Basic Information

Type: gene

Biological Identity

Species

rosa_chinensis

Chromosome

Orthogroup ID

OG0003176

Physical Location & Seq

Genomic Coordinates Reverse (-)

15057494 .. 15058661

Gene Structure 1168 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

N/A

Sequence Viewer

CDS Protein Promoter (2k)

Length: 972 bp

ATGAACGTTACACTTGGAGTCCCTCGGATAAAGGAGATAATAGATGGAGCAAAAAATATCAAGACACCCATCATCACTACAGTACTTGAGTGTGATAATAATGCGATGATTGCACGCATGGTGGCAGGTCGGATTGGGAGCACAAATTTAGGGCAGGTGGCTAAGAGTATAGGGATCCTAATGACTCCAAGACAGGCATGCATAGTCATCAAGCTTGATATGGTCATGATTCGAGATGCACAGTTGTCTATAGATGTTGATGTTGTGAAAGAATCAATTTTAAAAGTTCCCAGAATCAAACTGAAGCATGAGAATATTCAAGTTCCAGATAACGAAACTTTGGAAGTGTATTCTCCGGACAAGGATAGACGCAGACTTTATTTTGAGCTCTACAGATTAAAGAGTATCCTCCCCAATGTTACAGTAAGGGGCATAACGACAGTTCAGCGTGTTGTCATTGATGAAAGTGATGTGAAAAAGGATAAAGAAGATGTTCAAGTTAAAGGTGCAGATGTTGTTGGTAAGAAGTACAGGCTGTTTGCTGAAGGCAAGGGACTTCTGGCAGTAATGAGCACCGAAGGAGTAGATGGTTGTAAAACCACAAGTAATGACATTATTGAAGTGCAGCAGACACTTGGGATTGAAGCTGCGAGAATTTCTATCATAGAGGAGATAAAGTATACTATGAAGCAACATGGAATGAACATAGATGATCGCCATATGATGCTTTTAGCGGATGCAATGACTTCTAGGGGTCAAGTTCTTGGAATGACGAGATTTGGCCTTCAAAAGATGGACAAAAGTGTTTTAATGGGTGCTTCATTTGAGCGAACAGATGATCATCTGTTTAATGCTTGTGTGAAGGGGGCAGTGGACAAAATTGAAGGAGTAAGTGAAAGCATAATCATGGGTATACCAATGCCGATAGGAACTGGAATGTTCAAAGTTAAACACATCCTCCCTACTACATGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0001817 GO:0001819 GO:0002376 GO:0003674 GO:0003824 GO:0003899 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005666 GO:0005737 GO:0005829 GO:0006139 GO:0006351 GO:0006725 GO:0006807 GO:0006950 GO:0006952 GO:0006955 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009987 GO:0010467 GO:0016070 GO:0016740 GO:0016772 GO:0016779 GO:0018130 GO:0019438 GO:0030880 GO:0031974 GO:0031981 GO:0032479 GO:0032481 GO:0032648 GO:0032728 GO:0032774 GO:0032991 GO:0034062 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044444 GO:0044446 GO:0044451 GO:0044464 GO:0045087 GO:0046483 GO:0048518 GO:0050789 GO:0050896 GO:0051239 GO:0051240 GO:0055029 GO:0061695 GO:0065007 GO:0070013 GO:0071704 GO:0090304 GO:0097659 GO:0097747 GO:0140098 GO:1901360 GO:1901362 GO:1901576 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

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

Pfam Domains

Protein Families

RNA_pol_Rpb1_1 RNA_pol_Rpb1_2 RNA_pol_Rpb1_3 RNA_pol_Rpb1_4 RNA_pol_Rpb1_5

Protein Analysis

323

Amino Acids

35.8

Weight (kDa)

8.73

Isoelectric Point (pI)

30.81

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb1_5	PF04998	2 - 269	8.5e-29	RNA polymerase Rpb1, domain 5

