Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000003

Orthogroup ID

OG0000701

Physical Location & Seq

Genomic Coordinates Reverse (-)

43681299 .. 43684266

Gene Structure 2968 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_3G00249920.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 621 bp

ATGGCTCTATCAGAAGATGAAATCACGAGGCTTTACAGAACTCGAAGAACCGTGTTGCAAATGCTGAAAGATCGGGATTACTTAGTTACAGAAGCTGAGATCAACATGACAAAAGAACAATTCAAGAGCACATATGGAGAGAACATGAAAAGGGAAGATCTAGACATCAATAAAGAAAAGCGAAGTAACAGCTCTGATCAGATGTATGTCTTCTTCCCTAATGAGGCAAAGGTTGGGGTAAATACAATGAGGGACTACACCAAGCGCATGCAATCGCAGAATGTGTTCAGAGCAATCTTGGTGTCTCAAACAAAGCTGACTCCTTTTGCAAATAGATGTATAAGTGAGATGTCTACAAGGTTCCGCATGGAGGTTTTCCAGGAGGAAGAACTGTTGGTGAATATTAAAGAGCATGTTCTAGTTCCTGCGCATCAGGTGCTTACAAATGAGGAAAAGAAGAGTTTGCTGCAGAGGTATACCGTGAAAGAAACACAGCTTCCTCGGATGCAGGTGGTTGATCCAGTTGCAAGGTATTACGGGCTTTCACGTGGACAAGTTGTGAAGATAATCAGGCCAAGTGAGACTGCCGGAAGATACGTCACCTACCGTTATGTTGTGTAA

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

24.4

Weight (kDa)

9.42

Isoelectric Point (pI)

42.64

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb5_N	PF03871	5 - 90	4.2e-31	RNA polymerase Rpb5, N-terminal domain
RNA_pol_Rpb5_C	PF01191	133 - 205	5.7e-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

