Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000004

Orthogroup ID

OG0003607

Physical Location & Seq

Genomic Coordinates Forward (+)

60186994 .. 60190491

Gene Structure 3498 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_4G00327450.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 579 bp

ATGGCTGCCGTGGTGTTGGACGACGCCGTTTCGGGTGGCGGTGCAGGAGGCCGGGCGGGATGCATGACGAGCCACGACGTCGTCGGTGGAGGGAGCTTGGAGAGCTACAGGTACTACGTGTCTCGTCGTACGGTGATGGAGATGCTGAGCGACCGAGGCTACAACATTATGGTCATCTTCTGTGGAACTGATGAAATCAGAAAAGCGAGTGTTCGTGCCATTTATGCTGACCTCCTGAACAAAGATATAAGCTCTCTGATGCTTGTCCTGCAAAGTAAAATGAACTCCTATGCTCGAAAAGAACTGGAAAACTATCCTTACAAAGTTGAAACTTTCCACATTTCTGAACTGCTGGTCAATGTTACAAAGCATGTTTTACAGCCAAAGTATGAGATAGTTACAGCTGAAGAAAAGAAACATTTGCTAAGGAAGTACAAGTTGGAAGACAAGAAGCTCCCTCTCATGCTGGAAACCGATGCATTTGCACGCTACTATGGATTGGAGAAGGGACAGGTGGTAAAGATTACTTACCGTGGTGGAGCTGTTTGTGCCCTCAAAACTTACCGTTGCATTGTCTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000419 GO:0000428 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0030880 GO:0032991 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044464 GO:0055029 GO:0061695 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

192

Amino Acids

21.61

Weight (kDa)

9.03

Isoelectric Point (pI)

35.34

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb5_N	PF03871	34 - 56	8.9e-06	RNA polymerase Rpb5, N-terminal domain
RNA_pol_Rpb5_C	PF01191	119 - 191	1.7e-25	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

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Orthologous Genes (Group: OG0003607)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G54490
fragaria_vesca	FvH4_7g02710 FvH4_7g02710 FvH4_7g02710
malus_domestica	MD07G1036700.v1.1
prunus_persica	Prupe.2G032100_v2.0.a1
rosa_chinensis	RchiOBHm_Chr1g0321871 RchiOBHm_Chr1g0321951 RchiOBHm_Chr3g0472601
rosa_laevigata	RLG00000030400 RLG00000030402
rosa_multiflora	Rmu_sc0000427.1_g000005 Rmu_sc0002872.1_g000006 Rmu_sc0003510.1_g000023 Rmu_sc0015497.1_g000006
rosa_roxburghii	Rroxscaffold_4G00327410 Rroxscaffold_4G00327450
rosa_rugosa	Rorug01G0034400
rosa_samantha	Rh1AG047300 Rh1BG045400 Rh1CG051100 Rh1CG051500 Rh1DG055400 Rh1DG055800 Rh2CG536300 Rh3AG178800 Rh3BG204700 Rh3CG202100 Rh3CG224200 Rh5AG112100 Rh6AG330000
rosa_wichuraiana	Rw1G004250 Rw1G004290 Rw1G004310 Rw5G021040

