Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5A

Orthogroup ID

OG0002206

Physical Location & Seq

Genomic Coordinates Reverse (-)

38438961 .. 38440206

Gene Structure 1246 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5AG283600.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 903 bp

ATGGAGGAGCTGGTAGATGATACTTCAACATCACTTGATGGGAAGAATAAAGTTTTTCTCAATGGGGATTGGGTTGGCGTTTGTGAAGATTCCGGTGATTTTGTCATGAGACTAAGGACATTGAGACGCAGGAAAAAGTTGCTACAGCAGATGGAAATCAAAAGAGATGAGCAGCTCTGGGAAGTACAAATATATTCTGATGCTGGAAGGATTCTACGTCCTTTCCTGGTAGTTAAGAATTTGAATAAGATTAAAGCATCCAAGGGAAAAAAACACACGTTCCAAGATCTTCTTGGCAATGGAATAATCGAGCTCATTGGAGCTGAAGAAGAAGAGGATTGCTGTACAGCATGGGACGTCAGGCATCTATTTATGGAAGACAATGGGAAGTCAGCAGTCAAGTACACACACTGTGAACTGGACCTGTCATTTTTGTTAGGCTTAAGTTGTGGTATCATTCCCTTTTCAAACCATGATCATGCAAGGAGGGTTCTATACCAGTCTCAGAAGCACTCTCAGCAGGTCATTGGTTTTTCTACCACAAATCCTAACCACAGAGTGGTTACTCTGTCTCACCAACTATGCTACCCTCAGAGGCCGCTTTTTTGTAATATGATATCTGATTGCCTTAGCCAACCAGGAAACCCAGTGAGCCATAACAGAGTTATGTCCAAGCCTGAATACTTTAATGGCCAAAATGCAATTGTTGCATTCAATGTGCACCTAGGATATAACCAAGAAGATTCTATTGTGATGAACCGCGCATCTGTGCAACGTGGCATGTTCAAATCTGAGCACATACGGAGCTACAAGGCTGAAGCTGAAAACAAGTTCTCATTGGGAAAATACAGAGTAGATTTGGAAGTGTTGACAGCCTTGATGATGATGGATTCCCTCGTATAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000228 GO:0000418 GO:0000419 GO:0000428 GO:0000785 GO:0000790 GO:0000792 GO:0002682 GO:0003674 GO:0003824 GO:0003899 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005694 GO:0005720 GO:0005730 GO:0005736 GO:0006139 GO:0006259 GO:0006304 GO:0006305 GO:0006306 GO:0006396 GO:0006725 GO:0006807 GO:0006950 GO:0006952 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009605 GO:0009607 GO:0009620 GO:0009892 GO:0009987 GO:0010033 GO:0010467 GO:0010468 GO:0010605 GO:0010608 GO:0010629 GO:0014070 GO:0016020 GO:0016070 GO:0016246 GO:0016441 GO:0016458 GO:0016740 GO:0016772 GO:0016779 GO:0018130 GO:0019222 GO:0019438 GO:0030422 GO:0030880 GO:0031047 GO:0031050 GO:0031974 GO:0031981 GO:0032259 GO:0032774 GO:0032991 GO:0034062 GO:0034641 GO:0034654 GO:0035194 GO:0040029 GO:0042221 GO:0043170 GO:0043207 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0043331 GO:0043412 GO:0043414 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044427 GO:0044428 GO:0044446 GO:0044451 GO:0044452 GO:0044454 GO:0044464 GO:0044728 GO:0046483 GO:0048519 GO:0048583 GO:0050776 GO:0050789 GO:0050832 GO:0050896 GO:0051704 GO:0051707 GO:0051716 GO:0055029 GO:0060255 GO:0061695 GO:0065007 GO:0070013 GO:0070887 GO:0070918 GO:0071310 GO:0071359 GO:0071407 GO:0071704 GO:0090304 GO:0097747 GO:0098542 GO:0140098 GO:1901360 GO:1901362 GO:1901576 GO:1901698 GO:1901699 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 ko05016 ko05169 map00230 map00240 map01100 map03020 map05016 map05169

