Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr2B

Orthogroup ID

OG0004203

Physical Location & Seq

Genomic Coordinates Reverse (-)

45694080 .. 45697498

Gene Structure 3419 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh2BG342100.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 576 bp

ATGTGGGGCCTAGGCCTTGATGGCTTACACGTTGAAGAAGACACCACCAACCAAAACGACATGTCCTCAATTGCACTAAAAACGACATGTCGTGATCAAGGGAGCTCCAGTTTAAAAACCAGGAAACAAAAACGCAGAGGAATCCCAAGCCCTTCTTCGCACTCCTCCCGCGTCAAGTTTCGAGTCTTCATCGCCTGGAGTAATACCTCTCAGTCTCTCACCGTCCCACGATTCAGCAAGTTCTGTGAAGAAATGGAACTTGGGACACTTTCTGATCCCAGCCAATCCACATTCTCTTTGGTTGATGAGGACCACACATTTGCAAATGCTATCAGATTTACTTTGAATCAGGATCCAAGGACGAAATTCTGTGGGTACAGCATTCCTCATCCATCAGATAACCGGGTTAATATTAGAATCCAGACTACAGGTGATCCAGCGAAAGATGTATTCAAAGATGCATGTCAGGATCTCATGGTGATGTGCCAGCATGTGAGCAACACTTTTGACAAGGCTGTGGTTGATTTCAAAATGAGCAAGTCTGTGAATGGCATGGATATTGAATCAAATAGTTAA

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

191

Amino Acids

21.41

Weight (kDa)

6.95

Isoelectric Point (pI)

46.9

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_L_2	PF13656	96 - 167	6.2e-27	RNA polymerase Rpb3/Rpb11 dimerisation domain
RNA_pol_L	PF01193	97 - 159	9.6e-10	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

iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

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)
AccII	CGCG	1 cut(s)	171
AciI	CCGC	1 cut(s)	169
AclWI	GGATC	5 cut(s)	269, 347, 360, 428, 477
AcsI	RAATTY	1 cut(s)	365
AfaI	GTAC	1 cut(s)	377
AflIII	ACRYGT	3 cut(s)	28, 60, 86
AgsI	TTSAA	5 cut(s)	35, 346, 454, 529, 563
AjnI	CCWGG	2 cut(s)	119, 194
AjuI	GAANNNNNNNTTGG	4 cut(s)	139, 171, 243, 275
AluBI	AGCT	1 cut(s)	105
AluI	AGCT	1 cut(s)	105
Alw21I	GWGCWC	1 cut(s)	107
Alw26I	GTCTC	1 cut(s)	219
AlwI	GGATC	5 cut(s)	269, 347, 360, 428, 477
AoxI	GGCC	2 cut(s)	7, 13
ApoI	RAATTY	1 cut(s)	365
ArsI	GACNNNNNNTTYG	2 cut(s)	302, 334
AspA2I	CCTAGG	1 cut(s)	10
AspS9I	GGNCC	2 cut(s)	7, 310
AsuC2I	CCSGG	1 cut(s)	404
AsuHPI	GGTGA	3 cut(s)	211, 443, 490
AvaII	GGWCC	1 cut(s)	310
AvrII	CCTAGG	1 cut(s)	10
BamHI	GGATCC	1 cut(s)	352
BanII	GRGCYC	1 cut(s)	107
BbsI	GAAGAC	2 cut(s)	45, 178
Bbv12I	GWGCWC	1 cut(s)	107
BccI	CCATC	2 cut(s)	14, 400
BciT130I	CCWGG	2 cut(s)	121, 196
BclI	TGATCA	1 cut(s)	94
BcnI	CCSGG	1 cut(s)	404
BcoDI	GTCTC	1 cut(s)	219
BfaI	CTAG	1 cut(s)	11
BfmI	CTRYAG	1 cut(s)	426
BglI	GCCNNNNNGGC	1 cut(s)	21
BlnI	CCTAGG	1 cut(s)	10
Bme1390I	CCNGG	3 cut(s)	121, 196, 404
Bme18I	GGWCC	1 cut(s)	310
BmgT120I	GGNCC	2 cut(s)	7, 310
BmiI	GGNNCC	2 cut(s)	8, 354
BmrFI	CCNGG	3 cut(s)	121, 196, 404
BmsI	GCATC	1 cut(s)	448
BpiI	GAAGAC	2 cut(s)	45, 178
BpmI	CTGGAG	2 cut(s)	91, 217
BpuMI	CCSGG	1 cut(s)	404
BsaJI	CCNNGG	2 cut(s)	10, 356
BsaXI	ACNNNNNCTCC	2 cut(s)	94, 124
Bse1I	ACTGG	1 cut(s)	108
BseBI	CCWGG	2 cut(s)	121, 196
BseDI	CCNNGG	2 cut(s)	10, 356
BseGI	GGATG	1 cut(s)	388
BseMII	CTCAG	1 cut(s)	224
BseNI	ACTGG	1 cut(s)	108
BseRI	GAGGAG	1 cut(s)	154
BseYI	CCCAGC	1 cut(s)	278
Bsh1236I	CGCG	1 cut(s)	171
BshFI	GGCC	2 cut(s)	9, 15
BsiHKAI	GWGCWC	1 cut(s)	107
BsiSI	CCGG	1 cut(s)	403
BslFI	GGGAC	2 cut(s)	209, 277
BsmAI	GTCTC	1 cut(s)	219
BsmFI	GGGAC	2 cut(s)	209, 277
BsmI	GAATGC	1 cut(s)	381
BsnI	GGCC	2 cut(s)	9, 15
Bsp1286I	GDGCHC	1 cut(s)	107
Bsp143I	GATC	5 cut(s)	94, 274, 352, 433, 469
BspACI	CCGC	1 cut(s)	169
BspANI	GGCC	2 cut(s)	9, 15
BspCNI	CTCAG	1 cut(s)	223
BspFNI	CGCG	1 cut(s)	171
BspLI	GGNNCC	2 cut(s)	8, 354
BspPI	GGATC	5 cut(s)	269, 347, 360, 428, 477
BsrI	ACTGG	1 cut(s)	108
BssECI	CCNNGG	2 cut(s)	10, 356
BssMI	GATC	5 cut(s)	94, 274, 352, 433, 469
BssT1I	CCWWGG	2 cut(s)	10, 356
Bst2UI	CCWGG	2 cut(s)	121, 196
Bst4CI	ACNGT	1 cut(s)	223
BstC8I	GCNNGC	1 cut(s)	488
