Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000004

Orthogroup ID

OG0003607

Physical Location & Seq

Genomic Coordinates Forward (+)

60106679 .. 60109008

Gene Structure 2330 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_4G00327410.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 669 bp

ATGGCTACCGTGGTGTTGGACGACGCCGTTTCGGGTGGCGGTGGAGGAGGCCGGGCGGGATGCATGACGAGCCACGACGTCGTCGGTGGAGGGAGCTTGGAGAGCTACAGGTACCACGTGTCTCGTCGTACGGTGACGGAGATGCTGAGCGACCGAGGCTACAACGTCGCCGACTCGGACCTCACTCGCTCACTCACTGAGTTCCGTACCGCGTTCGGTCAAAACCCTGACCTCGACCGCCTCACCATCTGCGCCTCTCTCCGCTCCAATTCCAAGAACAAGATTATGGTCATCTTCTGTGGAATTGATGAAATCAGAAAAGCGAGTGTTCGTGCCATTTATGCTAACCTCCTGAACAAAGATATAAGCTCTCTGATGCTTGTCCTGCAAAGTAAAATGAACTCCTATGCTCGAAAAGAACTGGAAAACTATCCTTACAAAGTTGAAACTTTTCACATCTCTGAACTGCTGGTCAATGTTACAAAGCATGTTTTACAGCCAAAGTATGAGATGTTTTCTGCTGAAGAAAAGAAACATCTGCTAAGGAAGTACAAGTTGGAAGACAAGAAGGGGGCAGTCACTACTTCAACTGATGGTGGGGCAGCAGCGGATATTTTAGGCTTGCCATATCTTCTCAGTGTTTCAAACTTCTATGCCATAATCTGTTAA

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

222

Amino Acids

24.52

Weight (kDa)

8.58

Isoelectric Point (pI)

43.9

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb5_N	PF03871	34 - 115	5e-21	RNA polymerase Rpb5, N-terminal domain
RNA_pol_Rpb5_C	PF01191	158 - 189	4.1e-07	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