Pfam Domains

Protein Families

RNA_pol_Rpb2_1 RNA_pol_Rpb2_2 RNA_pol_Rpb2_3 RNA_pol_Rpb2_4 RNA_pol_Rpb2_5 RNA_pol_Rpb2_6 RNA_pol_Rpb2_7

Protein Analysis

300

Amino Acids

34.36

Weight (kDa)

7.16

Isoelectric Point (pI)

42.31

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb2_4	PF04566	18 - 79	1.5e-20	RNA polymerase Rpb2, domain 4
RNA_pol_Rpb2_5	PF04567	94 - 141	6.1e-09	RNA polymerase Rpb2, domain 5
RNA_pol_Rpb2_6	PF00562	150 - 276	3.5e-26	RNA polymerase Rpb2, domain 6

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

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0002206)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G18090 AT3G18090 AT3G18090 AT3G23780 AT3G23780
fragaria_vesca	FvH4_1g06870 FvH4_1g06870
malus_domestica	MD08G1057300.v1.1 MD15G1040100.v1.1
prunus_persica	Prupe.1G393500_v2.0.a1
pyrus_communis	pycom08g04680 pycom15g03760
rosa_chinensis	RchiOBHm_Chr2g0092681 RchiOBHm_Chr5g0042241 RchiOBHm_Chr5g0042281
rosa_laevigata	RLG00000016333 RLG00000034111 RLG00000034115
rosa_multiflora	Rmu_sc0001132.1_g000021 Rmu_sc0001715.1_g000028 Rmu_sc0017518.1_g000004 Rmu_sc0039596.1_g000001
rosa_roxburghii	Rroxscaffold_1G00038430 Rroxscaffold_2G00148910
rosa_rugosa	Rorug02G0028500 Rorug02G0028600 Rorug02G0028700 Rorug05G0198900
rosa_samantha	Rh2AG074500 Rh2BG075400 Rh2CG077200 Rh2DG073100 Rh5AG283600 Rh5AG284200 Rh5AG285200 Rh5BG289600 Rh5BG290100 Rh5CG320900 Rh5DG298900 Rh5DG299300
rosa_wichuraiana	Rw0G001490 Rw0G001760 Rw2G005860

