Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1B

Orthogroup ID

OG0004203

Physical Location & Seq

Genomic Coordinates Forward (+)

18906507 .. 18909476

Gene Structure 2970 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1BG110000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 711 bp

ATGACTCTTGGCTTATGGAGGCTGCGTAGAGGTGAAGGTGGTGTTAGGATGTTGATTGACGAGATCTGTGGCAATCTCGACTGGGTTCATGATGCGTGGCGGTGGTTGGTGGCTCTGTGGGCTTGGAGTCTGAAACTGGGGCGTTGGTTTGGGCTTGGGATGATGTATGGAGCTTGGTCAATCACCGACGGTTGGTTGGATATCAGGTGGTTAAATCGATTAGGGCAGTGGCTGTGCAGTGGGTGGGTGGCCGTCATTGGGCGGGTGGAGGTGGCGGTGCCTGAGTGGTTGCAACTCCTCTTCGGCTCATCTCTTCATAATTTTTGCTCAATATTTACTCACTCTTCTCAACTCTTGTTCAACTTCGGGCAGGGTTTTGTAAAAGAAATGGAACTTGGGTCCCTTTCTGATCCCACCCAATCCACATTCTCTTTAGTTGATGACGATCATACATTCGCAAATGCTGTCAGGTTTACTTTGAATCAGGATCCAAGGACGAAATTCTGTGGGTACAGCATTCCTCATCCATCAGATAACCGAGTTAATATTAGAATCCAGACTACAGGTGATCCAGCAAAAGATGTATTCAAAGATGCATGCCAGGATCTCATGGTGATGTGCCAGCATGTGAGCAACACTTTTAACAAGGCAGTGGTTGATTTCAAATTGAGCAACTCTGTGGAGGGCATGGATATTGAATCAGATAGTTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

No ontology terms assigned.

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 ko04623 ko05169 map00230 map00240 map01100 map03020 map04623 map05169

Pfam Domains

Protein Families

RNA_pol_L_2

Protein Analysis

236

Amino Acids

26.89

Weight (kDa)

5.46

Isoelectric Point (pI)

37.22

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_L_2	PF13656	141 - 212	2.8e-25	RNA polymerase Rpb3/Rpb11 dimerisation domain
RNA_pol_L	PF01193	142 - 204	3.5e-08	RNA polymerase Rpb3/Rpb11 dimerisation 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: OG0004203)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT2G29540 AT2G29540 AT2G29540
fragaria_vesca	FvH4_6g26980 FvH4_7g06540
malus_domestica	MD10G1078400.v1.1
prunus_persica	Prupe.2G047700_v2.0.a1 Prupe.2G047700_v2.0.a1 Prupe.3G125300_v2.0.a1 Prupe.3G125300_v2.0.a1
rosa_chinensis	RchiOBHm_Chr1g0334971 RchiOBHm_Chr2g0128821
rosa_laevigata	RLG00000019027
rosa_multiflora	Rmu_sc0007061.1_g000007 Rmu_sc0009556.1_g000001
rosa_roxburghii	Rroxscaffold_2G00115240 Rroxscaffold_4G00316330
rosa_rugosa	Rorug01G0118200 Rorug02G0281300 Rorug02G0281400 Rorug02G0281500 Rorug02G0281600 Rorug02G0281600
rosa_samantha	Rh1AG141500 Rh1BG110000 Rh1CG133400 Rh1DG146100 Rh2AG334100 Rh2BG342100 Rh2CG321000 Rh2DG358800
rosa_wichuraiana	Rw1G011740 Rw2G027000