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AatII	GACGTC	1 cut(s)	81
AciI	CCGC	2 cut(s)	39, 56
AcuI	CTGAAG	1 cut(s)	426
AcyI	GRCGYC	2 cut(s)	24, 78
AfaI	GTAC	3 cut(s)	113, 130, 434
AflIII	ACRYGT	1 cut(s)	117
AgsI	TTSAA	1 cut(s)	329
AjuI	GAANNNNNNNTTGG	2 cut(s)	422, 454
AluBI	AGCT	6 cut(s)	96, 105, 252, 404, 454, 542
AluI	AGCT	6 cut(s)	96, 105, 252, 404, 454, 542
Alw26I	GTCTC	1 cut(s)	126
AoxI	GGCC	1 cut(s)	49
ApeKI	GCWGC	1 cut(s)	5
AsuC2I	CCSGG	1 cut(s)	53
AsuHPI	GGTGA	1 cut(s)	145
BaeGI	GKGCMC	1 cut(s)	553
BbsI	GAAGAC	1 cut(s)	450
BccI	CCATC	1 cut(s)	130
BceAI	ACGGC	1 cut(s)	11
BcgI	CGANNNNNNTGC	2 cut(s)	464, 498
BcnI	CCSGG	1 cut(s)	53
BcoDI	GTCTC	1 cut(s)	126
BfmI	CTRYAG	1 cut(s)	106
BisI	GCNGC	1 cut(s)	6
BlpI	GCTNAGC	1 cut(s)	146
BlsI	GCNGC	1 cut(s)	7
Bme1390I	CCNGG	1 cut(s)	53
BmrFI	CCNGG	1 cut(s)	53
BmsI	GCATC	4 cut(s)	50, 132, 249, 466
BpiI	GAAGAC	1 cut(s)	450
Bpu10I	CCTNAGC	1 cut(s)	425
Bpu1102I	GCTNAGC	1 cut(s)	146
BpuMI	CCSGG	1 cut(s)	53
BsaAI	YACGTR	1 cut(s)	118
BsaHI	GRCGYC	2 cut(s)	24, 78
BsaJI	CCNNGG	3 cut(s)	9, 154, 532
Bse1I	ACTGG	1 cut(s)	309
BseDI	CCNNGG	3 cut(s)	9, 154, 532
BseGI	GGATG	1 cut(s)	65
BseMII	CTCAG	1 cut(s)	137
BseNI	ACTGG	1 cut(s)	309
BseSI	GKGCMC	1 cut(s)	553
BsgI	GTGCAG	1 cut(s)	63
Bsh1285I	CGRYCG	1 cut(s)	154
BshFI	GGCC	1 cut(s)	51
BsiEI	CGRYCG	1 cut(s)	154
BsiSI	CCGG	1 cut(s)	52
BsiWI	CGTACG	1 cut(s)	128
BslFI	GGGAC	1 cut(s)	522
BsmAI	GTCTC	1 cut(s)	126
BsmFI	GGGAC	1 cut(s)	522
BsnI	GGCC	1 cut(s)	51
Bsp1286I	GDGCHC	1 cut(s)	553
Bsp1720I	GCTNAGC	1 cut(s)	146
BspACI	CCGC	2 cut(s)	39, 56
BspANI	GGCC	1 cut(s)	51
BspCNI	CTCAG	1 cut(s)	138
BsrI	ACTGG	1 cut(s)	309
BssECI	CCNNGG	3 cut(s)	9, 154, 532
BssNI	GRCGYC	2 cut(s)	24, 78
Bst4CI	ACNGT	3 cut(s)	133, 533, 566
BstACI	GRCGYC	2 cut(s)	24, 78
BstBAI	YACGTR	1 cut(s)	118
BstC8I	GCNNGC	1 cut(s)	487
BstDEI	CTNAG	2 cut(s)	146, 425
BstDSI	CCRYGG	2 cut(s)	9, 532
BstF5I	GGATG	1 cut(s)	65
BstMAI	GTCTC	1 cut(s)	126
BstMCI	CGRYCG	1 cut(s)	154
BstMWI	GCNNNNNNNGC	6 cut(s)	69, 102, 156, 224, 268, 548
BstNSI	RCATGY	1 cut(s)	374
BstSCI	CCNGG	1 cut(s)	51
BstSFI	CTRYAG	1 cut(s)	106
BstSLI	GKGCMC	1 cut(s)	553
BstV2I	GAAGAC	1 cut(s)	450
BsuRI	GGCC	1 cut(s)	51
BtgI	CCRYGG	2 cut(s)	9, 532
BtsCI	GGATG	1 cut(s)	65
Cac8I	GCNNGC	1 cut(s)	487
CseI	GACGC	1 cut(s)	32
Csp6I	GTAC	3 cut(s)	112, 129, 433
CviAII	CATG	3 cut(s)	64, 371, 463
CviQI	GTAC	3 cut(s)	112, 129, 433