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

Tree File

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Orthologous Genes (Group: OG0003176)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G60040 AT5G60040
fragaria_vesca	FvH4_3g34290 FvH4_3g34290 FvH4_3g34290 FvH4_6g15631
malus_domestica	MD03G1106800.v1.1 MD09G1157000.v1.1
prunus_persica	Prupe.6G089600_v2.0.a1 Prupe.6G089600_v2.0.a1
pyrus_communis	pycom03g08620 pycom09g07570
rosa_chinensis	RchiOBHm_Chr3g0469301 RchiOBHm_Chr3g0469321 RchiOBHm_Chr5g0061861
rosa_laevigata	RLG00000024360 RLG00000035511
rosa_multiflora	Rmu_sc0004134.1_g000001 Rmu_sc0011641.1_g000013 Rmu_sc0011641.1_g000015 Rmu_sc0019271.1_g000001 Rmu_sc0022191.1_g000001
rosa_roxburghii	Rroxscaffold_1G00018870 Rroxscaffold_6G00411990 Rroxscaffold_6G00412000
rosa_rugosa	Rorug03G0100400 Rorug05G0344900 Rorug05G0345000
rosa_samantha	Rh3AG149800 Rh3BG173400 Rh3CG164500 Rh3DG202000 Rh5AG405500 Rh5BG418300 Rh5CG442800 Rh5DG432400
rosa_wichuraiana	Rw5G038070