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	1 cut(s)	277
AciI	CCGC	3 cut(s)	100, 262, 275
AclWI	GGATC	5 cut(s)	404, 482, 495, 563, 612
AcoI	YGGCCR	1 cut(s)	249
AcsI	RAATTY	1 cut(s)	500
AfaI	GTAC	1 cut(s)	512
AfiI	CCNNNNNNNGG	2 cut(s)	192, 258
AgsI	TTSAA	5 cut(s)	361, 481, 589, 664, 698
AjnI	CCWGG	1 cut(s)	600
AjuI	GAANNNNNNNTTGG	2 cut(s)	378, 410
AluBI	AGCT	1 cut(s)	173
AluI	AGCT	1 cut(s)	173
AlwI	GGATC	5 cut(s)	404, 482, 495, 563, 612
AlwNI	CAGNNNCTG	1 cut(s)	232
AoxI	GGCC	1 cut(s)	249
ApeKI	GCWGC	1 cut(s)	22
ApoI	RAATTY	1 cut(s)	500
AspS9I	GGNCC	1 cut(s)	399
AsuHPI	GGTGA	4 cut(s)	44, 175, 578, 625
AvaII	GGWCC	1 cut(s)	399
BamHI	GGATCC	1 cut(s)	487
BanI	GGYRCC	1 cut(s)	277
BbvI	GCAGC	1 cut(s)	9
BccI	CCATC	1 cut(s)	535
BceAI	ACGGC	1 cut(s)	236
BciT130I	CCWGG	1 cut(s)	602
BfmI	CTRYAG	1 cut(s)	561
BglII	AGATCT	1 cut(s)	63
BisI	GCNGC	1 cut(s)	23
BlsI	GCNGC	1 cut(s)	24
Bme1390I	CCNGG	1 cut(s)	602
Bme18I	GGWCC	1 cut(s)	399
BmgT120I	GGNCC	1 cut(s)	399
BmiI	GGNNCC	4 cut(s)	279, 400, 401, 489
BmrFI	CCNGG	1 cut(s)	602
BmrI	ACTGGG	2 cut(s)	91, 146
BmsI	GCATC	2 cut(s)	82, 583
BmuI	ACTGGG	2 cut(s)	91, 146
Bsa29I	ATCGAT	1 cut(s)	217
BsaBI	GATNNNNATC	1 cut(s)	444
BsaJI	CCNNGG	1 cut(s)	491
BsaXI	ACNNNNNCTCC	2 cut(s)	10, 40
Bsc4I	CCNNNNNNNGG	2 cut(s)	192, 258
Bse1I	ACTGG	2 cut(s)	86, 141
Bse8I	GATNNNNATC	1 cut(s)	444
BseBI	CCWGG	1 cut(s)	602
BseCI	ATCGAT	1 cut(s)	217
BseDI	CCNNGG	1 cut(s)	491
BseGI	GGATG	3 cut(s)	54, 165, 523
BseJI	GATNNNNATC	1 cut(s)	444
BseLI	CCNNNNNNNGG	2 cut(s)	192, 258
BseMII	CTCAG	1 cut(s)	273
BseNI	ACTGG	2 cut(s)	86, 141
BseRI	GAGGAG	1 cut(s)	287
BseXI	GCAGC	1 cut(s)	9
BsgI	GTGCAG	1 cut(s)	256
BshFI	GGCC	1 cut(s)	251
BshNI	GGYRCC	1 cut(s)	277
BshVI	ATCGAT	1 cut(s)	217
BslFI	GGGAC	1 cut(s)	385
BslI	CCNNNNNNNGG	2 cut(s)	192, 258
BsmFI	GGGAC	1 cut(s)	385
BsmI	GAATGC	1 cut(s)	516
BsnI	GGCC	1 cut(s)	251
Bsp143I	GATC	6 cut(s)	63, 409, 445, 487, 568, 604
BspACI	CCGC	3 cut(s)	100, 262, 275
BspANI	GGCC	1 cut(s)	251
BspCNI	CTCAG	1 cut(s)	274
BspDI	ATCGAT	1 cut(s)	217
BspHI	TCATGA	1 cut(s)	88
BspLI	GGNNCC	4 cut(s)	279, 400, 401, 489
BspPI	GGATC	5 cut(s)	404, 482, 495, 563, 612
BspT107I	GGYRCC	1 cut(s)	277
BsrI	ACTGG	2 cut(s)	86, 141
BssECI	CCNNGG	1 cut(s)	491
BssMI	GATC	6 cut(s)	63, 409, 445, 487, 568, 604
BssT1I	CCWWGG	1 cut(s)	491
Bst2UI	CCWGG	1 cut(s)	602
Bst4CI	ACNGT	1 cut(s)	191