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Publication-ready

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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
Acc65I	GGTACC	1 cut(s)	111
AccB1I	GGYRCC	1 cut(s)	111
AccBSI	CCGCTC	1 cut(s)	264
AccII	CGCG	1 cut(s)	212
AciI	CCGC	6 cut(s)	39, 56, 210, 238, 262, 608
AcuI	CTGAAG	1 cut(s)	543
AcvI	CACGTG	1 cut(s)	118
AcyI	GRCGYC	2 cut(s)	24, 78
AfaI	GTAC	4 cut(s)	113, 130, 208, 551
AflIII	ACRYGT	1 cut(s)	117
AgsI	TTSAA	3 cut(s)	446, 588, 645
AjuI	GAANNNNNNNTTGG	2 cut(s)	539, 571
AluBI	AGCT	3 cut(s)	96, 105, 369
AluI	AGCT	3 cut(s)	96, 105, 369
Alw26I	GTCTC	1 cut(s)	126
AoxI	GGCC	1 cut(s)	49
ApeKI	GCWGC	2 cut(s)	602, 605
Asp700I	GAANNNNTTC	1 cut(s)	450
Asp718I	GGTACC	1 cut(s)	111
AspLEI	GCGC	1 cut(s)	254
AspS9I	GGNCC	1 cut(s)	178
AsuC2I	CCSGG	1 cut(s)	53
AsuHPI	GGTGA	2 cut(s)	145, 235
AvaII	GGWCC	1 cut(s)	178
BanI	GGYRCC	1 cut(s)	111
BbrPI	CACGTG	1 cut(s)	118
BbsI	GAAGAC	1 cut(s)	567
BbvI	GCAGC	2 cut(s)	614, 617
BccI	CCATC	2 cut(s)	254, 587
BceAI	ACGGC	1 cut(s)	11
BcnI	CCSGG	1 cut(s)	53
BcoDI	GTCTC	1 cut(s)	126
BfmI	CTRYAG	1 cut(s)	106
BisI	GCNGC	2 cut(s)	603, 606
BlpI	GCTNAGC	1 cut(s)	146
BlsI	GCNGC	2 cut(s)	604, 607
Bme1390I	CCNGG	1 cut(s)	53
Bme18I	GGWCC	1 cut(s)	178
BmgT120I	GGNCC	1 cut(s)	178
BmiI	GGNNCC	1 cut(s)	113
BmrFI	CCNGG	1 cut(s)	53
BmsI	GCATC	3 cut(s)	50, 132, 366
BpiI	GAAGAC	1 cut(s)	567
Bpu10I	CCTNAGC	1 cut(s)	542
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	2 cut(s)	9, 154
Bse1I	ACTGG	1 cut(s)	426
BseDI	CCNNGG	2 cut(s)	9, 154
BseGI	GGATG	1 cut(s)	65
BseMII	CTCAG	3 cut(s)	137, 189, 649
BseNI	ACTGG	1 cut(s)	426
BseRI	GAGGAG	1 cut(s)	60
BseXI	GCAGC	2 cut(s)	614, 617
Bsh1236I	CGCG	1 cut(s)	212
Bsh1285I	CGRYCG	2 cut(s)	154, 238
BshFI	GGCC	1 cut(s)	51
BshNI	GGYRCC	1 cut(s)	111
BsiEI	CGRYCG	2 cut(s)	154, 238
BsiSI	CCGG	1 cut(s)	52
BsiWI	CGTACG	1 cut(s)	128
BsmAI	GTCTC	1 cut(s)	126
BsnI	GGCC	1 cut(s)	51
Bsp1720I	GCTNAGC	1 cut(s)	146
BspACI	CCGC	6 cut(s)	39, 56, 210, 238, 262, 608
BspANI	GGCC	1 cut(s)	51
BspCNI	CTCAG	3 cut(s)	138, 190, 648
BspFNI	CGCG	1 cut(s)	212
BspLI	GGNNCC	1 cut(s)	113
BspT107I	GGYRCC	1 cut(s)	111
BsrBI	CCGCTC	1 cut(s)	264
BsrI	ACTGG	1 cut(s)	426
BssECI	CCNNGG	2 cut(s)	9, 154
BssNI	GRCGYC	2 cut(s)	24, 78
Bst4CI	ACNGT	2 cut(s)	10, 133
BstACI	GRCGYC	2 cut(s)	24, 78
BstBAI	YACGTR	1 cut(s)	118
BstC8I	GCNNGC	1 cut(s)	623
BstDEI	CTNAG	4 cut(s)	146, 198, 542, 635
BstDSI	CCRYGG	1 cut(s)	9
BstF5I	GGATG	1 cut(s)	65
BstFNI	CGCG	1 cut(s)	212
BstHHI	GCGC	1 cut(s)	254
BstMAI	GTCTC	1 cut(s)	126
BstMCI	CGRYCG	2 cut(s)	154, 238
BstMWI	GCNNNNNNNGC	5 cut(s)	69, 102, 156, 341, 385
BstNSI	RCATGY	1 cut(s)	491
BstSCI	CCNGG	1 cut(s)	51
BstSFI	CTRYAG	1 cut(s)	106
BstUI	CGCG	1 cut(s)	212
BstV1I	GCAGC	2 cut(s)	614, 617
BstV2I	GAAGAC	1 cut(s)	567
BsuRI	GGCC	1 cut(s)	51
BtgI	CCRYGG	1 cut(s)	9
BtsCI	GGATG	1 cut(s)	65
BtsIMutI	CAGTG	2 cut(s)	195, 643
Cac8I	GCNNGC	1 cut(s)	623
CfoI	GCGC	1 cut(s)	254
Cfr13I	GGNCC	1 cut(s)	178
CseI	GACGC	1 cut(s)	32
Csp6I	GTAC	4 cut(s)	112, 129, 207, 550
CviAII	CATG	2 cut(s)	64, 488
CviJI	RGCY	9 cut(s)	5, 51, 72, 96, 105, 159, 369, 499, 621
CviKI_1	RGCY	9 cut(s)	5, 51, 72, 96, 105, 159, 369, 499, 621
CviQI	GTAC	4 cut(s)	112, 129, 207, 550
DdeI	CTNAG	4 cut(s)	146, 198, 542, 635
Eco47I	GGWCC	1 cut(s)	178
