Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1B

Orthogroup ID

OG0003607

Physical Location & Seq

Genomic Coordinates Reverse (-)

6034243 .. 6037435

Gene Structure 3193 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1BG045400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 696 bp

ATGGCTGCCGTGGTGTTGGACGACGCCGTTTCGGGTGGCGGTGGAGGAGGCCGGGCGGGATGCATGACGAGCCACGACGTCGTCGGTGGAGGGAGCTTGGAGAGCTCCAGGTACTACGTGTCTCGTCGTACGGTGATGGAGATGCTGAGCGACCGAGGCTACAACGTCGCCGACTCGGACCTCACTCGCTCACTCACTGAGTTCCGTACCGCGTTCGGCCAAAACCCTGACCTCGACCGCCTCACCATCTGCGCCTCTCTCCGCTCCAATTCCAAGAACAAGATTATGGTCATCTTCTGTGGAACTGATGAAATCAGAAAAGCGAGTGTTCGTGCCATTTATGCTAACCTCCTGAACAAAGATATAAGCTCGCTGATGCTTGTCCTGCAAAGTAAAATGAACTCCTATGCTCGAAAAGAACTGGAAAACTATCCTTACAAAGTTGAAACTTTCCACATCTCTGAACTGCTGGTCAATGTTACAAAGCATGTTTTACAGCCCAAGTATGAGATACTTTCTGCTGAAGAAAAGAAACATCTGCTAAGGAAGTACAAGTTGGAAGACAAGAAGCTCCCTCTCATGCTGGAAACTGATGCATTTGCACGCTACTTTGGATTGGAGAAGGGACAGGTGGTAAAGATTACTTACCATGGTGGAGCTGTTGGTGCCCTCAAAACTTACCGTTGCATTGTCTGA

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

231

Amino Acids

25.76

Weight (kDa)

9.14

Isoelectric Point (pI)

41.03

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb5_N	PF03871	34 - 115	6.7e-23	RNA polymerase Rpb5, N-terminal domain
RNA_pol_Rpb5_C	PF01191	158 - 230	1.8e-26	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)

