Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000004

Orthogroup ID

OG0003037

Physical Location & Seq

Genomic Coordinates Reverse (-)

5648679 .. 5651283

Gene Structure 2605 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_4G00283820.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1008 bp

ATGGACAAAAGCGAGTCCTCTGCTCCTCGCCGGAAGGGAAGGTTCAAGCCCAAAGCTCAACCCAGAAAGCCCAAACCCACTGTGCCCACAACTGAGGTTGAAGATGCTGAGAAAGAAGAAAGAGAAGCCAAGGCTCTGCTGCGAAAGTTCCAGATCATTGATTTATGTCCCTTGCATTTACAGGAGAAACAGGCGAGACGTGTGCCTAAAGCTGAGAAAAAATCTGCTGTGCAAGTGGCATTTGGTCCAGGAGCTCCATCCTCAAGCTCCTTGAGGACATATGGGGTGCCAAAGGTTGAAAATCTTGATCAGGGGAGCAGCTTTGGAGTGAAAGGCTCTGACAATGTTCAAATTCTGTCACCTTCACCTTTGGCTACCAGTGGAGCTGGAACTGATGCACCTATGGATATTGATATTGCGGATGCATCAATTTCGAATGTCAAGAATCAATATATAGAGATTTGGGATTATGAGAACAGCAAATATCCTACTACTCTTCCGCTGAGGAAGCCATACTCTGGAGACCCAGACATTCTTAATGAGAAGGAATTTGTTGAGGATGCTGCAAAGGAGTATGATGAGAGTACTATAAATTGTGCTTCAGAACTCGGGCTGCTGGAGCAAAATGCGAAAGAGAAGTTGCTCTTTGTTCAGCTGCCTCCTATTCTACCGTTGGTCAAGCGACCTACTAGTGCAAAGGGGAAAGAGAGAGTCGGAAGCTCAGCACCATCAGAGAAGGTAGGTGCTGCAAAGAAGGGTGGTAGTTTGGAAGAGTTATCTGAGGGGTATATGGGGAAGATGCTGGTTTACAAGAGTGGAGCAGTCAAGTTCAAGCTAGGAGATGCACTGTATGATGTTTCACCCGGTTCAGATTGTATATTTGCTCAAGATGTTGCTGCAATCAACACTGCAGCGAGAAAGTGTTGTGTTCTTGGAGAGCTTGGCCAGCGAGTTGTTATAACTCCTGATGTGGATTCCCTACTAGACGCAACGATTGAGTTGGACTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0001817 GO:0001819 GO:0002682 GO:0002684 GO:0003674 GO:0003682 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005666 GO:0005737 GO:0005829 GO:0008150 GO:0016604 GO:0016607 GO:0030880 GO:0031347 GO:0031349 GO:0031974 GO:0031981 GO:0032479 GO:0032481 GO:0032648 GO:0032728 GO:0032991 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044422 GO:0044424 GO:0044428 GO:0044444 GO:0044446 GO:0044451 GO:0044464 GO:0045088 GO:0045089 GO:0048518 GO:0048583 GO:0048584 GO:0050776 GO:0050778 GO:0050789 GO:0051239 GO:0051240 GO:0055029 GO:0061695 GO:0065007 GO:0070013 GO:0080134 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_Rpc4

Protein Analysis

335

Amino Acids

36.27

Weight (kDa)

5.83

Isoelectric Point (pI)

42.75

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpc4	PF05132	212 - 324	2.7e-25	RNA polymerase III RPC4

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: OG0003037)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G09380 AT5G09380 AT5G09380
fragaria_vesca	FvH4_1g08400 FvH4_1g08400 FvH4_7g27240 FvH4_7g27240
malus_domestica	MD01G1181300.v1.1 MD02G1088300.v1.1 MD07G1251400.v1.1
prunus_persica	Prupe.2G275200_v2.0.a1 Prupe.7G201300_v2.0.a1
pyrus_communis	pycom02g07090 pycom07g22410
rosa_chinensis	RchiOBHm_Chr1g0374021 RchiOBHm_Chr2g0094511 RchiOBHm_Chr3g0487921
rosa_laevigata	RLG00000016497 RLG00000026785
rosa_multiflora	Rmu_sc0004359.1_g000044 Rmu_sc0006924.1_g000006 Rmu_sc0009793.1_g000002
rosa_roxburghii	Rroxscaffold_2G00147110 Rroxscaffold_4G00283820
rosa_rugosa	Rorug01G0380300 Rorug02G0044300.1
rosa_samantha	Rh1AG390800 Rh1BG354900 Rh1CG368000 Rh1DG385600 Rh2AG092600 Rh2BG092800 Rh2CG095300 Rh2DG091700 Rh3AG285100 Rh6AG149200
rosa_wichuraiana	Rw1G034440 Rw6G012910