BstDEI	CTNAG	1 cut(s)	210
BstF5I	GGATG	1 cut(s)	388
BstFNI	CGCG	1 cut(s)	171
BstKTI	GATC	5 cut(s)	97, 277, 355, 436, 472
BstMAI	GTCTC	1 cut(s)	219
BstMBI	GATC	5 cut(s)	94, 274, 352, 433, 469
BstMWI	GCNNNNNNNGC	1 cut(s)	21
BstNI	CCWGG	2 cut(s)	121, 196
BstNSI	RCATGY	4 cut(s)	64, 90, 465, 494
BstSCI	CCNGG	3 cut(s)	119, 194, 402
BstSFI	CTRYAG	1 cut(s)	426
BstUI	CGCG	1 cut(s)	171
BstV2I	GAAGAC	2 cut(s)	45, 178
BstX2I	RGATCY	2 cut(s)	352, 469
BstYI	RGATCY	2 cut(s)	352, 469
BsuRI	GGCC	2 cut(s)	9, 15
BtgZI	GCGATG	1 cut(s)	175
BtsCI	GGATG	1 cut(s)	388
Cac8I	GCNNGC	1 cut(s)	488
Cfr13I	GGNCC	2 cut(s)	7, 310
CseI	GACGC	1 cut(s)	160
Csp6I	GTAC	1 cut(s)	376
CviAII	CATG	6 cut(s)	61, 87, 462, 475, 491, 553
CviJI	RGCY	7 cut(s)	9, 15, 24, 105, 150, 282, 515
CviKI_1	RGCY	7 cut(s)	9, 15, 24, 105, 150, 282, 515
CviQI	GTAC	1 cut(s)	376
DdeI	CTNAG	1 cut(s)	210
DpnI	GATC	5 cut(s)	96, 276, 354, 435, 471
DpnII	GATC	5 cut(s)	94, 274, 352, 433, 469
DraI	TTTAAA	1 cut(s)	114
Ecl136II	GAGCTC	1 cut(s)	105
Eco130I	CCWWGG	2 cut(s)	10, 356
Eco147I	AGGCCT	1 cut(s)	15
Eco24I	GRGCYC	1 cut(s)	107
Eco47I	GGWCC	1 cut(s)	310
Eco53kI	GAGCTC	1 cut(s)	105
EcoICRI	GAGCTC	1 cut(s)	105
EcoO109I	RGGNCCY	1 cut(s)	7
EcoRII	CCWGG	2 cut(s)	119, 194
EcoT14I	CCWWGG	2 cut(s)	10, 356
EcoT22I	ATGCAT	1 cut(s)	463
EcoT38I	GRGCYC	1 cut(s)	107
ErhI	CCWWGG	2 cut(s)	10, 356
FaeI	CATG	6 cut(s)	64, 90, 465, 478, 494, 556
FaiI	YATR	6 cut(s)	62, 88, 463, 476, 492, 554
FalI	AAGNNNNNCTT	2 cut(s)	139, 171
FaqI	GGGAC	2 cut(s)	209, 277
FatI	CATG	6 cut(s)	60, 86, 461, 474, 490, 552
FauI	CCCGC	1 cut(s)	176
FbaI	TGATCA	1 cut(s)	94
FokI	GGATG	1 cut(s)	375
FriOI	GRGCYC	1 cut(s)	107
FspBI	CTAG	1 cut(s)	11
GsaI	CCCAGC	1 cut(s)	282
GsuI	CTGGAG	2 cut(s)	91, 217
HaeIII	GGCC	2 cut(s)	9, 15
HapII	CCGG	1 cut(s)	403
HgaI	GACGC	1 cut(s)	160
Hin1II	CATG	6 cut(s)	64, 90, 465, 478, 494, 556
HinfI	GANTC	6 cut(s)	141, 183, 231, 346, 417, 563
HpaII	CCGG	1 cut(s)	403
HphI	GGTGA	3 cut(s)	211, 443, 490
Hpy188I	TCNGA	3 cut(s)	274, 335, 397
Hpy188III	TCNNGA	4 cut(s)	92, 350, 421, 467
HpyAV	CCTTC	1 cut(s)	162
HpyCH4III	ACNGT	1 cut(s)	223
HpyCH4IV	ACGT	1 cut(s)	30
HpyCH4V	TGCA	3 cut(s)	74, 323, 461
HpyF10VI	GCNNNNNNNGC	1 cut(s)	21
HpyF3I	CTNAG	1 cut(s)	210
HpySE526I	ACGT	1 cut(s)	30
Hsp92II	CATG	6 cut(s)	64, 90, 465, 478, 494, 556
Ksp22I	TGATCA	1 cut(s)	94
Kzo9I	GATC	5 cut(s)	94, 274, 352, 433, 469
LmnI	GCTCC	2 cut(s)	102, 110
LweI	GCATC	1 cut(s)	448
