGGGCTTAAGCGTGGACAAGTTGTGAAGATAATCCGGCCAAGTGAGACTGCAGGACGATATGTCACCTACCGTTACGTTATCTAA

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

206

Amino Acids

24.43

Weight (kDa)

9.41

Isoelectric Point (pI)

33.01

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb5_N	PF03871	5 - 90	3e-32	RNA polymerase Rpb5, N-terminal domain
RNA_pol_Rpb5_C	PF01191	133 - 205	2.6e-35	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)	233
AclWI	GGATC	1 cut(s)	512
AcoI	YGGCCR	1 cut(s)	572
AfaI	GTAC	2 cut(s)	362, 476
AfiI	CCNNNNNNNGG	1 cut(s)	233
AflII	CTTAAG	1 cut(s)	542
AhdI	GACNNNNNGTC	1 cut(s)	596
AjnI	CCWGG	1 cut(s)	378
AjuI	GAANNNNNNNTTGG	2 cut(s)	216, 248
AluBI	AGCT	2 cut(s)	496, 511
AluI	AGCT	2 cut(s)	496, 511
Alw26I	GTCTC	1 cut(s)	575
AlwI	GGATC	1 cut(s)	512
AoxI	GGCC	1 cut(s)	572
AspS9I	GGNCC	1 cut(s)	157
AsuHPI	GGTGA	3 cut(s)	197, 409, 592
AsuII	TTCGAA	1 cut(s)	43
AvaII	GGWCC	1 cut(s)	157
BauI	CACGAG	1 cut(s)	25
BbsI	GAAGAC	1 cut(s)	464
BciT130I	CCWGG	1 cut(s)	380
BclI	TGATCA	2 cut(s)	91, 196
BcoDI	GTCTC	1 cut(s)	575
BfaI	CTAG	1 cut(s)	419
BfmI	CTRYAG	1 cut(s)	585
BfrI	CTTAAG	1 cut(s)	542
BglII	AGATCT	1 cut(s)	372
Bme1390I	CCNGG	1 cut(s)	380
Bme18I	GGWCC	1 cut(s)	157
BmeRI	GACNNNNNGTC	1 cut(s)	596
BmgT120I	GGNCC	1 cut(s)	157
BmiI	GGNNCC	1 cut(s)	355
BmrFI	CCNGG	1 cut(s)	380
BmsI	GCATC	2 cut(s)	45, 439
BpiI	GAAGAC	1 cut(s)	464
BpmI	CTGGAG	1 cut(s)	488
Bpu10I	CCTNAGC	1 cut(s)	426
Bpu14I	TTCGAA	1 cut(s)	43
BsaAI	YACGTR	1 cut(s)	266
BsaBI	GATNNNNATC	1 cut(s)	96
Bsc4I	CCNNNNNNNGG	1 cut(s)	233
Bse3DI	GCAATG	1 cut(s)	258
Bse8I	GATNNNNATC	1 cut(s)	96
BseBI	CCWGG	1 cut(s)	380
BseJI	GATNNNNATC	1 cut(s)	96
BseLI	CCNNNNNNNGG	1 cut(s)	233
BseMI	GCAATG	1 cut(s)	258
BseMII	CTCAG	2 cut(s)	287, 417
BshFI	GGCC	1 cut(s)	574
BsiSI	CCGG	1 cut(s)	571
BslFI	GGGAC	1 cut(s)	89
BslI	CCNNNNNNNGG	1 cut(s)	233
BsmAI	GTCTC	1 cut(s)	575
BsmFI	GGGAC	1 cut(s)	89
BsnI	GGCC	1 cut(s)	574
Bsp119I	TTCGAA	1 cut(s)	43
Bsp143I	GATC	6 cut(s)	70, 91, 97, 196, 372, 517
BspANI	GGCC	1 cut(s)	574
BspCNI	CTCAG	2 cut(s)	286, 418
BspHI	TCATGA	1 cut(s)	94
BspLI	GGNNCC	1 cut(s)	355
BspMAI	CTGCAG	1 cut(s)	589
BspPI	GGATC	1 cut(s)	512
BspT104I	TTCGAA	1 cut(s)	43
BspTI	CTTAAG	1 cut(s)	542
BsrDI	GCAATG	1 cut(s)	258
BssMI	GATC	6 cut(s)	70, 91, 97, 196, 372, 517
BssSI	CACGAG	1 cut(s)	25
Bst2BI	CACGAG	1 cut(s)	25