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	959
AccB1I	GGYRCC	1 cut(s)	286
AccB7I	CCANNNNNTGG	1 cut(s)	518
AciI	CCGC	2 cut(s)	419, 500
AcoI	YGGCCR	1 cut(s)	943
AcsI	RAATTY	2 cut(s)	351, 548
AcuI	CTGAAG	1 cut(s)	585
AfaI	GTAC	1 cut(s)	586
AfiI	CCNNNNNNNGG	1 cut(s)	518
AflIII	ACRYGT	1 cut(s)	199
AgsI	TTSAA	5 cut(s)	46, 101, 299, 350, 832
AhlI	ACTAGT	1 cut(s)	689
AjiI	CACGTC	1 cut(s)	200
AjnI	CCWGG	1 cut(s)	247
Alw21I	GWGCWC	1 cut(s)	256
Alw26I	GTCTC	2 cut(s)	190, 516
Ama87I	CYCGRG	1 cut(s)	608
AoxI	GGCC	1 cut(s)	943
ApeKI	GCWGC	8 cut(s)	139, 318, 563, 613, 655, 746, 896, 911
ApoI	RAATTY	2 cut(s)	351, 548
AspS9I	GGNCC	1 cut(s)	245
AsuC2I	CCSGG	1 cut(s)	864
AsuHPI	GGTGA	3 cut(s)	351, 357, 852
AsuII	TTCGAA	1 cut(s)	434
AvaI	CYCGRG	1 cut(s)	608
AvaII	GGWCC	1 cut(s)	245
BaeGI	GKGCMC	1 cut(s)	87
BalI	TGGCCA	1 cut(s)	945
BanI	GGYRCC	1 cut(s)	286
BanII	GRGCYC	1 cut(s)	256
Bbv12I	GWGCWC	1 cut(s)	256
BbvCI	CCTCAGC	1 cut(s)	503
BbvI	GCAGC	8 cut(s)	126, 330, 550, 600, 642, 733, 883, 923
BccI	CCATC	2 cut(s)	265, 736
BcgI	CGANNNNNNTGC	5 cut(s)	36, 184, 218, 414, 448
BciT130I	CCWGG	1 cut(s)	249
BclI	TGATCA	1 cut(s)	307
BcnI	CCSGG	1 cut(s)	864
BcoDI	GTCTC	2 cut(s)	190, 516
BcuI	ACTAGT	1 cut(s)	689
BfaI	CTAG	3 cut(s)	690, 836, 983
BfmI	CTRYAG	1 cut(s)	909
BisI	GCNGC	8 cut(s)	140, 319, 564, 614, 656, 747, 897, 912
BlpI	GCTNAGC	1 cut(s)	721
BlsI	GCNGC	8 cut(s)	141, 320, 565, 615, 657, 748, 898, 913
BmcAI	AGTACT	1 cut(s)	586
Bme1390I	CCNGG	2 cut(s)	249, 864
Bme18I	GGWCC	1 cut(s)	245
BmeT110I	CYCGRG	1 cut(s)	608
BmgBI	CACGTC	1 cut(s)	200
BmgT120I	GGNCC	1 cut(s)	245
BmiI	GGNNCC	1 cut(s)	288
BmrFI	CCNGG	2 cut(s)	249, 864
BmsI	GCATC	7 cut(s)	94, 385, 412, 434, 550, 789, 832
BpmI	CTGGAG	2 cut(s)	540, 638
Bpu10I	CCTNAGC	1 cut(s)	503
Bpu1102I	GCTNAGC	1 cut(s)	721
Bpu14I	TTCGAA	1 cut(s)	434
BpuEI	CTTGAG	3 cut(s)	247, 292, 870
BpuMI	CCSGG	1 cut(s)	864
BsaI	GGTCTC	1 cut(s)	516
BsaJI	CCNNGG	1 cut(s)	129
Bsc4I	CCNNNNNNNGG	1 cut(s)	518
Bse1I	ACTGG	1 cut(s)	378
BseBI	CCWGG	1 cut(s)	249
BseDI	CCNNGG	1 cut(s)	129
BseGI	GGATG	3 cut(s)	257, 427, 565
BseLI	CCNNNNNNNGG	1 cut(s)	518