DdeI	CTNAG	2 cut(s)	146, 425
Eco57I	CTGAAG	1 cut(s)	426
EcoT22I	ATGCAT	2 cut(s)	65, 481
FaeI	CATG	3 cut(s)	67, 374, 466
FaiI	YATR	9 cut(s)	65, 170, 225, 248, 291, 372, 390, 464, 495
FaqI	GGGAC	1 cut(s)	522
FatI	CATG	3 cut(s)	63, 370, 462
FauI	CCCGC	1 cut(s)	49
Fnu4HI	GCNGC	1 cut(s)	6
FokI	GGATG	1 cut(s)	72
Fsp4HI	GCNGC	1 cut(s)	6
GluI	GCNGC	1 cut(s)	6
HaeIII	GGCC	1 cut(s)	51
HapII	CCGG	1 cut(s)	52
HgaI	GACGC	1 cut(s)	32
Hin1I	GRCGYC	2 cut(s)	24, 78
Hin1II	CATG	3 cut(s)	67, 374, 466
HpaII	CCGG	1 cut(s)	52
HphI	GGTGA	1 cut(s)	145
Hpy188I	TCNGA	4 cut(s)	200, 258, 346, 578
Hpy188III	TCNNGA	1 cut(s)	235
Hpy99I	CGWCG	5 cut(s)	26, 80, 83, 86, 129
HpyAV	CCTTC	1 cut(s)	499
HpyCH4III	ACNGT	3 cut(s)	133, 533, 566
HpyCH4IV	ACGT	2 cut(s)	78, 117
HpyCH4V	TGCA	6 cut(s)	44, 63, 271, 479, 485, 570
HpyF10VI	GCNNNNNNNGC	6 cut(s)	69, 102, 156, 224, 268, 548
HpyF3I	CTNAG	2 cut(s)	146, 425
HpySE526I	ACGT	2 cut(s)	78, 117
Hsp92I	GRCGYC	2 cut(s)	24, 78
Hsp92II	CATG	3 cut(s)	67, 374, 466
LmnI	GCTCC	3 cut(s)	93, 459, 539
LpnPI	CCDG	9 cut(s)	30, 65, 94, 248, 281, 290, 338, 452, 497
LweI	GCATC	4 cut(s)	50, 132, 249, 466
MaeII	ACGT	2 cut(s)	78, 117
MaeIII	GTNAC	2 cut(s)	361, 397
MboII	GAAGA	3 cut(s)	169, 419, 455
MhlI	GDGCHC	1 cut(s)	553
MmeI	TCCRAC	1 cut(s)	420
MnlI	CCTC	6 cut(s)	41, 83, 149, 242, 468, 563
Mph1103I	ATGCAT	2 cut(s)	65, 481
MspA1I	CMGCKG	1 cut(s)	404
MspI	CCGG	1 cut(s)	52
MspR9I	CCNGG	1 cut(s)	53
MwoI	GCNNNNNNNGC	6 cut(s)	69, 102, 156, 224, 268, 548
NciI	CCSGG	1 cut(s)	53
NlaIII	CATG	3 cut(s)	67, 374, 466
NsiI	ATGCAT	2 cut(s)	65, 481
NspI	RCATGY	1 cut(s)	374
Pfl23II	CGTACG	1 cut(s)	128
PflFI	GACNNNGTC	1 cut(s)	80
PkrI	GCNGC	1 cut(s)	7
Ppu21I	YACGTR	1 cut(s)	118
PspLI	CGTACG	1 cut(s)	128
PsyI	GACNNNGTC	1 cut(s)	80
PvuII	CAGCTG	1 cut(s)	404
RsaI	GTAC	3 cut(s)	113, 130, 434
RsaNI	GTAC	3 cut(s)	112, 129, 433
SatI	GCNGC	1 cut(s)	6
ScrFI	CCNGG	1 cut(s)	53
SduI	GDGCHC	1 cut(s)	553
SfaNI	GCATC	4 cut(s)	50, 132, 249, 466
SfcI	CTRYAG	1 cut(s)	106
SsiI	CCGC	2 cut(s)	39, 56
StyD4I	CCNGG	1 cut(s)	51
TaaI	ACNGT	3 cut(s)	133, 533, 566
TaiI	ACGT	2 cut(s)	81, 120
TaqI	TCGA	1 cut(s)	295
TaqII	GACCGA	1 cut(s)	168
TatI	WGTACW	1 cut(s)	432
TseI	GCWGC	1 cut(s)	5
TspDTI	ATGAA	2 cut(s)	207, 296
Tth111I	GACNNNGTC	1 cut(s)	80
XceI	RCATGY	1 cut(s)	374
ZraI	GACGTC	1 cut(s)	79
Zsp2I	ATGCAT	2 cut(s)	65, 481

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