Basic Information

Type: gene

Biological Identity

Species

rosa_chinensis

Chromosome

Orthogroup ID

OG0003607

Physical Location & Seq

Genomic Coordinates Reverse (-)

9395798 .. 9399736

Gene Structure 3939 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

PRQ55190

Sequence Viewer

CDS Protein Promoter (2k)

Length: 450 bp

ATGGAGATGCTGAGCGACCGAGGCTACGACGTCGCCGACTCGGACCTCACTCGCTCGCTCACTGAGTTCCGTACCGGGTTCGGCCAAAACCCTGACCTCGACCGCCTCACCATCTGCGCCTCTCTCCGCTCCAATTCCAAGAACAAGATTATGGTCATCTTCTGTGGAACTGATGAAATCAGAAAGGCGAGTGTTCGTGCCATTTATGCTAACCTCCTGAACAAAGATATAAGCTCTCTCATGCTTGTCCTGCAAAGTAAAATGAACTCCTATGCTCGAAAAGAACTGGAAAACTATCCTTACAAAGTTGAAACTTTTCACATCTCTGAACTGCTGGTCAATGTTACAAAGCATGTTTTACAGCCAAAGTATGAGATACTTTCTACTGAAGAAAAGAAACATCTGCTAAGGAAGTACAAGTTGGAAGACAAGAAGGTAACTATTTGCTGA

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

149

Amino Acids

17.26

Weight (kDa)

8.91

Isoelectric Point (pI)

46.54

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb5_N	PF03871	1 - 70	7.6e-17	RNA polymerase Rpb5, N-terminal domain
RNA_pol_Rpb5_C	PF01191	113 - 145	3.5e-08	RNA polymerase Rpb5, C-terminal domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