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AatII	GACGTC	1 cut(s)	360
Acc36I	ACCTGC	1 cut(s)	511
AccB7I	CCANNNNNTGG	1 cut(s)	559
AccII	CGCG	1 cut(s)	762
AciI	CCGC	2 cut(s)	599, 760
AcoI	YGGCCR	1 cut(s)	691
AcsI	RAATTY	1 cut(s)	238
AcuI	CTGAAG	2 cut(s)	345, 837
AcyI	GRCGYC	1 cut(s)	357
AdeI	CACNNNGTG	2 cut(s)	413, 559
AfaI	GTAC	3 cut(s)	186, 346, 404
AfiI	CCNNNNNNNGG	1 cut(s)	559
AflII	CTTAAG	1 cut(s)	442
AflIII	ACRYGT	1 cut(s)	276
AgsI	TTSAA	5 cut(s)	27, 244, 468, 715, 787
AjnI	CCWGG	2 cut(s)	225, 637
AluBI	AGCT	6 cut(s)	10, 175, 313, 323, 807, 821
AluI	AGCT	6 cut(s)	10, 175, 313, 323, 807, 821
Alw21I	GWGCWC	3 cut(s)	315, 723, 798
Alw26I	GTCTC	4 cut(s)	103, 118, 507, 576
Alw44I	GTGCAC	1 cut(s)	719
AoxI	GGCC	2 cut(s)	596, 691
ApaLI	GTGCAC	1 cut(s)	719
ApeKI	GCWGC	1 cut(s)	172
ApoI	RAATTY	1 cut(s)	238
AspA2I	CCTAGG	1 cut(s)	724
AspLEI	GCGC	1 cut(s)	764
AspS9I	GGNCC	1 cut(s)	421
AsuHPI	GGTGA	2 cut(s)	107, 566
AvaII	GGWCC	1 cut(s)	421
AvrII	CCTAGG	1 cut(s)	724
BaeGI	GKGCMC	1 cut(s)	723
BalI	TGGCCA	1 cut(s)	693
BanII	GRGCYC	1 cut(s)	315
BbsI	GAAGAC	1 cut(s)	384
Bbv12I	GWGCWC	3 cut(s)	315, 723, 798
BbvI	GCAGC	1 cut(s)	184
BccI	CCATC	3 cut(s)	32, 145, 880
BciT130I	CCWGG	2 cut(s)	227, 639
BclI	TGATCA	1 cut(s)	475
BcoDI	GTCTC	4 cut(s)	103, 118, 507, 576
BfaI	CTAG	1 cut(s)	725
BfmI	CTRYAG	1 cut(s)	143
BfrI	CTTAAG	1 cut(s)	442
BfuAI	ACCTGC	1 cut(s)	511
BglII	AGATCT	1 cut(s)	286
BisI	GCNGC	2 cut(s)	173, 599
BlnI	CCTAGG	1 cut(s)	724
BlsI	GCNGC	2 cut(s)	174, 600
Bme1390I	CCNGG	2 cut(s)	227, 639
Bme18I	GGWCC	1 cut(s)	421
BmgT120I	GGNCC	1 cut(s)	421
BmrFI	CCNGG	2 cut(s)	227, 639
BmrI	ACTGGG	1 cut(s)	641
BmsI	GCATC	4 cut(s)	190, 266, 373, 773
BmuI	ACTGGG	1 cut(s)	641
BpiI	GAAGAC	1 cut(s)	384
Bpu10I	CCTNAGC	1 cut(s)	629
BsaBI	GATNNNNATC	1 cut(s)	155
BsaHI	GRCGYC	1 cut(s)	357
BsaJI	CCNNGG	2 cut(s)	261, 724
BsaWI	WCCGGW	1 cut(s)	92
Bsc4I	CCNNNNNNNGG	1 cut(s)	559
Bse1I	ACTGG	3 cut(s)	423, 499, 647
Bse3DI	GCAATG	1 cut(s)	304
Bse8I	GATNNNNATC	1 cut(s)	155
BseBI	CCWGG	2 cut(s)	227, 639
BseDI	CCNNGG	2 cut(s)	261, 724
BseGI	GGATG	1 cut(s)	257
BseJI	GATNNNNATC	1 cut(s)	155
BseLI	CCNNNNNNNGG	1 cut(s)	559
BseMI	GCAATG	1 cut(s)	304
BseMII	CTCAG	4 cut(s)	518, 530, 605, 783