Style Settings

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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)
AarI	CACCTGC	1 cut(s)	499
Acc16I	TGCGCA	1 cut(s)	429
Acc36I	ACCTGC	1 cut(s)	499
AccI	GTMKAC	2 cut(s)	353, 476
AciI	CCGC	1 cut(s)	364
AclWI	GGATC	1 cut(s)	512
AcvI	CACGTG	1 cut(s)	548
AfiI	CCNNNNNNNGG	2 cut(s)	223, 370
AgsI	TTSAA	1 cut(s)	124
AjnI	CCWGG	1 cut(s)	378
AluBI	AGCT	4 cut(s)	95, 192, 316, 496
AluI	AGCT	4 cut(s)	95, 192, 316, 496
Alw21I	GWGCWC	1 cut(s)	131
Alw26I	GTCTC	2 cut(s)	309, 575
AlwI	GGATC	1 cut(s)	512
AlwNI	CAGNNNCTG	1 cut(s)	95
AoxI	GGCC	1 cut(s)	572
ApeKI	GCWGC	1 cut(s)	466
Asp700I	GAANNNNTTC	1 cut(s)	284
AspLEI	GCGC	2 cut(s)	267, 430
AsuHPI	GGTGA	2 cut(s)	409, 592
BarI	GAAGNNNNNNTAC	2 cut(s)	197, 229
BauI	CACGAG	1 cut(s)	25
BbrPI	CACGTG	1 cut(s)	548
BbsI	GAAGAC	1 cut(s)	202
Bbv12I	GWGCWC	1 cut(s)	131
BbvI	GCAGC	1 cut(s)	453
BciT130I	CCWGG	1 cut(s)	380
BclI	TGATCA	1 cut(s)	196
BcoDI	GTCTC	2 cut(s)	309, 575
BfaI	CTAG	2 cut(s)	161, 419
BfmI	CTRYAG	1 cut(s)	467
BfuAI	ACCTGC	1 cut(s)	499
BglII	AGATCT	1 cut(s)	157
BisI	GCNGC	1 cut(s)	467
BlsI	GCNGC	1 cut(s)	468
Bme1390I	CCNGG	1 cut(s)	380
BmiI	GGNNCC	1 cut(s)	362
BmrFI	CCNGG	1 cut(s)	380
BmsI	GCATC	2 cut(s)	439, 495
BpiI	GAAGAC	1 cut(s)	202
BsaAI	YACGTR	1 cut(s)	548
BsaJI	CCNNGG	1 cut(s)	500
Bsc4I	CCNNNNNNNGG	2 cut(s)	223, 370
Bse1I	ACTGG	1 cut(s)	521
BseBI	CCWGG	1 cut(s)	380
BseDI	CCNNGG	1 cut(s)	500
BseGI	GGATG	1 cut(s)	510
BseLI	CCNNNNNNNGG	2 cut(s)	223, 370
BseMII	CTCAG	1 cut(s)	87
BseNI	ACTGG	1 cut(s)	521
BseXI	GCAGC	1 cut(s)	453
BshFI	GGCC	1 cut(s)	574
BsiHKAI	GWGCWC	1 cut(s)	131
BsiSI	CCGG	1 cut(s)	588
BslFI	GGGAC	1 cut(s)	266
BslI	CCNNNNNNNGG	2 cut(s)	223, 370
BsmAI	GTCTC	2 cut(s)	309, 575
BsmFI	GGGAC	1 cut(s)	266
BsnI	GGCC	1 cut(s)	574
Bsp1286I	GDGCHC	1 cut(s)	131
Bsp143I	GATC	5 cut(s)	70, 99, 157, 196, 517
BspACI	CCGC	1 cut(s)	364
BspANI	GGCC	1 cut(s)	574
BspCNI	CTCAG	1 cut(s)	88
BspLI	GGNNCC	1 cut(s)	362
BspMAI	CTGCAG	1 cut(s)	471
BspMI	ACCTGC	1 cut(s)	499
BspPI	GGATC	1 cut(s)	512
BsrI	ACTGG	1 cut(s)	521
BssECI	CCNNGG	1 cut(s)	500
BssMI	GATC	5 cut(s)	70, 99, 157, 196, 517
BssNAI	GTATAC	1 cut(s)	477
BssSI	CACGAG	1 cut(s)	25
Bst1107I	GTATAC	1 cut(s)	477
Bst2BI	CACGAG	1 cut(s)	25
Bst2UI	CCWGG	1 cut(s)	380
Bst4CI	ACNGT	4 cut(s)	52, 393, 481, 608
Bst6I	CTCTTC	1 cut(s)	452
BstAPI	GCANNNNNTGC	1 cut(s)	436
BstBAI	YACGTR	1 cut(s)	548
BstC8I	GCNNGC	1 cut(s)	269
BstDEI	CTNAG	2 cut(s)	82, 96
BstF5I	GGATG	1 cut(s)	510
BstHHI	GCGC	2 cut(s)	267, 430
BstKTI	GATC	5 cut(s)	73, 102, 160, 199, 520
BstMAI	GTCTC	2 cut(s)	309, 575
BstMBI	GATC	5 cut(s)	70, 99, 157, 196, 517
BstMWI	GCNNNNNNNGC	1 cut(s)	436
BstNI	CCWGG	1 cut(s)	380
BstNSI	RCATGY	2 cut(s)	271, 416
BstSCI	CCNGG	1 cut(s)	378
BstSFI	CTRYAG	1 cut(s)	467
BstV1I	GCAGC	1 cut(s)	453
BstV2I	GAAGAC	1 cut(s)	202
BstX2I	RGATCY	1 cut(s)	157
BstYI	RGATCY	1 cut(s)	157
BstZ17I	GTATAC	1 cut(s)	477
BsuRI	GGCC	1 cut(s)	574
BtsCI	GGATG	1 cut(s)	510
BveI	ACCTGC	1 cut(s)	499
Cac8I	GCNNGC	1 cut(s)	269
CaiI	CAGNNNCTG	1 cut(s)	95
CfoI	GCGC	2 cut(s)	267, 430
CviAII	CATG	5 cut(s)	106, 145, 268, 367, 413
CviJI	RGCY	8 cut(s)	5, 31, 95, 192, 316, 496, 541, 574
CviKI_1	RGCY	8 cut(s)	5, 31, 95, 192, 316, 496, 541, 574
DdeI	CTNAG	2 cut(s)	82, 96
DpnI	GATC	5 cut(s)	72, 101, 159, 198, 519
DpnII	GATC	5 cut(s)	70, 99, 157, 196, 517
Eam1104I	CTCTTC	1 cut(s)	452
EarI	CTCTTC	1 cut(s)	452