BseMII	CTCAG	6 cut(s)	84, 99, 204, 494, 735, 771
BseNI	ACTGG	1 cut(s)	378
BseRI	GAGGAG	1 cut(s)	15
BseSI	GKGCMC	1 cut(s)	87
BseXI	GCAGC	8 cut(s)	126, 330, 550, 600, 642, 733, 883, 923
BshFI	GGCC	1 cut(s)	945
BshNI	GGYRCC	1 cut(s)	286
BsiHKAI	GWGCWC	1 cut(s)	256
BsiHKCI	CYCGRG	1 cut(s)	608
BsiSI	CCGG	2 cut(s)	31, 864
BslFI	GGGAC	1 cut(s)	153
BslI	CCNNNNNNNGG	1 cut(s)	518
BsmAI	GTCTC	2 cut(s)	190, 516
BsmBI	CGTCTC	1 cut(s)	190
BsmFI	GGGAC	1 cut(s)	153
BsnI	GGCC	1 cut(s)	945
Bso31I	GGTCTC	1 cut(s)	516
BsoBI	CYCGRG	1 cut(s)	608
Bsp119I	TTCGAA	1 cut(s)	434
Bsp1286I	GDGCHC	2 cut(s)	87, 256
Bsp143I	GATC	2 cut(s)	153, 307
Bsp1720I	GCTNAGC	1 cut(s)	721
BspACI	CCGC	2 cut(s)	419, 500
BspANI	GGCC	1 cut(s)	945
BspCNI	CTCAG	6 cut(s)	85, 100, 205, 495, 734, 772
BspLI	GGNNCC	1 cut(s)	288
BspMAI	CTGCAG	1 cut(s)	913
BspT104I	TTCGAA	1 cut(s)	434
BspT107I	GGYRCC	1 cut(s)	286
BspTNI	GGTCTC	1 cut(s)	516
BsrI	ACTGG	1 cut(s)	378
BssECI	CCNNGG	1 cut(s)	129
BssMI	GATC	2 cut(s)	153, 307
BssT1I	CCWWGG	1 cut(s)	129
Bst2UI	CCWGG	1 cut(s)	249
Bst4CI	ACNGT	3 cut(s)	82, 672, 849
Bst6I	CTCTTC	2 cut(s)	501, 765
BstBI	TTCGAA	1 cut(s)	434
BstC8I	GCNNGC	1 cut(s)	947
BstDEI	CTNAG	6 cut(s)	93, 108, 213, 503, 721, 780
BstF5I	GGATG	3 cut(s)	257, 427, 565
BstKTI	GATC	2 cut(s)	156, 310
BstMAI	GTCTC	2 cut(s)	190, 516
BstMBI	GATC	2 cut(s)	153, 307
BstMWI	GCNNNNNNNGC	3 cut(s)	508, 619, 946
BstNI	CCWGG	1 cut(s)	249
BstSCI	CCNGG	2 cut(s)	247, 862
BstSFI	CTRYAG	1 cut(s)	909
BstSLI	GKGCMC	1 cut(s)	87
BstV1I	GCAGC	8 cut(s)	126, 330, 550, 600, 642, 733, 883, 923
BsuRI	GGCC	1 cut(s)	945
BtrI	CACGTC	1 cut(s)	200
BtsCI	GGATG	3 cut(s)	257, 427, 565
BtsI	GCAGTG	1 cut(s)	906
BtsIMutI	CAGTG	4 cut(s)	78, 385, 845, 906
Cac8I	GCNNGC	1 cut(s)	947
Cfr13I	GGNCC	1 cut(s)	245
CseI	GACGC	1 cut(s)	995
Csp6I	GTAC	1 cut(s)	585
CviQI	GTAC	1 cut(s)	585
DdeI	CTNAG	6 cut(s)	93, 108, 213, 503, 721, 780
DpnI	GATC	2 cut(s)	155, 309
DpnII	GATC	2 cut(s)	153, 307
EaeI	YGGCCR	1 cut(s)	943
Eam1104I	CTCTTC	2 cut(s)	501, 765
EarI	CTCTTC	2 cut(s)	501, 765
Ecl136II	GAGCTC	1 cut(s)	254
Eco130I	CCWWGG	1 cut(s)	129
Eco24I	GRGCYC	1 cut(s)	256
