Basic Information

Type: gene

Biological Identity

Species

rosa_laevigata

Chromosome

Chr6

Orthogroup ID

OG0003607

Physical Location & Seq

Genomic Coordinates Forward (+)

60976023 .. 60979139

Gene Structure 3117 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

RLM00000030402

Sequence Viewer

CDS Protein Promoter (2k)

Length: 684 bp

ATGCATGACGAGCCACGACGTTGTCGGTGGAGGGAGCTTGGAGAGCTACAGGTACTACGTGTCTACTACGTGTCTCGTCGTACGGTGATGGAGATGCTGTGCGACCGAGGCTACAACGTCGCCGACTCGGACCTCACTCGCTCACTCACTGAGTTCCGTACGGCGTTCGGCCAAAACCCTGACCTCGACCACCTCACCATCTGCGCCTCTCTCCGCTCCAATTCCAAGAACAAGATTATGGTCATCTTCTGTGGAACTGATGAAATCAGAAAAGTGAGTGTTCGTGCCATTTATGCTAACCTCCTGAACAAAGATATAAGCTCTCTGATGCTTGTCCTGCAAAGTAAAATGAACTCCTATGCTCGAAAAGAACTGGAAAACTATCCTTACAAAGTTGAAACTTTCCACATAAGTTGCCTCATAATTATTCTACGTTATTGTACTATTTCTGAACCGCTGGTCAATGTTACAAAGCATGTTTTACAGCCAAAGTATGAGATACTTGCTGCTGAAGAAAAGAAACATCTGCTAAGGAAGTACAAGTTGGAAGACAAGAAGCTTCCTCTTATGCTGGAAACCGATGCATTTGCACGCTACTATGGATTGGAGAAGGGACAGGTGGTAAAGATTACATACCGAGGTGGAGCTGTTGGTGCCCTCAAAACTTACCGTTGCATTGTCTGA

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

228

Amino Acids

26.44

Weight (kDa)

9.3

Isoelectric Point (pI)

49.16

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb5_N	PF03871	22 - 99	7.3e-20	RNA polymerase Rpb5, N-terminal domain
RNA_pol_Rpb5_C	PF01191	154 - 226	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