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Genomic Context

Gene Family Tree

Species Filter

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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)	33
AccBSI	CCGCTC	1 cut(s)	129
AciI	CCGC	2 cut(s)	103, 127
AcoI	YGGCCR	1 cut(s)	82
AcuI	CTGAAG	1 cut(s)	408
AcyI	GRCGYC	1 cut(s)	30
AfaI	GTAC	2 cut(s)	73, 416
AgsI	TTSAA	1 cut(s)	311
AjuI	GAANNNNNNNTTGG	2 cut(s)	404, 436
AluBI	AGCT	1 cut(s)	234
AluI	AGCT	1 cut(s)	234
AoxI	GGCC	1 cut(s)	82
Asp700I	GAANNNNTTC	1 cut(s)	315
AspLEI	GCGC	1 cut(s)	119
AspS9I	GGNCC	1 cut(s)	43
AsuC2I	CCSGG	1 cut(s)	76
AsuHPI	GGTGA	1 cut(s)	100
AvaII	GGWCC	1 cut(s)	43
BbsI	GAAGAC	1 cut(s)	432
BccI	CCATC	1 cut(s)	119
BcnI	CCSGG	1 cut(s)	76
BlpI	GCTNAGC	1 cut(s)	11
Bme1390I	CCNGG	1 cut(s)	76
Bme18I	GGWCC	1 cut(s)	43
BmgT120I	GGNCC	1 cut(s)	43
BmrFI	CCNGG	1 cut(s)	76
BpiI	GAAGAC	1 cut(s)	432
Bpu10I	CCTNAGC	1 cut(s)	407
Bpu1102I	GCTNAGC	1 cut(s)	11
BpuMI	CCSGG	1 cut(s)	76
BsaHI	GRCGYC	1 cut(s)	30
BsaJI	CCNNGG	1 cut(s)	19
Bse1I	ACTGG	1 cut(s)	291
BseDI	CCNNGG	1 cut(s)	19
BseMII	CTCAG	1 cut(s)	54
BseNI	ACTGG	1 cut(s)	291
Bsh1285I	CGRYCG	2 cut(s)	19, 103
BshFI	GGCC	1 cut(s)	84
BsiEI	CGRYCG	2 cut(s)	19, 103
BsiSI	CCGG	1 cut(s)	75
BsnI	GGCC	1 cut(s)	84
Bsp1720I	GCTNAGC	1 cut(s)	11
BspACI	CCGC	2 cut(s)	103, 127
BspANI	GGCC	1 cut(s)	84
BspCNI	CTCAG	1 cut(s)	55
BsrBI	CCGCTC	1 cut(s)	129
BsrI	ACTGG	1 cut(s)	291
BssECI	CCNNGG	1 cut(s)	19
BssNI	GRCGYC	1 cut(s)	30
BstACI	GRCGYC	1 cut(s)	30
BstC8I	GCNNGC	1 cut(s)	56
BstDEI	CTNAG	3 cut(s)	11, 63, 407
BstHHI	GCGC	1 cut(s)	119
BstMCI	CGRYCG	2 cut(s)	19, 103
BstMWI	GCNNNNNNNGC	3 cut(s)	21, 206, 250
BstNSI	RCATGY	1 cut(s)	356
BstSCI	CCNGG	1 cut(s)	74
BstV2I	GAAGAC	1 cut(s)	432
BsuRI	GGCC	1 cut(s)	84
BtsIMutI	CAGTG	1 cut(s)	60
Cac8I	GCNNGC	1 cut(s)	56
CfoI	GCGC	1 cut(s)	119
Cfr13I	GGNCC	1 cut(s)	43
Csp6I	GTAC	2 cut(s)	72, 415
CviAII	CATG	2 cut(s)	241, 353
CviJI	RGCY	4 cut(s)	24, 84, 234, 364
CviKI_1	RGCY	4 cut(s)	24, 84, 234, 364
CviQI	GTAC	2 cut(s)	72, 415
DdeI	CTNAG	3 cut(s)	11, 63, 407
EaeI	YGGCCR	1 cut(s)	82
Eco47I	GGWCC	1 cut(s)	43
Eco57I	CTGAAG	1 cut(s)	408
FaeI	CATG	2 cut(s)	244, 356
FaiI	YATR	7 cut(s)	152, 207, 230, 242, 273, 354, 372
FatI	CATG	2 cut(s)	240, 352
GlaI	GCGC	1 cut(s)	118
HaeIII	GGCC	1 cut(s)	84
HapII	CCGG	1 cut(s)	75
HhaI	GCGC	1 cut(s)	119
Hin1I	GRCGYC	1 cut(s)	30
Hin1II	CATG	2 cut(s)	244, 356
Hin6I	GCGC	1 cut(s)	117
HinP1I	GCGC	1 cut(s)	117
HinfI	GANTC	1 cut(s)	38
HpaII	CCGG	1 cut(s)	75
HphI	GGTGA	1 cut(s)	100
Hpy188I	TCNGA	3 cut(s)	43, 182, 328
Hpy188III	TCNNGA	1 cut(s)	217
Hpy99I	CGWCG	2 cut(s)	32, 35
HpyAV	CCTTC	1 cut(s)	427
HpyCH4IV	ACGT	1 cut(s)	30
HpyCH4V	TGCA	1 cut(s)	253
HpyF10VI	GCNNNNNNNGC	3 cut(s)	21, 206, 250
HpyF3I	CTNAG	3 cut(s)	11, 63, 407
HpySE526I	ACGT	1 cut(s)	30
Hsp92I	GRCGYC	1 cut(s)	30
Hsp92II	CATG	2 cut(s)	244, 356
HspAI	GCGC	1 cut(s)	117
LmnI	GCTCC	1 cut(s)	134
LpnPI	CCDG	6 cut(s)	88, 105, 230, 263, 272, 320
MaeII	ACGT	1 cut(s)	30
MaeIII	GTNAC	2 cut(s)	343, 436
MbiI	CCGCTC	1 cut(s)	129
MboII	GAAGA	3 cut(s)	151, 401, 437
MluCI	AATT	1 cut(s)	133
MlyI	GAGTC	1 cut(s)	32
MmeI	TCCRAC	1 cut(s)	402
MnlI	CCTC	6 cut(s)	14, 56, 107, 116, 130, 224
MroXI	GAANNNNTTC	1 cut(s)	315
MspI	CCGG	1 cut(s)	75
MspR9I	CCNGG	1 cut(s)	76
MwoI	GCNNNNNNNGC	3 cut(s)	21, 206, 250
NciI	CCSGG	1 cut(s)	76
NlaIII	CATG	2 cut(s)	244, 356
NspI	RCATGY	1 cut(s)	356
PcsI	WCGNNNNNNNCGW	1 cut(s)	33
PdmI	GAANNNNTTC	1 cut(s)	315
PleI	GAGTC	1 cut(s)	32
PpsI	GAGTC	1 cut(s)	32
PspPI	GGNCC	1 cut(s)	43
RsaI	GTAC	2 cut(s)	73, 416
RsaNI	GTAC	2 cut(s)	72, 415
Sau96I	GGNCC	1 cut(s)	43
SchI	GAGTC	1 cut(s)	32
ScrFI	CCNGG	1 cut(s)	76
SetI	ASST	6 cut(s)	33, 48, 99, 216, 236, 438
SinI	GGWCC	1 cut(s)	43
Sse9I	AATT	1 cut(s)	133
SsiI	CCGC	2 cut(s)	103, 127
StyD4I	CCNGG	1 cut(s)	74
TaiI	ACGT	1 cut(s)	33
TaqI	TCGA	2 cut(s)	99, 277
TaqII	GACCGA	1 cut(s)	33
TasI	AATT	1 cut(s)	133
TatI	WGTACW	1 cut(s)	414
TscAI	CASTG	1 cut(s)	67
TspDTI	ATGAA	2 cut(s)	189, 278
TspGWI	ACGGA	1 cut(s)	59
TspRI	CASTG	1 cut(s)	67
VpaK11BI	GGWCC	1 cut(s)	43
XceI	RCATGY	1 cut(s)	356
XmnI	GAANNNNTTC	1 cut(s)	315
ZraI	GACGTC	1 cut(s)	31

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