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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
AccB1I	GGYRCC	1 cut(s)	665
AccBSI	CCGCTC	1 cut(s)	264
AccII	CGCG	1 cut(s)	212
AciI	CCGC	5 cut(s)	39, 56, 210, 238, 262
AcoI	YGGCCR	1 cut(s)	217
AcuI	CTGAAG	1 cut(s)	543
AcyI	GRCGYC	2 cut(s)	24, 78
AfaI	GTAC	4 cut(s)	113, 130, 208, 551
AflIII	ACRYGT	1 cut(s)	117
AgsI	TTSAA	1 cut(s)	446
AjnI	CCWGG	1 cut(s)	107
AjuI	GAANNNNNNNTTGG	2 cut(s)	539, 571
AluBI	AGCT	5 cut(s)	96, 105, 369, 571, 659
AluI	AGCT	5 cut(s)	96, 105, 369, 571, 659
Alw21I	GWGCWC	1 cut(s)	107
Alw26I	GTCTC	1 cut(s)	126
AoxI	GGCC	2 cut(s)	49, 217
ApeKI	GCWGC	1 cut(s)	5
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
BaeGI	GKGCMC	1 cut(s)	670
BanI	GGYRCC	1 cut(s)	665
BanII	GRGCYC	1 cut(s)	107
BbsI	GAAGAC	1 cut(s)	567
Bbv12I	GWGCWC	1 cut(s)	107
BccI	CCATC	2 cut(s)	130, 254
BceAI	ACGGC	1 cut(s)	11
BciT130I	CCWGG	1 cut(s)	109
BcnI	CCSGG	1 cut(s)	53
BcoDI	GTCTC	1 cut(s)	126
BisI	GCNGC	1 cut(s)	6
BlpI	GCTNAGC	1 cut(s)	146
BlsI	GCNGC	1 cut(s)	7
Bme1390I	CCNGG	2 cut(s)	53, 109
Bme18I	GGWCC	1 cut(s)	178
BmgT120I	GGNCC	1 cut(s)	178
BmiI	GGNNCC	1 cut(s)	667
BmrFI	CCNGG	2 cut(s)	53, 109
BmsI	GCATC	4 cut(s)	50, 132, 366, 583
BpiI	GAAGAC	1 cut(s)	567
BpmI	CTGGAG	1 cut(s)	91
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	3 cut(s)	9, 154, 649
Bse1I	ACTGG	1 cut(s)	426
BseBI	CCWGG	1 cut(s)	109
BseDI	CCNNGG	3 cut(s)	9, 154, 649
BseGI	GGATG	1 cut(s)	65
BseMII	CTCAG	2 cut(s)	137, 189
BseNI	ACTGG	1 cut(s)	426
BseRI	GAGGAG	1 cut(s)	60
BseSI	GKGCMC	1 cut(s)	670
Bsh1236I	CGCG	1 cut(s)	212
Bsh1285I	CGRYCG	2 cut(s)	154, 238
BshFI	GGCC	2 cut(s)	51, 219
BshNI	GGYRCC	1 cut(s)	665
BsiEI	CGRYCG	2 cut(s)	154, 238
BsiHKAI	GWGCWC	1 cut(s)	107
BsiSI	CCGG	1 cut(s)	52
BsiWI	CGTACG	1 cut(s)	128
BslFI	GGGAC	1 cut(s)	639
BsmAI	GTCTC	1 cut(s)	126
BsmFI	GGGAC	1 cut(s)	639
BsnI	GGCC	2 cut(s)	51, 219
Bsp1286I	GDGCHC	2 cut(s)	107, 670
Bsp1720I	GCTNAGC	1 cut(s)	146
Bsp19I	CCATGG	1 cut(s)	649
BspACI	CCGC	5 cut(s)	39, 56, 210, 238, 262
BspANI	GGCC	2 cut(s)	51, 219
BspCNI	CTCAG	2 cut(s)	138, 190
BspFNI	CGCG	1 cut(s)	212
BspLI	GGNNCC	1 cut(s)	667
BspT107I	GGYRCC	1 cut(s)	665
BsrBI	CCGCTC	1 cut(s)	264
BsrI	ACTGG	1 cut(s)	426
BssECI	CCNNGG	3 cut(s)	9, 154, 649
BssNI	GRCGYC	2 cut(s)	24, 78
BssT1I	CCWWGG	1 cut(s)	649
Bst2UI	CCWGG	1 cut(s)	109
Bst4CI	ACNGT	2 cut(s)	133, 683
BstACI	GRCGYC	2 cut(s)	24, 78
BstBAI	YACGTR	1 cut(s)	118
BstC8I	GCNNGC	2 cut(s)	371, 604
BstDEI	CTNAG	3 cut(s)	146, 198, 542
BstDSI	CCRYGG	2 cut(s)	9, 649
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	6 cut(s)	69, 102, 156, 341, 385, 665
BstNI	CCWGG	1 cut(s)	109
BstNSI	RCATGY	1 cut(s)	491
BstSCI	CCNGG	2 cut(s)	51, 107
BstSLI	GKGCMC	1 cut(s)	670
BstUI	CGCG	1 cut(s)	212
BstV2I	GAAGAC	1 cut(s)	567
BsuRI	GGCC	2 cut(s)	51, 219
BtgI	CCRYGG	2 cut(s)	9, 649
BtsCI	GGATG	1 cut(s)	65
BtsIMutI	CAGTG	1 cut(s)	195
Cac8I	GCNNGC	2 cut(s)	371, 604
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	4 cut(s)	64, 488, 580, 650
CviQI	GTAC	4 cut(s)	112, 129, 207, 550
DdeI	CTNAG	3 cut(s)	146, 198, 542
EaeI	YGGCCR	1 cut(s)	217
Ecl136II	GAGCTC	1 cut(s)	105