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	145
Acc36I	ACCTGC	2 cut(s)	116, 145
AccI	GTMKAC	2 cut(s)	680, 913
AccIII	TCCGGA	1 cut(s)	355
AciI	CCGC	1 cut(s)	734
AclI	AACGTT	1 cut(s)	6
AclWI	GGATC	2 cut(s)	169, 182
AcsI	RAATTY	2 cut(s)	145, 654
AcuI	CTGAAG	2 cut(s)	323, 564
AfaI	GTAC	2 cut(s)	84, 530
AgsI	TTSAA	7 cut(s)	320, 497, 620, 644, 788, 884, 943
AluBI	AGCT	3 cut(s)	214, 388, 647
AluI	AGCT	3 cut(s)	214, 388, 647
Alw21I	GWGCWC	3 cut(s)	143, 390, 575
AlwI	GGATC	2 cut(s)	169, 182
Aor13HI	TCCGGA	1 cut(s)	355
AoxI	GGCC	1 cut(s)	781
ApeKI	GCWGC	2 cut(s)	625, 647
ApoI	RAATTY	2 cut(s)	145, 654
Asp700I	GAANNNNTTC	1 cut(s)	492
BamHI	GGATCC	1 cut(s)	174
BanII	GRGCYC	1 cut(s)	390
Bbv12I	GWGCWC	3 cut(s)	143, 390, 575
BbvI	GCAGC	2 cut(s)	634, 637
BccI	CCATC	4 cut(s)	38, 77, 581, 787
BciVI	GTATCC	1 cut(s)	416
BclI	TGATCA	1 cut(s)	838
BfaI	CTAG	1 cut(s)	750
BfmI	CTRYAG	3 cut(s)	78, 249, 391
BfuAI	ACCTGC	2 cut(s)	116, 145
BfuI	GTATCC	1 cut(s)	416
BisI	GCNGC	2 cut(s)	626, 648
BlsI	GCNGC	2 cut(s)	627, 649
BmcAI	AGTACT	1 cut(s)	84
BmiI	GGNNCC	1 cut(s)	176
BmsI	GCATC	3 cut(s)	226, 714, 727
BpuEI	CTTGAG	1 cut(s)	107
BsaBI	GATNNNNATC	1 cut(s)	840
BsaJI	CCNNGG	1 cut(s)	23
BsaWI	WCCGGW	1 cut(s)	355
BsaXI	ACNNNNNCTCC	4 cut(s)	662, 692, 942, 972
Bse1I	ACTGG	1 cut(s)	937
Bse3DI	GCAATG	1 cut(s)	747
Bse8I	GATNNNNATC	1 cut(s)	840
BseAI	TCCGGA	1 cut(s)	355
BseDI	CCNNGG	1 cut(s)	23
BseGI	GGATG	2 cut(s)	742, 954
BseJI	GATNNNNATC	1 cut(s)	840
BseMI	GCAATG	1 cut(s)	747
BseNI	ACTGG	1 cut(s)	937
BseRI	GAGGAG	1 cut(s)	683
BseXI	GCAGC	2 cut(s)	634, 637
BsgI	GTGCAG	2 cut(s)	528, 644
BshFI	GGCC	1 cut(s)	783
BsiHKAI	GWGCWC	3 cut(s)	143, 390, 575
BsiSI	CCGG	1 cut(s)	356
BslFI	GGGAC	2 cut(s)	5, 567
BsmFI	GGGAC	2 cut(s)	5, 567
BsnI	GGCC	1 cut(s)	783
Bsp1286I	GDGCHC	3 cut(s)	143, 390, 575
Bsp13I	TCCGGA	1 cut(s)	355
Bsp143I	GATC	3 cut(s)	174, 712, 838
BspACI	CCGC	1 cut(s)	734
BspANI	GGCC	1 cut(s)	783
BspEI	TCCGGA	1 cut(s)	355
BspHI	TCATGA	1 cut(s)	225
BspLI	GGNNCC	1 cut(s)	176
BspMI	ACCTGC	2 cut(s)	116, 145
BspPI	GGATC	2 cut(s)	169, 182
BsrDI	GCAATG	1 cut(s)	747
BsrI	ACTGG	1 cut(s)	937
BssECI	CCNNGG	1 cut(s)	23
BssMI	GATC	3 cut(s)	174, 712, 838
BssNAI	GTATAC	2 cut(s)	681, 914
Bst1107I	GTATAC	2 cut(s)	681, 914
Bst4CI	ACNGT	4 cut(s)	82, 243, 424, 442
BstC8I	GCNNGC	2 cut(s)	115, 199
BstDEI	CTNAG	1 cut(s)	162
BstF5I	GGATG	2 cut(s)	742, 954
BstKTI	GATC	3 cut(s)	177, 715, 841