Eco31I	GGTCTC	1 cut(s)	516
Eco47I	GGWCC	1 cut(s)	245
Eco53kI	GAGCTC	1 cut(s)	254
Eco57I	CTGAAG	1 cut(s)	585
Eco88I	CYCGRG	1 cut(s)	608
EcoICRI	GAGCTC	1 cut(s)	254
EcoRII	CCWGG	1 cut(s)	247
EcoT14I	CCWWGG	1 cut(s)	129
EcoT22I	ATGCAT	1 cut(s)	427
EcoT38I	GRGCYC	1 cut(s)	256
ErhI	CCWWGG	1 cut(s)	129
Esp3I	CGTCTC	1 cut(s)	190
FalI	AAGNNNNNCTT	2 cut(s)	629, 661
FaqI	GGGAC	1 cut(s)	153
FauNDI	CATATG	1 cut(s)	280
FbaI	TGATCA	1 cut(s)	307
Fnu4HI	GCNGC	8 cut(s)	140, 319, 564, 614, 656, 747, 897, 912
FokI	GGATG	3 cut(s)	244, 434, 572
FriOI	GRGCYC	1 cut(s)	256
Fsp4HI	GCNGC	8 cut(s)	140, 319, 564, 614, 656, 747, 897, 912
FspBI	CTAG	3 cut(s)	690, 836, 983
GluI	GCNGC	8 cut(s)	140, 319, 564, 614, 656, 747, 897, 912
GsuI	CTGGAG	2 cut(s)	540, 638
HaeIII	GGCC	1 cut(s)	945
HapII	CCGG	2 cut(s)	31, 864
HgaI	GACGC	1 cut(s)	995
HinfI	GANTC	4 cut(s)	14, 445, 711, 974
HpaII	CCGG	2 cut(s)	31, 864
HphI	GGTGA	3 cut(s)	351, 357, 852
Hpy166II	GTNNAC	1 cut(s)	808
Hpy188I	TCNGA	6 cut(s)	340, 604, 716, 733, 781, 871
Hpy188III	TCNNGA	6 cut(s)	151, 305, 442, 519, 887, 965
Hpy8I	GTNNAC	1 cut(s)	808
HpyAV	CCTTC	6 cut(s)	28, 33, 372, 538, 730, 748
HpyCH4III	ACNGT	3 cut(s)	82, 672, 849
HpyCH4IV	ACGT	1 cut(s)	199
HpyF10VI	GCNNNNNNNGC	3 cut(s)	508, 619, 946
HpyF3I	CTNAG	6 cut(s)	93, 108, 213, 503, 721, 780
HpySE526I	ACGT	1 cut(s)	199
Ksp22I	TGATCA	1 cut(s)	307
Kzo9I	GATC	2 cut(s)	153, 307
LmnI	GCTCC	8 cut(s)	28, 251, 259, 272, 315, 383, 619, 818
Lsp1109I	GCAGC	8 cut(s)	126, 330, 550, 600, 642, 733, 883, 923
LweI	GCATC	7 cut(s)	94, 385, 412, 434, 550, 789, 832
MaeI	CTAG	3 cut(s)	690, 836, 983
MaeII	ACGT	1 cut(s)	199
MaeIII	GTNAC	1 cut(s)	357
MalI	GATC	2 cut(s)	155, 309
MboI	GATC	2 cut(s)	153, 307
MboII	GAAGA	5 cut(s)	113, 128, 488, 782, 808
MhlI	GDGCHC	2 cut(s)	87, 256
MlsI	TGGCCA	1 cut(s)	945
MluCI	AATT	4 cut(s)	351, 429, 548, 592
MluNI	TGGCCA	1 cut(s)	945
MlyI	GAGTC	2 cut(s)	23, 720
MmeI	TCCRAC	2 cut(s)	694, 981
MnlI	CCTC	9 cut(s)	28, 36, 88, 267, 271, 498, 550, 669, 775
Mox20I	TGGCCA	1 cut(s)	945
Mph1103I	ATGCAT	1 cut(s)	427
MscI	TGGCCA	1 cut(s)	945
MseI	TTAA	1 cut(s)	537
Msp20I	TGGCCA	1 cut(s)	945