Style Settings

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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)
AccB1I	GGYRCC	1 cut(s)	653
AccBSI	CCGCTC	1 cut(s)	216
AccI	GTMKAC	1 cut(s)	63
AciI	CCGC	2 cut(s)	214, 455
AcoI	YGGCCR	1 cut(s)	169
AcuI	CTGAAG	1 cut(s)	531
AfaI	GTAC	5 cut(s)	54, 82, 160, 442, 539
AflIII	ACRYGT	2 cut(s)	58, 69
AgsI	TTSAA	1 cut(s)	398
AjuI	GAANNNNNNNTTGG	2 cut(s)	527, 559
AluBI	AGCT	5 cut(s)	37, 46, 321, 559, 647
AluI	AGCT	5 cut(s)	37, 46, 321, 559, 647
Alw26I	GTCTC	1 cut(s)	78
AoxI	GGCC	1 cut(s)	169
ApeKI	GCWGC	1 cut(s)	506
AspLEI	GCGC	1 cut(s)	206
AspS9I	GGNCC	1 cut(s)	130
AsuHPI	GGTGA	2 cut(s)	97, 187
AvaII	GGWCC	1 cut(s)	130
BaeGI	GKGCMC	1 cut(s)	658
BanI	GGYRCC	1 cut(s)	653
BbsI	GAAGAC	1 cut(s)	555
BbvI	GCAGC	1 cut(s)	493
BccI	CCATC	2 cut(s)	82, 206
BceAI	ACGGC	1 cut(s)	177
BcgI	CGANNNNNNTGC	2 cut(s)	569, 603
BcoDI	GTCTC	1 cut(s)	78
BfmI	CTRYAG	1 cut(s)	47
BisI	GCNGC	1 cut(s)	507
BlsI	GCNGC	1 cut(s)	508
Bme18I	GGWCC	1 cut(s)	130
BmgT120I	GGNCC	1 cut(s)	130
BmiI	GGNNCC	1 cut(s)	655
BmsI	GCATC	3 cut(s)	84, 318, 571
BpiI	GAAGAC	1 cut(s)	555
Bpu10I	CCTNAGC	1 cut(s)	530
BsaAI	YACGTR	2 cut(s)	59, 70
BsaJI	CCNNGG	2 cut(s)	106, 637
BsaXI	ACNNNNNCTCC	2 cut(s)	83, 113
Bse1I	ACTGG	1 cut(s)	378
BseDI	CCNNGG	2 cut(s)	106, 637
BseMII	CTCAG	1 cut(s)	141
BseNI	ACTGG	1 cut(s)	378
BseSI	GKGCMC	1 cut(s)	658
BseXI	GCAGC	1 cut(s)	493
Bsh1285I	CGRYCG	1 cut(s)	106
BshFI	GGCC	1 cut(s)	171
BshNI	GGYRCC	1 cut(s)	653
BsiEI	CGRYCG	1 cut(s)	106
BsiWI	CGTACG	2 cut(s)	80, 158
BslFI	GGGAC	1 cut(s)	627
BsmAI	GTCTC	1 cut(s)	78
BsmFI	GGGAC	1 cut(s)	627
BsnI	GGCC	1 cut(s)	171
Bsp1286I	GDGCHC	1 cut(s)	658
BspACI	CCGC	2 cut(s)	214, 455
BspANI	GGCC	1 cut(s)	171
BspCNI	CTCAG	1 cut(s)	142
BspLI	GGNNCC	1 cut(s)	655
BspT107I	GGYRCC	1 cut(s)	653
BsrBI	CCGCTC	1 cut(s)	216
BsrI	ACTGG	1 cut(s)	378
BssECI	CCNNGG	2 cut(s)	106, 637
Bst4CI	ACNGT	2 cut(s)	85, 671
BstBAI	YACGTR	2 cut(s)	59, 70
BstC8I	GCNNGC	1 cut(s)	592
BstDEI	CTNAG	2 cut(s)	150, 530
BstHHI	GCGC	1 cut(s)	206
BstMAI	GTCTC	1 cut(s)	78
BstMCI	CGRYCG	1 cut(s)	106
BstMWI	GCNNNNNNNGC	6 cut(s)	10, 43, 108, 293, 337, 653
BstNSI	RCATGY	1 cut(s)	479
BstSFI	CTRYAG	1 cut(s)	47
BstSLI	GKGCMC	1 cut(s)	658
BstV1I	GCAGC	1 cut(s)	493
BstV2I	GAAGAC	1 cut(s)	555
BsuRI	GGCC	1 cut(s)	171
BtsIMutI	CAGTG	1 cut(s)	147
Cac8I	GCNNGC	1 cut(s)	592
CfoI	GCGC	1 cut(s)	206
Cfr13I	GGNCC	1 cut(s)	130
Csp6I	GTAC	5 cut(s)	53, 81, 159, 441, 538
CspCI	CAANNNNNGTGG	2 cut(s)	395, 430
CviAII	CATG	2 cut(s)	5, 476
CviJI	RGCY	9 cut(s)	13, 37, 46, 111, 171, 321, 487, 559, 647
CviKI_1	RGCY	9 cut(s)	13, 37, 46, 111, 171, 321, 487, 559, 647
CviQI	GTAC	5 cut(s)	53, 81, 159, 441, 538
DdeI	CTNAG	2 cut(s)	150, 530
EaeI	YGGCCR	1 cut(s)	169