BstMBI	GATC	3 cut(s)	174, 712, 838
BstMWI	GCNNNNNNNGC	1 cut(s)	110
BstNSI	RCATGY	1 cut(s)	201
BstSFI	CTRYAG	3 cut(s)	78, 249, 391
BstV1I	GCAGC	2 cut(s)	634, 637
BstX2I	RGATCY	1 cut(s)	174
BstYI	RGATCY	1 cut(s)	174
BstZ17I	GTATAC	2 cut(s)	681, 914
BsuI	GTATCC	1 cut(s)	416
BsuRI	GGCC	1 cut(s)	783
BtgZI	GCGATG	1 cut(s)	119
BtsCI	GGATG	2 cut(s)	742, 954
BtsI	GCAGTG	1 cut(s)	876
BtsIMutI	CAGTG	1 cut(s)	876
BveI	ACCTGC	2 cut(s)	116, 145
Cac8I	GCNNGC	2 cut(s)	115, 199
CciI	TCATGA	1 cut(s)	225
CseI	GACGC	1 cut(s)	378
Csp6I	GTAC	2 cut(s)	83, 529
CviAII	CATG	7 cut(s)	118, 198, 226, 308, 695, 907, 969
CviJI	RGCY	6 cut(s)	161, 214, 388, 535, 647, 783
CviKI_1	RGCY	6 cut(s)	161, 214, 388, 535, 647, 783
CviQI	GTAC	2 cut(s)	83, 529
DdeI	CTNAG	1 cut(s)	162
DpnI	GATC	3 cut(s)	176, 714, 840
DpnII	GATC	3 cut(s)	174, 712, 838
DraI	TTTAAA	1 cut(s)	282
Ecl136II	GAGCTC	1 cut(s)	388
Eco24I	GRGCYC	1 cut(s)	390
Eco53kI	GAGCTC	1 cut(s)	388
Eco57I	CTGAAG	2 cut(s)	323, 564
EcoICRI	GAGCTC	1 cut(s)	388
EcoT22I	ATGCAT	1 cut(s)	203
EcoT38I	GRGCYC	1 cut(s)	390
FaeI	CATG	7 cut(s)	121, 201, 229, 311, 698, 910, 972
FaqI	GGGAC	2 cut(s)	5, 567
FatI	CATG	7 cut(s)	117, 197, 225, 307, 694, 906, 968
FauNDI	CATATG	1 cut(s)	720
FbaI	TGATCA	1 cut(s)	838
FblI	GTMKAC	2 cut(s)	680, 913
Fnu4HI	GCNGC	2 cut(s)	626, 648
FokI	GGATG	2 cut(s)	749, 941
FriOI	GRGCYC	1 cut(s)	390
Fsp4HI	GCNGC	2 cut(s)	626, 648
FspBI	CTAG	1 cut(s)	750
GluI	GCNGC	2 cut(s)	626, 648
HaeIII	GGCC	1 cut(s)	783
HapII	CCGG	1 cut(s)	356
HgaI	GACGC	1 cut(s)	378
Hin1II	CATG	7 cut(s)	121, 201, 229, 311, 698, 910, 972
HindIII	AAGCTT	1 cut(s)	212
HinfI	GANTC	5 cut(s)	18, 184, 229, 272, 294
HpaII	CCGG	1 cut(s)	356
Hpy166II	GTNNAC	3 cut(s)	681, 874, 914
Hpy188I	TCNGA	2 cut(s)	27, 132
Hpy188III	TCNNGA	5 cut(s)	61, 226, 233, 326, 356
Hpy8I	GTNNAC	3 cut(s)	681, 874, 914
HpyAV	CCTTC	5 cut(s)	539, 572, 794, 856, 878
HpyCH4III	ACNGT	4 cut(s)	82, 243, 424, 442
HpyCH4IV	ACGT	1 cut(s)	6
HpyCH4V	TGCA	6 cut(s)	113, 201, 239, 509, 625, 740
HpyF10VI	GCNNNNNNNGC	1 cut(s)	110
HpyF3I	CTNAG	1 cut(s)	162
HpySE526I	ACGT	1 cut(s)	6
Hsp92II	CATG	7 cut(s)	121, 201, 229, 311, 698, 910, 972
Kpn2I	TCCGGA	1 cut(s)	355
Ksp22I	TGATCA	1 cut(s)	838
Kzo9I	GATC	3 cut(s)	174, 712, 838
LmnI	GCTCC	2 cut(s)	47, 138
LpnPI	CCDG	9 cut(s)	111, 140, 179, 304, 339, 369, 517, 545, 918
Lsp1109I	GCAGC	2 cut(s)	634, 637
LweI	GCATC	3 cut(s)	226, 714, 727
MaeI	CTAG	1 cut(s)	750