Eco130I	CCWWGG	1 cut(s)	649
Eco24I	GRGCYC	1 cut(s)	107
Eco47I	GGWCC	1 cut(s)	178
Eco53kI	GAGCTC	1 cut(s)	105
Eco57I	CTGAAG	1 cut(s)	543
EcoICRI	GAGCTC	1 cut(s)	105
EcoRII	CCWGG	1 cut(s)	107
EcoT14I	CCWWGG	1 cut(s)	649
EcoT22I	ATGCAT	2 cut(s)	65, 598
EcoT38I	GRGCYC	1 cut(s)	107
ErhI	CCWWGG	1 cut(s)	649
FaeI	CATG	4 cut(s)	67, 491, 583, 653
FaiI	YATR	9 cut(s)	65, 287, 342, 365, 408, 489, 507, 581, 651
FaqI	GGGAC	1 cut(s)	639
FatI	CATG	4 cut(s)	63, 487, 579, 649
FauI	CCCGC	1 cut(s)	49
Fnu4HI	GCNGC	1 cut(s)	6
FokI	GGATG	1 cut(s)	72
FriOI	GRGCYC	1 cut(s)	107
Fsp4HI	GCNGC	1 cut(s)	6
GlaI	GCGC	1 cut(s)	253
GluI	GCNGC	1 cut(s)	6
GsuI	CTGGAG	1 cut(s)	91
HaeIII	GGCC	2 cut(s)	51, 219
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	4 cut(s)	67, 491, 583, 653
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, 463, 695
Hpy188III	TCNNGA	1 cut(s)	352
Hpy99I	CGWCG	6 cut(s)	26, 80, 83, 86, 129, 170
HpyAV	CCTTC	1 cut(s)	616
HpyCH4III	ACNGT	2 cut(s)	133, 683
HpyCH4IV	ACGT	3 cut(s)	78, 117, 165
HpyCH4V	TGCA	5 cut(s)	63, 388, 596, 602, 687
HpyF10VI	GCNNNNNNNGC	6 cut(s)	69, 102, 156, 341, 385, 665
HpyF3I	CTNAG	3 cut(s)	146, 198, 542
HpySE526I	ACGT	3 cut(s)	78, 117, 165
Hsp92I	GRCGYC	2 cut(s)	24, 78
Hsp92II	CATG	4 cut(s)	67, 491, 583, 653
HspAI	GCGC	1 cut(s)	252
LmnI	GCTCC	5 cut(s)	93, 110, 269, 576, 656
LweI	GCATC	4 cut(s)	50, 132, 366, 583
MaeII	ACGT	3 cut(s)	78, 117, 165
MaeIII	GTNAC	1 cut(s)	478
MbiI	CCGCTC	1 cut(s)	264
MboII	GAAGA	3 cut(s)	286, 536, 572
MhlI	GDGCHC	2 cut(s)	107, 670
MluCI	AATT	1 cut(s)	268
MlyI	GAGTC	1 cut(s)	167
MmeI	TCCRAC	1 cut(s)	537
Mph1103I	ATGCAT	2 cut(s)	65, 598
MspI	CCGG	1 cut(s)	52
MspR9I	CCNGG	2 cut(s)	53, 109
MvaI	CCWGG	1 cut(s)	109
MvnI	CGCG	1 cut(s)	212
MwoI	GCNNNNNNNGC	6 cut(s)	69, 102, 156, 341, 385, 665
NciI	CCSGG	1 cut(s)	53
NcoI	CCATGG	1 cut(s)	649
NlaIII	CATG	4 cut(s)	67, 491, 583, 653
NlaIV	GGNNCC	1 cut(s)	667
NsiI	ATGCAT	2 cut(s)	65, 598
NspI	RCATGY	1 cut(s)	491
Pfl23II	CGTACG	1 cut(s)	128
PflFI	GACNNNGTC	1 cut(s)	80
PkrI	GCNGC	1 cut(s)	7
PleI	GAGTC	1 cut(s)	167
PpsI	GAGTC	1 cut(s)	167
Ppu21I	YACGTR	1 cut(s)	118
Psp124BI	GAGCTC	1 cut(s)	107
Psp6I	CCWGG	1 cut(s)	107
PspGI	CCWGG	1 cut(s)	107
PspLI	CGTACG	1 cut(s)	128
PspN4I	GGNNCC	1 cut(s)	667
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
SacI	GAGCTC	1 cut(s)	107
SatI	GCNGC	1 cut(s)	6
Sau96I	GGNCC	1 cut(s)	178
SchI	GAGTC	1 cut(s)	167
ScrFI	CCNGG	2 cut(s)	53, 109
SduI	GDGCHC	2 cut(s)	107, 670
SfaNI	GCATC	4 cut(s)	50, 132, 366, 583
SinI	GGWCC	1 cut(s)	178
Sse9I	AATT	1 cut(s)	268
SsiI	CCGC	5 cut(s)	39, 56, 210, 238, 262
SstI	GAGCTC	1 cut(s)	107
StyD4I	CCNGG	2 cut(s)	51, 107
StyI	CCWWGG	1 cut(s)	649
TaaI	ACNGT	2 cut(s)	133, 683
TaiI	ACGT	3 cut(s)	81, 120, 168
TaqI	TCGA	2 cut(s)	234, 412
TaqII	GACCGA	1 cut(s)	168
TasI	AATT	1 cut(s)	268
TatI	WGTACW	1 cut(s)	549
TscAI	CASTG	1 cut(s)	202
TseI	GCWGC	1 cut(s)	5
TspDTI	ATGAA	2 cut(s)	324, 413
TspGWI	ACGGA	1 cut(s)	194
TspRI	CASTG	1 cut(s)	202
Tth111I	GACNNNGTC	1 cut(s)	80
VpaK11BI	GGWCC	1 cut(s)	178
XceI	RCATGY	1 cut(s)	491
ZraI	GACGTC	1 cut(s)	79
Zsp2I	ATGCAT	2 cut(s)	65, 598

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