Eco57I	CTGAAG	1 cut(s)	543
Eco72I	CACGTG	1 cut(s)	118
EcoT22I	ATGCAT	1 cut(s)	65
FaeI	CATG	2 cut(s)	67, 491
FatI	CATG	2 cut(s)	63, 487
FauI	CCCGC	1 cut(s)	49
Fnu4HI	GCNGC	2 cut(s)	603, 606
FokI	GGATG	1 cut(s)	72
Fsp4HI	GCNGC	2 cut(s)	603, 606
GlaI	GCGC	1 cut(s)	253
GluI	GCNGC	2 cut(s)	603, 606
HaeIII	GGCC	1 cut(s)	51
HapII	CCGG	1 cut(s)	52
HgaI	GACGC	1 cut(s)	32
HhaI	GCGC	1 cut(s)	254
Hin1I	GRCGYC	2 cut(s)	24, 78
Hin1II	CATG	2 cut(s)	67, 491
Hin6I	GCGC	1 cut(s)	252
HinP1I	GCGC	1 cut(s)	252
HinfI	GANTC	1 cut(s)	173
HpaII	CCGG	1 cut(s)	52
HphI	GGTGA	2 cut(s)	145, 235
Hpy188I	TCNGA	4 cut(s)	178, 317, 375, 463
Hpy188III	TCNNGA	1 cut(s)	352
Hpy99I	CGWCG	6 cut(s)	26, 80, 83, 86, 129, 170
HpyAV	CCTTC	1 cut(s)	562
HpyCH4III	ACNGT	2 cut(s)	10, 133
HpyCH4IV	ACGT	3 cut(s)	78, 117, 165
HpyCH4V	TGCA	2 cut(s)	63, 388
HpyF10VI	GCNNNNNNNGC	5 cut(s)	69, 102, 156, 341, 385
HpyF3I	CTNAG	4 cut(s)	146, 198, 542, 635
HpySE526I	ACGT	3 cut(s)	78, 117, 165
Hsp92I	GRCGYC	2 cut(s)	24, 78
Hsp92II	CATG	2 cut(s)	67, 491
HspAI	GCGC	1 cut(s)	252
KpnI	GGTACC	1 cut(s)	115
LmnI	GCTCC	2 cut(s)	93, 269
LpnPI	CCDG	7 cut(s)	65, 94, 240, 365, 398, 407, 455
Lsp1109I	GCAGC	2 cut(s)	614, 617
LweI	GCATC	3 cut(s)	50, 132, 366
MaeII	ACGT	3 cut(s)	78, 117, 165
MaeIII	GTNAC	3 cut(s)	133, 478, 577
MbiI	CCGCTC	1 cut(s)	264
MboII	GAAGA	4 cut(s)	286, 536, 572, 623
MluCI	AATT	2 cut(s)	268, 303
MlyI	GAGTC	1 cut(s)	167
MmeI	TCCRAC	1 cut(s)	537
MnlI	CCTC	9 cut(s)	38, 41, 83, 149, 191, 242, 251, 265, 359
Mph1103I	ATGCAT	1 cut(s)	65
MroXI	GAANNNNTTC	1 cut(s)	450
MseI	TTAA	1 cut(s)	667
MspA1I	CMGCKG	1 cut(s)	608
MspI	CCGG	1 cut(s)	52
MspR9I	CCNGG	1 cut(s)	53
MvnI	CGCG	1 cut(s)	212
MwoI	GCNNNNNNNGC	5 cut(s)	69, 102, 156, 341, 385
NciI	CCSGG	1 cut(s)	53
NlaIII	CATG	2 cut(s)	67, 491
NlaIV	GGNNCC	1 cut(s)	113
NmuCI	GTSAC	2 cut(s)	133, 577
NsiI	ATGCAT	1 cut(s)	65
NspI	RCATGY	1 cut(s)	491
PdmI	GAANNNNTTC	1 cut(s)	450
Pfl23II	CGTACG	1 cut(s)	128
PflFI	GACNNNGTC	1 cut(s)	80
PkrI	GCNGC	2 cut(s)	604, 607
PleI	GAGTC	1 cut(s)	167
PmaCI	CACGTG	1 cut(s)	118
PmlI	CACGTG	1 cut(s)	118
PpsI	GAGTC	1 cut(s)	167
Ppu21I	YACGTR	1 cut(s)	118
PspCI	CACGTG	1 cut(s)	118
PspLI	CGTACG	1 cut(s)	128
PspN4I	GGNNCC	1 cut(s)	113
PspPI	GGNCC	1 cut(s)	178
PsyI	GACNNNGTC	1 cut(s)	80
RsaI	GTAC	4 cut(s)	113, 130, 208, 551
RsaNI	GTAC	4 cut(s)	112, 129, 207, 550
SaqAI	TTAA	1 cut(s)	667
SatI	GCNGC	2 cut(s)	603, 606
Sau96I	GGNCC	1 cut(s)	178
SchI	GAGTC	1 cut(s)	167
ScrFI	CCNGG	1 cut(s)	53
SfaNI	GCATC	3 cut(s)	50, 132, 366
SfcI	CTRYAG	1 cut(s)	106
SinI	GGWCC	1 cut(s)	178
Sse9I	AATT	2 cut(s)	268, 303
SsiI	CCGC	6 cut(s)	39, 56, 210, 238, 262, 608
StyD4I	CCNGG	1 cut(s)	51
TaaI	ACNGT	2 cut(s)	10, 133
TaiI	ACGT	3 cut(s)	81, 120, 168
TaqI	TCGA	2 cut(s)	234, 412
TaqII	GACCGA	2 cut(s)	168, 206
TasI	AATT	2 cut(s)	268, 303
TatI	WGTACW	1 cut(s)	549
Tru1I	TTAA	1 cut(s)	667
Tru9I	TTAA	1 cut(s)	667
TscAI	CASTG	2 cut(s)	202, 643
TseFI	GTSAC	2 cut(s)	133, 577
TseI	GCWGC	2 cut(s)	602, 605
Tsp45I	GTSAC	2 cut(s)	133, 577
TspDTI	ATGAA	2 cut(s)	324, 413
TspGWI	ACGGA	2 cut(s)	152, 194
TspRI	CASTG	2 cut(s)	202, 643
Tth111I	GACNNNGTC	1 cut(s)	80
VpaK11BI	GGWCC	1 cut(s)	178
XceI	RCATGY	1 cut(s)	491
XmnI	GAANNNNTTC	1 cut(s)	450
ZraI	GACGTC	1 cut(s)	79
Zsp2I	ATGCAT	1 cut(s)	65

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