Bst6I	CTCTTC	3 cut(s)	305, 318, 349
BstC8I	GCNNGC	2 cut(s)	598, 623
BstDEI	CTNAG	1 cut(s)	282
BstF5I	GGATG	3 cut(s)	54, 165, 523
BstKTI	GATC	6 cut(s)	66, 412, 448, 490, 571, 607
BstMBI	GATC	6 cut(s)	63, 409, 445, 487, 568, 604
BstMWI	GCNNNNNNNGC	1 cut(s)	119
BstNI	CCWGG	1 cut(s)	602
BstNSI	RCATGY	2 cut(s)	600, 629
BstSCI	CCNGG	1 cut(s)	600
BstSFI	CTRYAG	1 cut(s)	561
BstV1I	GCAGC	1 cut(s)	9
BstX2I	RGATCY	3 cut(s)	63, 487, 604
BstYI	RGATCY	3 cut(s)	63, 487, 604
Bsu15I	ATCGAT	1 cut(s)	217
BsuRI	GGCC	1 cut(s)	251
BsuTUI	ATCGAT	1 cut(s)	217
BtsCI	GGATG	3 cut(s)	54, 165, 523
BtsI	GCAGTG	3 cut(s)	233, 244, 657
BtsIMutI	CAGTG	3 cut(s)	233, 244, 657
Cac8I	GCNNGC	2 cut(s)	598, 623
CaiI	CAGNNNCTG	1 cut(s)	232
CciI	TCATGA	1 cut(s)	88
Cfr13I	GGNCC	1 cut(s)	399
ClaI	ATCGAT	1 cut(s)	217
Csp6I	GTAC	1 cut(s)	511
CviAII	CATG	5 cut(s)	89, 597, 610, 626, 688
CviJI	RGCY	9 cut(s)	12, 22, 113, 122, 154, 173, 232, 251, 306
CviKI_1	RGCY	9 cut(s)	12, 22, 113, 122, 154, 173, 232, 251, 306
CviQI	GTAC	1 cut(s)	511
DdeI	CTNAG	1 cut(s)	282
DpnI	GATC	6 cut(s)	65, 411, 447, 489, 570, 606
DpnII	GATC	6 cut(s)	63, 409, 445, 487, 568, 604
EaeI	YGGCCR	1 cut(s)	249
Eam1104I	CTCTTC	3 cut(s)	305, 318, 349
EarI	CTCTTC	3 cut(s)	305, 318, 349
Eco130I	CCWWGG	1 cut(s)	491
Eco32I	GATATC	1 cut(s)	202
Eco47I	GGWCC	1 cut(s)	399
EcoO109I	RGGNCCY	1 cut(s)	399
EcoRII	CCWGG	1 cut(s)	600
EcoRV	GATATC	1 cut(s)	202
EcoT14I	CCWWGG	1 cut(s)	491
EcoT22I	ATGCAT	1 cut(s)	598
ErhI	CCWWGG	1 cut(s)	491
FaeI	CATG	5 cut(s)	92, 600, 613, 629, 691
FaiI	YATR	9 cut(s)	16, 90, 168, 318, 450, 598, 611, 627, 689
FaqI	GGGAC	1 cut(s)	385
FatI	CATG	5 cut(s)	88, 596, 609, 625, 687
FauI	CCCGC	1 cut(s)	255
Fnu4HI	GCNGC	1 cut(s)	23
FokI	GGATG	3 cut(s)	61, 172, 510
Fsp4HI	GCNGC	1 cut(s)	23
GluI	GCNGC	1 cut(s)	23
HaeIII	GGCC	1 cut(s)	251
Hin1II	CATG	5 cut(s)	92, 600, 613, 629, 691
HinfI	GANTC	5 cut(s)	4, 127, 481, 552, 698
HphI	GGTGA	4 cut(s)	44, 175, 578, 625
Hpy166II	GTNNAC	1 cut(s)	474
Hpy188I	TCNGA	4 cut(s)	132, 409, 532, 703
Hpy188III	TCNNGA	4 cut(s)	77, 89, 485, 556
Hpy8I	GTNNAC	1 cut(s)	474
Hpy99I	CGWCG	1 cut(s)	191
HpyAV	CCTTC	1 cut(s)	29
HpyCH4III	ACNGT	1 cut(s)	191
HpyCH4V	TGCA	3 cut(s)	237, 292, 596
HpyF10VI	GCNNNNNNNGC	1 cut(s)	119
HpyF3I	CTNAG	1 cut(s)	282
Hsp92II	CATG	5 cut(s)	92, 600, 613, 629, 691
KflI	GGGWCCC	1 cut(s)	399