Bst2UI	CCWGG	1 cut(s)	380
Bst4CI	ACNGT	3 cut(s)	52, 481, 608
Bst6I	CTCTTC	2 cut(s)	173, 245
BstAFI	CTTAAG	1 cut(s)	542
BstBAI	YACGTR	1 cut(s)	266
BstBI	TTCGAA	1 cut(s)	43
BstDEI	CTNAG	3 cut(s)	273, 298, 426
BstKTI	GATC	6 cut(s)	73, 94, 100, 199, 375, 520
BstMAI	GTCTC	1 cut(s)	575
BstMBI	GATC	6 cut(s)	70, 91, 97, 196, 372, 517
BstNI	CCWGG	1 cut(s)	380
BstNSI	RCATGY	1 cut(s)	416
BstSCI	CCNGG	1 cut(s)	378
BstSFI	CTRYAG	1 cut(s)	585
BstV2I	GAAGAC	1 cut(s)	464
BstX2I	RGATCY	1 cut(s)	372
BstYI	RGATCY	1 cut(s)	372
BsuRI	GGCC	1 cut(s)	574
BtsIMutI	CAGTG	2 cut(s)	57, 477
CciI	TCATGA	1 cut(s)	94
Cfr13I	GGNCC	1 cut(s)	157
Csp6I	GTAC	2 cut(s)	361, 475
CviAII	CATG	4 cut(s)	95, 106, 145, 413
CviJI	RGCY	5 cut(s)	31, 496, 511, 541, 574
CviKI_1	RGCY	5 cut(s)	31, 496, 511, 541, 574
CviQI	GTAC	2 cut(s)	361, 475
DdeI	CTNAG	3 cut(s)	273, 298, 426
DpnI	GATC	6 cut(s)	72, 93, 99, 198, 374, 519
DpnII	GATC	6 cut(s)	70, 91, 97, 196, 372, 517
DriI	GACNNNNNGTC	1 cut(s)	596
EaeI	YGGCCR	1 cut(s)	572
Eam1104I	CTCTTC	2 cut(s)	173, 245
Eam1105I	GACNNNNNGTC	1 cut(s)	596
EarI	CTCTTC	2 cut(s)	173, 245
Eco47I	GGWCC	1 cut(s)	157
EcoO109I	RGGNCCY	1 cut(s)	157
EcoRII	CCWGG	1 cut(s)	378
FaeI	CATG	4 cut(s)	98, 109, 148, 416
FaiI	YATR	9 cut(s)	36, 96, 107, 135, 146, 207, 269, 414, 597
FalI	AAGNNNNNCTT	2 cut(s)	350, 382
FaqI	GGGAC	1 cut(s)	89
FatI	CATG	4 cut(s)	94, 105, 144, 412
FbaI	TGATCA	2 cut(s)	91, 196
FspBI	CTAG	1 cut(s)	419
GsuI	CTGGAG	1 cut(s)	488
HaeIII	GGCC	1 cut(s)	574
HapII	CCGG	1 cut(s)	571
Hin1II	CATG	4 cut(s)	98, 109, 148, 416
HinfI	GANTC	2 cut(s)	191, 271
HpaII	CCGG	1 cut(s)	571
HphI	GGTGA	3 cut(s)	197, 409, 592
Hpy166II	GTNNAC	2 cut(s)	477, 551
Hpy188I	TCNGA	3 cut(s)	196, 201, 318
Hpy188III	TCNNGA	6 cut(s)	25, 74, 95, 241, 275, 425
Hpy8I	GTNNAC	2 cut(s)	477, 551
HpyAV	CCTTC	1 cut(s)	168
HpyCH4III	ACNGT	3 cut(s)	52, 481, 608
HpyCH4IV	ACGT	2 cut(s)	265, 612
HpyCH4V	TGCA	5 cut(s)	58, 263, 329, 527, 587
HpyF3I	CTNAG	3 cut(s)	273, 298, 426
HpySE526I	ACGT	2 cut(s)	265, 612
Hsp92II	CATG	4 cut(s)	98, 109, 148, 416
Ksp22I	TGATCA	2 cut(s)	91, 196
Kzo9I	GATC	6 cut(s)	70, 91, 97, 196, 372, 517
LpnPI	CCDG	8 cut(s)	231, 260, 365, 392, 438, 452, 573, 584
LweI	GCATC	2 cut(s)	45, 439
MaeI	CTAG	1 cut(s)	419
MaeII	ACGT	2 cut(s)	265, 612
MaeIII	GTNAC	4 cut(s)	185, 254, 598, 608
MalI	GATC	6 cut(s)	72, 93, 99, 198, 374, 519