BseNI	ACTGG	3 cut(s)	423, 499, 647
BseRI	GAGGAG	1 cut(s)	20
BseSI	GKGCMC	1 cut(s)	723
BseXI	GCAGC	1 cut(s)	184
Bsh1236I	CGCG	1 cut(s)	762
BshFI	GGCC	2 cut(s)	598, 693
BsiHKAI	GWGCWC	3 cut(s)	315, 723, 798
BsiSI	CCGG	1 cut(s)	93
BslFI	GGGAC	1 cut(s)	368
BslI	CCNNNNNNNGG	1 cut(s)	559
BsmAI	GTCTC	4 cut(s)	103, 118, 507, 576
BsmBI	CGTCTC	1 cut(s)	118
BsmFI	GGGAC	1 cut(s)	368
BsmI	GAATGC	1 cut(s)	710
BsnI	GGCC	2 cut(s)	598, 693
Bsp1286I	GDGCHC	3 cut(s)	315, 723, 798
Bsp1407I	TGTACA	1 cut(s)	344
Bsp143I	GATC	2 cut(s)	286, 475
BspACI	CCGC	2 cut(s)	599, 760
BspANI	GGCC	2 cut(s)	598, 693
BspCNI	CTCAG	4 cut(s)	517, 529, 604, 784
BspFNI	CGCG	1 cut(s)	762
BspHI	TCATGA	1 cut(s)	105
BspMI	ACCTGC	1 cut(s)	511
BspTI	CTTAAG	1 cut(s)	442
BsrDI	GCAATG	1 cut(s)	304
BsrGI	TGTACA	1 cut(s)	344
BsrI	ACTGG	3 cut(s)	423, 499, 647
BssECI	CCNNGG	2 cut(s)	261, 724
BssMI	GATC	2 cut(s)	286, 475
BssNI	GRCGYC	1 cut(s)	357
BssT1I	CCWWGG	2 cut(s)	261, 724
Bst2UI	CCWGG	2 cut(s)	227, 639
Bst4CI	ACNGT	1 cut(s)	413
Bst6I	CTCTTC	1 cut(s)	327
BstACI	GRCGYC	1 cut(s)	357
BstAFI	CTTAAG	1 cut(s)	442
BstAPI	GCANNNNNTGC	1 cut(s)	707
BstAUI	TGTACA	1 cut(s)	344
BstDEI	CTNAG	6 cut(s)	113, 504, 516, 591, 629, 792
BstF5I	GGATG	1 cut(s)	257
BstFNI	CGCG	1 cut(s)	762
BstHHI	GCGC	1 cut(s)	764
BstKTI	GATC	2 cut(s)	289, 478
BstMAI	GTCTC	4 cut(s)	103, 118, 507, 576
BstMBI	GATC	2 cut(s)	286, 475
BstMWI	GCNNNNNNNGC	2 cut(s)	517, 707
BstNI	CCWGG	2 cut(s)	227, 639
BstNSI	RCATGY	1 cut(s)	784
BstSCI	CCNGG	2 cut(s)	225, 637
BstSFI	CTRYAG	1 cut(s)	143
BstSLI	GKGCMC	1 cut(s)	723
BstUI	CGCG	1 cut(s)	762
BstV1I	GCAGC	1 cut(s)	184
BstV2I	GAAGAC	1 cut(s)	384
BstX2I	RGATCY	1 cut(s)	286
BstYI	RGATCY	1 cut(s)	286
BsuRI	GGCC	2 cut(s)	598, 693
BtsCI	GGATG	1 cut(s)	257
BtsIMutI	CAGTG	2 cut(s)	409, 654
BveI	ACCTGC	1 cut(s)	511
CciI	TCATGA	1 cut(s)	105
CfoI	GCGC	1 cut(s)	764
Cfr13I	GGNCC	1 cut(s)	421
CseI	GACGC	1 cut(s)	135
Csp6I	GTAC	3 cut(s)	185, 345, 403
CviAII	CATG	5 cut(s)	106, 351, 473, 479, 781
CviQI	GTAC	3 cut(s)	185, 345, 403
DdeI	CTNAG	6 cut(s)	113, 504, 516, 591, 629, 792
DpnI	GATC	2 cut(s)	288, 477
DpnII	GATC	2 cut(s)	286, 475
DraIII	CACNNNGTG	2 cut(s)	413, 559
EaeI	YGGCCR	1 cut(s)	691
Eam1104I	CTCTTC	1 cut(s)	327