MspA1I	CMGCKG	2 cut(s)	502, 655
MspI	CCGG	2 cut(s)	31, 864
MspR9I	CCNGG	2 cut(s)	249, 864
MvaI	CCWGG	1 cut(s)	249
MwoI	GCNNNNNNNGC	3 cut(s)	508, 619, 946
NciI	CCSGG	1 cut(s)	864
NdeI	CATATG	1 cut(s)	280
NdeII	GATC	2 cut(s)	153, 307
NlaIV	GGNNCC	1 cut(s)	288
NmuCI	GTSAC	1 cut(s)	357
NsiI	ATGCAT	1 cut(s)	427
NspV	TTCGAA	1 cut(s)	434
PfeI	GAWTC	2 cut(s)	445, 974
PflMI	CCANNNNNTGG	1 cut(s)	518
PfoI	TCCNGGA	1 cut(s)	247
PkrI	GCNGC	8 cut(s)	141, 320, 565, 615, 657, 748, 898, 913
PleI	GAGTC	2 cut(s)	22, 719
PpsI	GAGTC	2 cut(s)	22, 719
PsiI	TTATAA	1 cut(s)	959
Psp124BI	GAGCTC	1 cut(s)	256
Psp6I	CCWGG	1 cut(s)	247
PspGI	CCWGG	1 cut(s)	247
PspN4I	GGNNCC	1 cut(s)	288
PspPI	GGNCC	1 cut(s)	245
PstI	CTGCAG	1 cut(s)	913
PvuII	CAGCTG	1 cut(s)	655
RsaI	GTAC	1 cut(s)	586
RsaNI	GTAC	1 cut(s)	585
SacI	GAGCTC	1 cut(s)	256
SaqAI	TTAA	1 cut(s)	537
SatI	GCNGC	8 cut(s)	140, 319, 564, 614, 656, 747, 897, 912
Sau3AI	GATC	2 cut(s)	153, 307
Sau96I	GGNCC	1 cut(s)	245
ScaI	AGTACT	1 cut(s)	586
SchI	GAGTC	2 cut(s)	23, 720
ScrFI	CCNGG	2 cut(s)	249, 864
SduI	GDGCHC	2 cut(s)	87, 256
SfaNI	GCATC	7 cut(s)	94, 385, 412, 434, 550, 789, 832
SfcI	CTRYAG	1 cut(s)	909
SfuI	TTCGAA	1 cut(s)	434
SinI	GGWCC	1 cut(s)	245
SmlI	CTYRAG	3 cut(s)	262, 271, 885
SmoI	CTYRAG	3 cut(s)	262, 271, 885
SpeI	ACTAGT	1 cut(s)	689
Sse9I	AATT	4 cut(s)	351, 429, 548, 592
SsiI	CCGC	2 cut(s)	419, 500
SspMI	CTAG	3 cut(s)	690, 836, 983
SstI	GAGCTC	1 cut(s)	256
StyD4I	CCNGG	2 cut(s)	247, 862
StyI	CCWWGG	1 cut(s)	129
TaaI	ACNGT	3 cut(s)	82, 672, 849
TaiI	ACGT	1 cut(s)	202
TaqI	TCGA	1 cut(s)	434
TasI	AATT	4 cut(s)	351, 429, 548, 592
TatI	WGTACW	1 cut(s)	584
TfiI	GAWTC	2 cut(s)	445, 974
Tru1I	TTAA	1 cut(s)	537
Tru9I	TTAA	1 cut(s)	537
TscAI	CASTG	4 cut(s)	85, 385, 852, 913
TseFI	GTSAC	1 cut(s)	357
TseI	GCWGC	8 cut(s)	139, 318, 563, 613, 655, 746, 896, 911
Tsp45I	GTSAC	1 cut(s)	357
TspRI	CASTG	4 cut(s)	85, 385, 852, 913
Van91I	CCANNNNNTGG	1 cut(s)	518
VpaK11BI	GGWCC	1 cut(s)	245
XapI	RAATTY	2 cut(s)	351, 548
XspI	CTAG	3 cut(s)	690, 836, 983
ZrmI	AGTACT	1 cut(s)	586
Zsp2I	ATGCAT	1 cut(s)	427

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