Kzo9I	GATC	6 cut(s)	63, 409, 445, 487, 568, 604
LmnI	GCTCC	1 cut(s)	170
Lsp1109I	GCAGC	1 cut(s)	9
LweI	GCATC	2 cut(s)	82, 583
MalI	GATC	6 cut(s)	65, 411, 447, 489, 570, 606
MboI	GATC	6 cut(s)	63, 409, 445, 487, 568, 604
MboII	GAAGA	3 cut(s)	292, 305, 336
MflI	RGATCY	3 cut(s)	63, 487, 604
MluCI	AATT	3 cut(s)	319, 500, 665
MlyI	GAGTC	1 cut(s)	136
MmeI	TCCRAC	1 cut(s)	177
MnlI	CCTC	6 cut(s)	12, 23, 262, 308, 531, 676
Mph1103I	ATGCAT	1 cut(s)	598
MseI	TTAA	4 cut(s)	212, 543, 642, 709
MslI	CAYNNNNRTG	1 cut(s)	614
MspR9I	CCNGG	1 cut(s)	602
Mva1269I	GAATGC	1 cut(s)	516
MvaI	CCWGG	1 cut(s)	602
MwoI	GCNNNNNNNGC	1 cut(s)	119
NdeII	GATC	6 cut(s)	63, 409, 445, 487, 568, 604
NlaIII	CATG	5 cut(s)	92, 600, 613, 629, 691
NlaIV	GGNNCC	4 cut(s)	279, 400, 401, 489
NsiI	ATGCAT	1 cut(s)	598
NspI	RCATGY	2 cut(s)	600, 629
PaeI	GCATGC	1 cut(s)	600
PagI	TCATGA	1 cut(s)	88
PctI	GAATGC	1 cut(s)	516
PfeI	GAWTC	3 cut(s)	481, 552, 698
PkrI	GCNGC	1 cut(s)	24
PleI	GAGTC	1 cut(s)	135
PpsI	GAGTC	1 cut(s)	135
PpuMI	RGGWCCY	1 cut(s)	399
Psp5II	RGGWCCY	1 cut(s)	399
Psp6I	CCWGG	1 cut(s)	600
PspGI	CCWGG	1 cut(s)	600
PspN4I	GGNNCC	4 cut(s)	279, 400, 401, 489
PspPI	GGNCC	1 cut(s)	399
PspPPI	RGGWCCY	1 cut(s)	399
PstNI	CAGNNNCTG	1 cut(s)	232
PsuI	RGATCY	3 cut(s)	63, 487, 604
RsaI	GTAC	1 cut(s)	512
RsaNI	GTAC	1 cut(s)	511
RseI	CAYNNNNRTG	1 cut(s)	614
SaqAI	TTAA	4 cut(s)	212, 543, 642, 709
SatI	GCNGC	1 cut(s)	23
Sau3AI	GATC	6 cut(s)	63, 409, 445, 487, 568, 604
Sau96I	GGNCC	1 cut(s)	399
SchI	GAGTC	1 cut(s)	136
ScrFI	CCNGG	1 cut(s)	602
SetI	ASST	7 cut(s)	34, 40, 175, 209, 273, 473, 568
SfaNI	GCATC	2 cut(s)	82, 583
SfcI	CTRYAG	1 cut(s)	561
SinI	GGWCC	1 cut(s)	399
SmiMI	CAYNNNNRTG	1 cut(s)	614
SphI	GCATGC	1 cut(s)	600
Sse9I	AATT	3 cut(s)	319, 500, 665
SsiI	CCGC	3 cut(s)	100, 262, 275
SspI	AATATT	2 cut(s)	333, 547
StyD4I	CCNGG	1 cut(s)	600
StyI	CCWWGG	1 cut(s)	491
TaaI	ACNGT	1 cut(s)	191
TaqI	TCGA	2 cut(s)	78, 217
TasI	AATT	3 cut(s)	319, 500, 665
TfiI	GAWTC	3 cut(s)	481, 552, 698
Tru1I	TTAA	4 cut(s)	212, 543, 642, 709
Tru9I	TTAA	4 cut(s)	212, 543, 642, 709
TscAI	CASTG	3 cut(s)	233, 244, 657
TseI	GCWGC	1 cut(s)	22
TspDTI	ATGAA	2 cut(s)	77, 305
TspRI	CASTG	3 cut(s)	233, 244, 657
VpaK11BI	GGWCC	1 cut(s)	399
XapI	RAATTY	1 cut(s)	500
XceI	RCATGY	2 cut(s)	600, 629
Zsp2I	ATGCAT	1 cut(s)	598

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