EarI	CTCTTC	1 cut(s)	327
Ecl136II	GAGCTC	1 cut(s)	313
Eco130I	CCWWGG	2 cut(s)	261, 724
Eco24I	GRGCYC	1 cut(s)	315
Eco32I	GATATC	1 cut(s)	618
Eco47I	GGWCC	1 cut(s)	421
Eco53kI	GAGCTC	1 cut(s)	313
Eco57I	CTGAAG	2 cut(s)	345, 837
EcoICRI	GAGCTC	1 cut(s)	313
EcoRII	CCWGG	2 cut(s)	225, 637
EcoRV	GATATC	1 cut(s)	618
EcoT14I	CCWWGG	2 cut(s)	261, 724
EcoT38I	GRGCYC	1 cut(s)	315
ErhI	CCWWGG	2 cut(s)	261, 724
Esp3I	CGTCTC	1 cut(s)	118
FaeI	CATG	5 cut(s)	109, 354, 476, 482, 784
FalI	AAGNNNNNCTT	2 cut(s)	276, 308
FaqI	GGGAC	1 cut(s)	368
FatI	CATG	5 cut(s)	105, 350, 472, 478, 780
FbaI	TGATCA	1 cut(s)	475
Fnu4HI	GCNGC	2 cut(s)	173, 599
FokI	GGATG	1 cut(s)	244
FriOI	GRGCYC	1 cut(s)	315
Fsp4HI	GCNGC	2 cut(s)	173, 599
FspBI	CTAG	1 cut(s)	725
GlaI	GCGC	1 cut(s)	763
GluI	GCNGC	2 cut(s)	173, 599
HaeIII	GGCC	2 cut(s)	598, 693
HapII	CCGG	1 cut(s)	93
HgaI	GACGC	1 cut(s)	135
HhaI	GCGC	1 cut(s)	764
Hin1I	GRCGYC	1 cut(s)	357
Hin1II	CATG	5 cut(s)	109, 354, 476, 482, 784
Hin6I	GCGC	1 cut(s)	762
HinP1I	GCGC	1 cut(s)	762
HincII	GTYRAC	1 cut(s)	870
HindII	GTYRAC	1 cut(s)	870
HinfI	GANTC	4 cut(s)	89, 211, 743, 890
HpaII	CCGG	1 cut(s)	93
HphI	GGTGA	2 cut(s)	107, 566
Hpy166II	GTNNAC	4 cut(s)	405, 416, 721, 870
Hpy188I	TCNGA	5 cut(s)	199, 507, 594, 622, 793
Hpy188III	TCNNGA	1 cut(s)	106
Hpy8I	GTNNAC	4 cut(s)	405, 416, 721, 870
HpyAV	CCTTC	1 cut(s)	201
HpyCH4III	ACNGT	1 cut(s)	413
HpyCH4IV	ACGT	4 cut(s)	217, 278, 357, 775
HpyCH4V	TGCA	5 cut(s)	482, 701, 710, 721, 772
HpyF10VI	GCNNNNNNNGC	2 cut(s)	517, 707
HpyF3I	CTNAG	6 cut(s)	113, 504, 516, 591, 629, 792
HpySE526I	ACGT	4 cut(s)	217, 278, 357, 775
Hsp92I	GRCGYC	1 cut(s)	357
Hsp92II	CATG	5 cut(s)	109, 354, 476, 482, 784
HspAI	GCGC	1 cut(s)	762
Ksp22I	TGATCA	1 cut(s)	475
Kzo9I	GATC	2 cut(s)	286, 475
LmnI	GCTCC	3 cut(s)	7, 320, 804
Lsp1109I	GCAGC	1 cut(s)	184
LweI	GCATC	4 cut(s)	190, 266, 373, 773
MaeI	CTAG	1 cut(s)	725
MaeII	ACGT	4 cut(s)	217, 278, 357, 775
MaeIII	GTNAC	1 cut(s)	562
MalI	GATC	2 cut(s)	288, 477
MboI	GATC	2 cut(s)	286, 475
MboII	GAAGA	8 cut(s)	55, 98, 281, 338, 341, 344, 389, 752
MfeI	CAATTG	1 cut(s)	702
MflI	RGATCY	1 cut(s)	286
MhlI	GDGCHC	3 cut(s)	315, 723, 798
MlsI	TGGCCA	1 cut(s)	693
MluCI	AATT	2 cut(s)	238, 702
MluNI	TGGCCA	1 cut(s)	693