MaeI	CTAG	1 cut(s)	11
MaeII	ACGT	1 cut(s)	30
MalI	GATC	5 cut(s)	96, 276, 354, 435, 471
MboI	GATC	5 cut(s)	94, 274, 352, 433, 469
MboII	GAAGA	5 cut(s)	47, 50, 147, 178, 260
MfeI	CAATTG	1 cut(s)	69
MflI	RGATCY	2 cut(s)	352, 469
MhlI	GDGCHC	1 cut(s)	107
MluCI	AATT	2 cut(s)	69, 365
MlyI	GAGTC	1 cut(s)	192
MnlI	CCTC	6 cut(s)	76, 131, 175, 217, 301, 396
Mph1103I	ATGCAT	1 cut(s)	463
MseI	TTAA	3 cut(s)	113, 408, 574
MslI	CAYNNNNRTG	1 cut(s)	479
MspI	CCGG	1 cut(s)	403
MspR9I	CCNGG	3 cut(s)	121, 196, 404
MunI	CAATTG	1 cut(s)	69
Mva1269I	GAATGC	1 cut(s)	381
MvaI	CCWGG	2 cut(s)	121, 196
MvnI	CGCG	1 cut(s)	171
MwoI	GCNNNNNNNGC	1 cut(s)	21
NciI	CCSGG	1 cut(s)	404
NdeII	GATC	5 cut(s)	94, 274, 352, 433, 469
NlaIII	CATG	6 cut(s)	64, 90, 465, 478, 494, 556
NlaIV	GGNNCC	2 cut(s)	8, 354
NsiI	ATGCAT	1 cut(s)	463
NspI	RCATGY	4 cut(s)	64, 90, 465, 494
PceI	AGGCCT	1 cut(s)	15
PciI	ACATGT	2 cut(s)	60, 86
PctI	GAATGC	1 cut(s)	381
PfeI	GAWTC	5 cut(s)	141, 231, 346, 417, 563
PleI	GAGTC	1 cut(s)	191
PpsI	GAGTC	1 cut(s)	191
PscI	ACATGT	2 cut(s)	60, 86
Psp124BI	GAGCTC	1 cut(s)	107
Psp6I	CCWGG	2 cut(s)	119, 194
PspFI	CCCAGC	1 cut(s)	278
PspGI	CCWGG	2 cut(s)	119, 194
PspN4I	GGNNCC	2 cut(s)	8, 354
PspPI	GGNCC	2 cut(s)	7, 310
PsuI	RGATCY	2 cut(s)	352, 469
RsaI	GTAC	1 cut(s)	377
RsaNI	GTAC	1 cut(s)	376
RseI	CAYNNNNRTG	1 cut(s)	479
SacI	GAGCTC	1 cut(s)	107
SaqAI	TTAA	3 cut(s)	113, 408, 574
Sau3AI	GATC	5 cut(s)	94, 274, 352, 433, 469
Sau96I	GGNCC	2 cut(s)	7, 310
SchI	GAGTC	1 cut(s)	192
ScrFI	CCNGG	3 cut(s)	121, 196, 404
SduI	GDGCHC	1 cut(s)	107
SetI	ASST	4 cut(s)	33, 107, 209, 433
SfaNI	GCATC	1 cut(s)	448
SfcI	CTRYAG	1 cut(s)	426
SinI	GGWCC	1 cut(s)	310
SmiMI	CAYNNNNRTG	1 cut(s)	479
Sse9I	AATT	2 cut(s)	69, 365
SseBI	AGGCCT	1 cut(s)	15
SsiI	CCGC	1 cut(s)	169
SspI	AATATT	1 cut(s)	412
SspMI	CTAG	1 cut(s)	11
SstI	GAGCTC	1 cut(s)	107
StuI	AGGCCT	1 cut(s)	15
StyD4I	CCNGG	3 cut(s)	119, 194, 402
StyI	CCWWGG	2 cut(s)	10, 356
TaaI	ACNGT	1 cut(s)	223
TaiI	ACGT	1 cut(s)	33
TaqI	TCGA	1 cut(s)	181
TasI	AATT	2 cut(s)	69, 365
TfiI	GAWTC	5 cut(s)	141, 231, 346, 417, 563
Tru1I	TTAA	3 cut(s)	113, 408, 574
Tru9I	TTAA	3 cut(s)	113, 408, 574
TspDTI	ATGAA	1 cut(s)	178
VpaK11BI	GGWCC	1 cut(s)	310
XapI	RAATTY	1 cut(s)	365
XceI	RCATGY	4 cut(s)	64, 90, 465, 494
XcmI	CCANNNNNNNNNTGG	1 cut(s)	295
XmaJI	CCTAGG	1 cut(s)	10
XspI	CTAG	1 cut(s)	11
Zsp2I	ATGCAT	1 cut(s)	463

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