MaeII	ACGT	1 cut(s)	6
MaeIII	GTNAC	2 cut(s)	7, 418
MalI	GATC	3 cut(s)	176, 714, 840
MboI	GATC	3 cut(s)	174, 712, 838
MboII	GAAGA	1 cut(s)	500
MflI	RGATCY	1 cut(s)	174
MhlI	GDGCHC	3 cut(s)	143, 390, 575
MluCI	AATT	4 cut(s)	145, 276, 654, 879
MlyI	GAGTC	2 cut(s)	27, 178
MmeI	TCCRAC	1 cut(s)	110
MnlI	CCTC	4 cut(s)	33, 419, 661, 968
Mph1103I	ATGCAT	1 cut(s)	203
MroI	TCCGGA	1 cut(s)	355
MroXI	GAANNNNTTC	1 cut(s)	492
MseI	TTAA	6 cut(s)	281, 398, 501, 809, 849, 948
MslI	CAYNNNNRTG	1 cut(s)	905
MspI	CCGG	1 cut(s)	356
MwoI	GCNNNNNNNGC	1 cut(s)	110
NdeI	CATATG	1 cut(s)	720
NdeII	GATC	3 cut(s)	174, 712, 838
NlaIII	CATG	7 cut(s)	121, 201, 229, 311, 698, 910, 972
NlaIV	GGNNCC	1 cut(s)	176
NsiI	ATGCAT	1 cut(s)	203
NspI	RCATGY	1 cut(s)	201
PaeI	GCATGC	1 cut(s)	201
PagI	TCATGA	1 cut(s)	225
PaqCI	CACCTGC	1 cut(s)	145
PdmI	GAANNNNTTC	1 cut(s)	492
PfeI	GAWTC	3 cut(s)	229, 272, 294
PkrI	GCNGC	2 cut(s)	627, 649
PleI	GAGTC	2 cut(s)	26, 178
PpsI	GAGTC	2 cut(s)	26, 178
Psp124BI	GAGCTC	1 cut(s)	390
Psp1406I	AACGTT	1 cut(s)	6
PspN4I	GGNNCC	1 cut(s)	176
PsuI	RGATCY	1 cut(s)	174
RsaI	GTAC	2 cut(s)	84, 530
RsaNI	GTAC	2 cut(s)	83, 529
RseI	CAYNNNNRTG	1 cut(s)	905
SacI	GAGCTC	1 cut(s)	390
SaqAI	TTAA	6 cut(s)	281, 398, 501, 809, 849, 948
SatI	GCNGC	2 cut(s)	626, 648
Sau3AI	GATC	3 cut(s)	174, 712, 838
ScaI	AGTACT	1 cut(s)	84
SchI	GAGTC	2 cut(s)	27, 178
SduI	GDGCHC	3 cut(s)	143, 390, 575
SetI	ASST	7 cut(s)	9, 130, 159, 216, 390, 508, 649
SfaNI	GCATC	3 cut(s)	226, 714, 727
SfcI	CTRYAG	3 cut(s)	78, 249, 391
SmiMI	CAYNNNNRTG	1 cut(s)	905
SmlI	CTYRAG	1 cut(s)	86
SmoI	CTYRAG	1 cut(s)	86
SphI	GCATGC	1 cut(s)	201
Sse9I	AATT	4 cut(s)	145, 276, 654, 879
SsiI	CCGC	1 cut(s)	734
SspI	AATATT	1 cut(s)	316
SspMI	CTAG	1 cut(s)	750
SstI	GAGCTC	1 cut(s)	390
TaaI	ACNGT	4 cut(s)	82, 243, 424, 442
TaiI	ACGT	1 cut(s)	9
TaqI	TCGA	1 cut(s)	232
TasI	AATT	4 cut(s)	145, 276, 654, 879
TatI	WGTACW	2 cut(s)	82, 528
TfiI	GAWTC	3 cut(s)	229, 272, 294
Tru1I	TTAA	6 cut(s)	281, 398, 501, 809, 849, 948
Tru9I	TTAA	6 cut(s)	281, 398, 501, 809, 849, 948
TscAI	CASTG	1 cut(s)	876
TseI	GCWGC	2 cut(s)	625, 647
TspDTI	ATGAA	5 cut(s)	17, 477, 701, 716, 810
TspRI	CASTG	1 cut(s)	876
XapI	RAATTY	2 cut(s)	145, 654
XceI	RCATGY	1 cut(s)	201
XmiI	GTMKAC	2 cut(s)	680, 913
XmnI	GAANNNNTTC	1 cut(s)	492
XspI	CTAG	1 cut(s)	750
ZrmI	AGTACT	1 cut(s)	84
Zsp2I	ATGCAT	1 cut(s)	203

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