MnlI	CCTC	4 cut(s)	328, 480, 588, 600
Mox20I	TGGCCA	1 cut(s)	693
MscI	TGGCCA	1 cut(s)	693
MseI	TTAA	4 cut(s)	234, 252, 443, 687
MslI	CAYNNNNRTG	1 cut(s)	477
Msp20I	TGGCCA	1 cut(s)	693
MspCI	CTTAAG	1 cut(s)	442
MspI	CCGG	1 cut(s)	93
MspR9I	CCNGG	2 cut(s)	227, 639
MunI	CAATTG	1 cut(s)	702
Mva1269I	GAATGC	1 cut(s)	710
MvaI	CCWGG	2 cut(s)	227, 639
MvnI	CGCG	1 cut(s)	762
MwoI	GCNNNNNNNGC	2 cut(s)	517, 707
NdeII	GATC	2 cut(s)	286, 475
NlaIII	CATG	5 cut(s)	109, 354, 476, 482, 784
NspI	RCATGY	1 cut(s)	784
PagI	TCATGA	1 cut(s)	105
PctI	GAATGC	1 cut(s)	710
PfeI	GAWTC	4 cut(s)	89, 211, 743, 890
PflMI	CCANNNNNTGG	1 cut(s)	559
PkrI	GCNGC	2 cut(s)	174, 600
Psp124BI	GAGCTC	1 cut(s)	315
Psp6I	CCWGG	2 cut(s)	225, 637
PspGI	CCWGG	2 cut(s)	225, 637
PspPI	GGNCC	1 cut(s)	421
PsuI	RGATCY	1 cut(s)	286
RsaI	GTAC	3 cut(s)	186, 346, 404
RsaNI	GTAC	3 cut(s)	185, 345, 403
RseI	CAYNNNNRTG	1 cut(s)	477
SacI	GAGCTC	1 cut(s)	315
SaqAI	TTAA	4 cut(s)	234, 252, 443, 687
SatI	GCNGC	2 cut(s)	173, 599
Sau3AI	GATC	2 cut(s)	286, 475
Sau96I	GGNCC	1 cut(s)	421
ScrFI	CCNGG	2 cut(s)	227, 639
SduI	GDGCHC	3 cut(s)	315, 723, 798
SfaNI	GCATC	4 cut(s)	190, 266, 373, 773
SfcI	CTRYAG	1 cut(s)	143
SinI	GGWCC	1 cut(s)	421
SmiMI	CAYNNNNRTG	1 cut(s)	477
SmlI	CTYRAG	1 cut(s)	442
SmoI	CTYRAG	1 cut(s)	442
Sse9I	AATT	2 cut(s)	238, 702
SsiI	CCGC	2 cut(s)	599, 760
SspMI	CTAG	1 cut(s)	725
SstI	GAGCTC	1 cut(s)	315
StyD4I	CCNGG	2 cut(s)	225, 637
StyI	CCWWGG	2 cut(s)	261, 724
TaaI	ACNGT	1 cut(s)	413
TaiI	ACGT	4 cut(s)	220, 281, 360, 778
TaqI	TCGA	1 cut(s)	309
TasI	AATT	2 cut(s)	238, 702
TatI	WGTACW	3 cut(s)	184, 344, 402
TauI	GCSGC	1 cut(s)	601
TfiI	GAWTC	4 cut(s)	89, 211, 743, 890
Tru1I	TTAA	4 cut(s)	234, 252, 443, 687
Tru9I	TTAA	4 cut(s)	234, 252, 443, 687
TscAI	CASTG	2 cut(s)	416, 654
TseI	GCWGC	1 cut(s)	172
TspDTI	ATGAA	1 cut(s)	770
TspGWI	ACGGA	1 cut(s)	817
TspRI	CASTG	2 cut(s)	416, 654
Van91I	CCANNNNNTGG	1 cut(s)	559
Vha464I	CTTAAG	1 cut(s)	442
VneI	GTGCAC	1 cut(s)	719
VpaK11BI	GGWCC	1 cut(s)	421
XapI	RAATTY	1 cut(s)	238
XceI	RCATGY	1 cut(s)	784
XcmI	CCANNNNNNNNNTGG	1 cut(s)	290
XmaJI	CCTAGG	1 cut(s)	724
XspI	CTAG	1 cut(s)	725
ZraI	GACGTC	1 cut(s)	358

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