Eco47I	GGWCC	1 cut(s)	130
Eco57I	CTGAAG	1 cut(s)	531
EcoT22I	ATGCAT	2 cut(s)	6, 586
FaeI	CATG	2 cut(s)	8, 479
FaqI	GGGAC	1 cut(s)	627
FatI	CATG	2 cut(s)	4, 475
FblI	GTMKAC	1 cut(s)	63
Fnu4HI	GCNGC	1 cut(s)	507
Fsp4HI	GCNGC	1 cut(s)	507
GlaI	GCGC	1 cut(s)	205
GluI	GCNGC	1 cut(s)	507
HaeIII	GGCC	1 cut(s)	171
HhaI	GCGC	1 cut(s)	206
Hin1II	CATG	2 cut(s)	8, 479
Hin6I	GCGC	1 cut(s)	204
HinP1I	GCGC	1 cut(s)	204
HindIII	AAGCTT	1 cut(s)	557
HinfI	GANTC	1 cut(s)	125
HphI	GGTGA	2 cut(s)	97, 187
Hpy166II	GTNNAC	1 cut(s)	64
Hpy188I	TCNGA	5 cut(s)	130, 269, 327, 451, 683
Hpy188III	TCNNGA	1 cut(s)	304
Hpy8I	GTNNAC	1 cut(s)	64
Hpy99I	CGWCG	3 cut(s)	21, 81, 122
HpyAV	CCTTC	1 cut(s)	604
HpyCH4III	ACNGT	2 cut(s)	85, 671
HpyCH4IV	ACGT	5 cut(s)	19, 58, 69, 117, 433
HpyCH4V	TGCA	5 cut(s)	4, 340, 584, 590, 675
HpyF10VI	GCNNNNNNNGC	6 cut(s)	10, 43, 108, 293, 337, 653
HpyF3I	CTNAG	2 cut(s)	150, 530
HpySE526I	ACGT	5 cut(s)	19, 58, 69, 117, 433
Hsp92II	CATG	2 cut(s)	8, 479
HspAI	GCGC	1 cut(s)	204
LmnI	GCTCC	3 cut(s)	34, 221, 644
LpnPI	CCDG	8 cut(s)	35, 192, 317, 350, 359, 443, 557, 602
Lsp1109I	GCAGC	1 cut(s)	493
LweI	GCATC	3 cut(s)	84, 318, 571
MaeII	ACGT	5 cut(s)	19, 58, 69, 117, 433
MaeIII	GTNAC	1 cut(s)	466
MbiI	CCGCTC	1 cut(s)	216
MboII	GAAGA	3 cut(s)	238, 524, 560
MhlI	GDGCHC	1 cut(s)	658
MluCI	AATT	2 cut(s)	220, 423
MlyI	GAGTC	1 cut(s)	119
MmeI	TCCRAC	1 cut(s)	525
Mph1103I	ATGCAT	2 cut(s)	6, 586
MspA1I	CMGCKG	1 cut(s)	457
MwoI	GCNNNNNNNGC	6 cut(s)	10, 43, 108, 293, 337, 653
NlaIII	CATG	2 cut(s)	8, 479
NlaIV	GGNNCC	1 cut(s)	655
NsiI	ATGCAT	2 cut(s)	6, 586
NspI	RCATGY	1 cut(s)	479
Pfl23II	CGTACG	2 cut(s)	80, 158
PflFI	GACNNNGTC	1 cut(s)	21
PkrI	GCNGC	1 cut(s)	508
PleI	GAGTC	1 cut(s)	119
PpsI	GAGTC	1 cut(s)	119
Ppu21I	YACGTR	2 cut(s)	59, 70
PspLI	CGTACG	2 cut(s)	80, 158
PspN4I	GGNNCC	1 cut(s)	655
PspPI	GGNCC	1 cut(s)	130
PsyI	GACNNNGTC	1 cut(s)	21
RsaI	GTAC	5 cut(s)	54, 82, 160, 442, 539
RsaNI	GTAC	5 cut(s)	53, 81, 159, 441, 538
SatI	GCNGC	1 cut(s)	507
Sau96I	GGNCC	1 cut(s)	130
SchI	GAGTC	1 cut(s)	119
SduI	GDGCHC	1 cut(s)	658
SfaNI	GCATC	3 cut(s)	84, 318, 571
SfcI	CTRYAG	1 cut(s)	47
SinI	GGWCC	1 cut(s)	130
Sse9I	AATT	2 cut(s)	220, 423
SsiI	CCGC	2 cut(s)	214, 455
TaaI	ACNGT	2 cut(s)	85, 671
TaiI	ACGT	5 cut(s)	22, 61, 72, 120, 436
TaqI	TCGA	2 cut(s)	186, 364
TaqII	GACCGA	1 cut(s)	120
TasI	AATT	2 cut(s)	220, 423
TatI	WGTACW	2 cut(s)	440, 537
TscAI	CASTG	1 cut(s)	154
TseI	GCWGC	1 cut(s)	506
TspDTI	ATGAA	2 cut(s)	276, 365
TspGWI	ACGGA	1 cut(s)	146
TspRI	CASTG	1 cut(s)	154
Tth111I	GACNNNGTC	1 cut(s)	21
VpaK11BI	GGWCC	1 cut(s)	130
XceI	RCATGY	1 cut(s)	479
XmiI	GTMKAC	1 cut(s)	63
Zsp2I	ATGCAT	2 cut(s)	6, 586

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