MboI	GATC	6 cut(s)	70, 91, 97, 196, 372, 517
MboII	GAAGA	7 cut(s)	26, 29, 190, 262, 367, 469, 574
MfeI	CAATTG	1 cut(s)	522
MflI	RGATCY	1 cut(s)	372
MluCI	AATT	3 cut(s)	84, 389, 522
MlyI	GAGTC	2 cut(s)	200, 265
MnlI	CCTC	8 cut(s)	21, 148, 176, 346, 376, 442, 465, 510
MseI	TTAA	3 cut(s)	123, 405, 543
MslI	CAYNNNNRTG	1 cut(s)	110
MspA1I	CMGCKG	1 cut(s)	511
MspCI	CTTAAG	1 cut(s)	542
MspI	CCGG	1 cut(s)	571
MspR9I	CCNGG	1 cut(s)	380
MunI	CAATTG	1 cut(s)	522
MvaI	CCWGG	1 cut(s)	380
NdeII	GATC	6 cut(s)	70, 91, 97, 196, 372, 517
NlaIII	CATG	4 cut(s)	98, 109, 148, 416
NlaIV	GGNNCC	1 cut(s)	355
NmuCI	GTSAC	2 cut(s)	185, 598
NspI	RCATGY	1 cut(s)	416
NspV	TTCGAA	1 cut(s)	43
PagI	TCATGA	1 cut(s)	94
PflFI	GACNNNGTC	1 cut(s)	112
PflMI	CCANNNNNTGG	1 cut(s)	233
PfoI	TCCNGGA	1 cut(s)	378
PleI	GAGTC	2 cut(s)	199, 265
PpsI	GAGTC	2 cut(s)	199, 265
Ppu21I	YACGTR	1 cut(s)	266
PpuMI	RGGWCCY	1 cut(s)	157
Psp5II	RGGWCCY	1 cut(s)	157
Psp6I	CCWGG	1 cut(s)	378
PspGI	CCWGG	1 cut(s)	378
PspN4I	GGNNCC	1 cut(s)	355
PspPI	GGNCC	1 cut(s)	157
PspPPI	RGGWCCY	1 cut(s)	157
PstI	CTGCAG	1 cut(s)	589
PsuI	RGATCY	1 cut(s)	372
PsyI	GACNNNGTC	1 cut(s)	112
PvuII	CAGCTG	1 cut(s)	511
RsaI	GTAC	2 cut(s)	362, 476
RsaNI	GTAC	2 cut(s)	361, 475
RseI	CAYNNNNRTG	1 cut(s)	110
SaqAI	TTAA	3 cut(s)	123, 405, 543
Sau3AI	GATC	6 cut(s)	70, 91, 97, 196, 372, 517
Sau96I	GGNCC	1 cut(s)	157
SchI	GAGTC	2 cut(s)	200, 265
ScrFI	CCNGG	1 cut(s)	380
SfaNI	GCATC	2 cut(s)	45, 439
SfcI	CTRYAG	1 cut(s)	585
SfuI	TTCGAA	1 cut(s)	43
SinI	GGWCC	1 cut(s)	157
SmiMI	CAYNNNNRTG	1 cut(s)	110
SmlI	CTYRAG	1 cut(s)	542
SmoI	CTYRAG	1 cut(s)	542
Sse9I	AATT	3 cut(s)	84, 389, 522
SspI	AATATT	1 cut(s)	403
SspMI	CTAG	1 cut(s)	419
StyD4I	CCNGG	1 cut(s)	378
TaaI	ACNGT	3 cut(s)	52, 481, 608
TaiI	ACGT	2 cut(s)	268, 615
TaqI	TCGA	1 cut(s)	43
TasI	AATT	3 cut(s)	84, 389, 522
Tru1I	TTAA	3 cut(s)	123, 405, 543
Tru9I	TTAA	3 cut(s)	123, 405, 543
TscAI	CASTG	2 cut(s)	57, 484
TseFI	GTSAC	2 cut(s)	185, 598
Tsp45I	GTSAC	2 cut(s)	185, 598
TspDTI	ATGAA	2 cut(s)	161, 263
TspRI	CASTG	2 cut(s)	57, 484
Tth111I	GACNNNGTC	1 cut(s)	112
Van91I	CCANNNNNTGG	1 cut(s)	233
Vha464I	CTTAAG	1 cut(s)	542
VpaK11BI	GGWCC	1 cut(s)	157
XceI	RCATGY	1 cut(s)	416
XcmI	CCANNNNNNNNNTGG	1 cut(s)	364
XspI	CTAG	1 cut(s)	419

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