Eco72I	CACGTG	1 cut(s)	548
EcoRII	CCWGG	1 cut(s)	378
FaeI	CATG	5 cut(s)	109, 148, 271, 370, 416
FaqI	GGGAC	1 cut(s)	266
FatI	CATG	5 cut(s)	105, 144, 267, 366, 412
FauNDI	CATATG	1 cut(s)	133
FbaI	TGATCA	1 cut(s)	196
FblI	GTMKAC	2 cut(s)	353, 476
Fnu4HI	GCNGC	1 cut(s)	467
FokI	GGATG	1 cut(s)	517
Fsp4HI	GCNGC	1 cut(s)	467
FspBI	CTAG	2 cut(s)	161, 419
FspI	TGCGCA	1 cut(s)	429
GlaI	GCGC	2 cut(s)	266, 429
GluI	GCNGC	1 cut(s)	467
HaeIII	GGCC	1 cut(s)	574
HapII	CCGG	1 cut(s)	588
HhaI	GCGC	2 cut(s)	267, 430
Hin1II	CATG	5 cut(s)	109, 148, 271, 370, 416
Hin6I	GCGC	2 cut(s)	265, 428
HinP1I	GCGC	2 cut(s)	265, 428
HinfI	GANTC	1 cut(s)	319
HpaII	CCGG	1 cut(s)	588
HphI	GGTGA	2 cut(s)	409, 592
Hpy166II	GTNNAC	3 cut(s)	354, 477, 551
Hpy188I	TCNGA	5 cut(s)	13, 196, 201, 290, 504
Hpy188III	TCNNGA	4 cut(s)	25, 74, 124, 161
Hpy8I	GTNNAC	3 cut(s)	354, 477, 551
HpyCH4III	ACNGT	4 cut(s)	52, 393, 481, 608
HpyCH4IV	ACGT	2 cut(s)	547, 597
HpyCH4V	TGCA	6 cut(s)	58, 271, 329, 469, 508, 527
HpyF10VI	GCNNNNNNNGC	1 cut(s)	436
HpyF3I	CTNAG	2 cut(s)	82, 96
HpySE526I	ACGT	2 cut(s)	547, 597
Hsp92II	CATG	5 cut(s)	109, 148, 271, 370, 416
HspAI	GCGC	2 cut(s)	265, 428
Ksp22I	TGATCA	1 cut(s)	196
Kzo9I	GATC	5 cut(s)	70, 99, 157, 196, 517
LpnPI	CCDG	8 cut(s)	365, 392, 419, 438, 494, 534, 556, 601
Lsp1109I	GCAGC	1 cut(s)	453
LweI	GCATC	2 cut(s)	439, 495
MaeI	CTAG	2 cut(s)	161, 419
MaeII	ACGT	2 cut(s)	547, 597
MaeIII	GTNAC	3 cut(s)	85, 185, 598
MalI	GATC	5 cut(s)	72, 101, 159, 198, 519
MboI	GATC	5 cut(s)	70, 99, 157, 196, 517
MboII	GAAGA	9 cut(s)	26, 57, 167, 202, 205, 398, 469, 574, 603
MflI	RGATCY	1 cut(s)	157
MhlI	GDGCHC	1 cut(s)	131
MluCI	AATT	1 cut(s)	119
MlyI	GAGTC	1 cut(s)	313
MnlI	CCTC	8 cut(s)	21, 217, 243, 364, 376, 442, 465, 510
MroXI	GAANNNNTTC	1 cut(s)	284
MseI	TTAA	1 cut(s)	405
MspI	CCGG	1 cut(s)	588
MspR9I	CCNGG	1 cut(s)	380
MvaI	CCWGG	1 cut(s)	380
MwoI	GCNNNNNNNGC	1 cut(s)	436
NdeI	CATATG	1 cut(s)	133
NdeII	GATC	5 cut(s)	70, 99, 157, 196, 517
NlaIII	CATG	5 cut(s)	109, 148, 271, 370, 416
NlaIV	GGNNCC	1 cut(s)	362
NmuCI	GTSAC	1 cut(s)	598
NsbI	TGCGCA	1 cut(s)	429
NspI	RCATGY	2 cut(s)	271, 416
PaeI	GCATGC	1 cut(s)	271
PaqCI	CACCTGC	1 cut(s)	499
PdmI	GAANNNNTTC	1 cut(s)	284
PfoI	TCCNGGA	1 cut(s)	378
PkrI	GCNGC	1 cut(s)	468
PleI	GAGTC	1 cut(s)	313
PmaCI	CACGTG	1 cut(s)	548
PmlI	CACGTG	1 cut(s)	548
PpsI	GAGTC	1 cut(s)	313
Ppu21I	YACGTR	1 cut(s)	548
Psp6I	CCWGG	1 cut(s)	378
PspCI	CACGTG	1 cut(s)	548
PspGI	CCWGG	1 cut(s)	378
PspN4I	GGNNCC	1 cut(s)	362
PstI	CTGCAG	1 cut(s)	471
PstNI	CAGNNNCTG	1 cut(s)	95
PsuI	RGATCY	1 cut(s)	157
SaqAI	TTAA	1 cut(s)	405
SatI	GCNGC	1 cut(s)	467
Sau3AI	GATC	5 cut(s)	70, 99, 157, 196, 517
SchI	GAGTC	1 cut(s)	313
ScrFI	CCNGG	1 cut(s)	380
SduI	GDGCHC	1 cut(s)	131
SfaNI	GCATC	2 cut(s)	439, 495
SfcI	CTRYAG	1 cut(s)	467
SphI	GCATGC	1 cut(s)	271
Sse9I	AATT	1 cut(s)	119
SsiI	CCGC	1 cut(s)	364
SspI	AATATT	1 cut(s)	403
SspMI	CTAG	2 cut(s)	161, 419
StyD4I	CCNGG	1 cut(s)	378
TaaI	ACNGT	4 cut(s)	52, 393, 481, 608
TaiI	ACGT	2 cut(s)	550, 600
TaqI	TCGA	1 cut(s)	43
TasI	AATT	1 cut(s)	119
Tru1I	TTAA	1 cut(s)	405
Tru9I	TTAA	1 cut(s)	405
TseFI	GTSAC	1 cut(s)	598
TseI	GCWGC	1 cut(s)	466
Tsp45I	GTSAC	1 cut(s)	598
TspDTI	ATGAA	2 cut(s)	33, 161
XbaI	TCTAGA	1 cut(s)	160
XceI	RCATGY	2 cut(s)	271, 416
XmiI	GTMKAC	2 cut(s)	353, 476
XmnI	GAANNNNTTC	1 cut(s)	284
XspI	CTAG	2 cut(s)	161, 419

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