Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1A

Orthogroup ID

OG0003037

Physical Location & Seq

Genomic Coordinates Forward (+)

61997271 .. 61999720

Gene Structure 2450 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1AG390800.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 978 bp

ATGGACAAAAACGAGTCCTCTGCTCCTCGCCGGAAGGGAAGGTTCAAGCCCAAAGCTCAACCCAGAAAGCCCAAACCCACTGTGCTGACAACTGAGGTTGAAGATGCTGAGAAAGAAGAAAGAGAAGCCAAGGCTCTGCTGCGAAAGTTCCAGGAGAAACAGGCTAGACGTGCGCCTAAAGCTGAGAAAAAATCTACTGTGCAAGTAGCATTTGGTCCAGGAGCTGCATCCTCAAGCTCCTTGAGGACATATGGGGTACCGAAGGTAGAAAATCTTGATCAAGGGAGCAGCTTAGGAGTGAAAGGCTCTGACAATGATCAAATTCTGTCACCTTCACCTTTGGCTACCAGTGGAGCTGGAACTGATGCACCTATGGATATTGATATTGCGGATGCATCAATTTCAAATGTCAAGAATCAATATATAGAGATTTGGGATTATGAGAACAGCAAATATCCTACTACTCTTCCTCTGAGGAAGCCATACTCTGGAGACCCAGACATTCTTAATCAGACTGAATTTGTTGAGGATGCTGCAAAGGAGTATGATGAGAGTACTATTAATTGTGCTTCAGAACTCGGGCTGCTGGAGCAAAATGCGAAAGAGAAGTTGCTCTTTGTTCAGTTGCCTCCTACTCTACCATTGGTCAAGCGACCTACTAGTGCAAAGGGGAAAGAGAAAGTCGGAAGCTCAGCACCATCAGAGAAGGTAGGTGCTGCAAAGAAGGGCGGTAGTTTGGAAGAGTTATCTGAGGGGTATATGGGGAAGATGCTGGTTTACAAGAGTGGAGCAGTCAAGTTCAAGCTAGGAGATGCACTGTATGATGTTTCACCCGGTTCAGATTGTATATTTGCTCAAGATGTTGCTGCAATCAACACTGCAGCGAGAAAGTGTTGTGTTCTTGGAGAGCTTGGCCAGCGAGTTGTTATAACTCCTGATGTGGATTCCCTACTAGACGCAACGATTGAGTTGGACTAA

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

325

Amino Acids

35.06

Weight (kDa)

5.67

Isoelectric Point (pI)

39.3

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpc4	PF05132	202 - 314	1.6e-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)	929
Acc65I	GGTACC	1 cut(s)	256
AccB1I	GGYRCC	1 cut(s)	256
AccB7I	CCANNNNNTGG	1 cut(s)	488
AciI	CCGC	2 cut(s)	389, 729
AcoI	YGGCCR	1 cut(s)	913
AcsI	RAATTY	2 cut(s)	321, 518
AcuI	CTGAAG	1 cut(s)	555
AfaI	GTAC	2 cut(s)	258, 556
AfiI	CCNNNNNNNGG	1 cut(s)	488
AgsI	TTSAA	4 cut(s)	46, 101, 405, 802
AhlI	ACTAGT	1 cut(s)	659
AjiI	CACGTC	1 cut(s)	170
AjnI	CCWGG	2 cut(s)	150, 217
AluBI	AGCT	9 cut(s)	56, 182, 224, 237, 291, 356, 690, 805, 910
AluI	AGCT	9 cut(s)	56, 182, 224, 237, 291, 356, 690, 805, 910
Alw26I	GTCTC	1 cut(s)	486
AlwNI	CAGNNNCTG	1 cut(s)	224
Ama87I	CYCGRG	1 cut(s)	578
AoxI	GGCC	1 cut(s)	913
ApeKI	GCWGC	8 cut(s)	139, 224, 288, 533, 583, 716, 866, 881
ApoI	RAATTY	2 cut(s)	321, 518
AseI	ATTAAT	1 cut(s)	561
Asp718I	GGTACC	1 cut(s)	256
AspLEI	GCGC	1 cut(s)	175
AspS9I	GGNCC	1 cut(s)	215
AsuC2I	CCSGG	1 cut(s)	834
AsuHPI	GGTGA	3 cut(s)	321, 327, 822
AvaI	CYCGRG	1 cut(s)	578
AvaII	GGWCC	1 cut(s)	215
BalI	TGGCCA	1 cut(s)	915
BanI	GGYRCC	1 cut(s)	256
BbvI	GCAGC	8 cut(s)	126, 211, 300, 520, 570, 703, 853, 893
BccI	CCATC	1 cut(s)	706
BcgI	CGANNNNNNTGC	1 cut(s)	36
BciT130I	CCWGG	2 cut(s)	152, 219
BclI	TGATCA	2 cut(s)	277, 316
BcnI	CCSGG	1 cut(s)	834
BcoDI	GTCTC	1 cut(s)	486
BcuI	ACTAGT	1 cut(s)	659
BfaI	CTAG	4 cut(s)	165, 660, 806, 953
BfmI	CTRYAG	1 cut(s)	879
BisI	GCNGC	8 cut(s)	140, 225, 289, 534, 584, 717, 867, 882
BlpI	GCTNAGC	1 cut(s)	691
BlsI	GCNGC	8 cut(s)	141, 226, 290, 535, 585, 718, 868, 883
BmcAI	AGTACT	1 cut(s)	556
Bme1390I	CCNGG	3 cut(s)	152, 219, 834
Bme18I	GGWCC	1 cut(s)	215
BmeT110I	CYCGRG	1 cut(s)	578
BmgBI	CACGTC	1 cut(s)	170
BmgT120I	GGNCC	1 cut(s)	215
BmiI	GGNNCC	1 cut(s)	258
BmrFI	CCNGG	3 cut(s)	152, 219, 834
BmsI	GCATC	8 cut(s)	94, 236, 355, 382, 404, 520, 759, 802
BpmI	CTGGAG	2 cut(s)	510, 608
Bpu10I	CCTNAGC	1 cut(s)	292
Bpu1102I	GCTNAGC	1 cut(s)	691
BpuEI	CTTGAG	3 cut(s)	217, 262, 840
BpuMI	CCSGG	1 cut(s)	834
BsaI	GGTCTC	1 cut(s)	486
BsaJI	CCNNGG	1 cut(s)	129
Bsc4I	CCNNNNNNNGG	1 cut(s)	488
Bse1I	ACTGG	1 cut(s)	348
BseBI	CCWGG	2 cut(s)	152, 219
BseDI	CCNNGG	1 cut(s)	129
BseGI	GGATG	3 cut(s)	227, 397, 535
BseLI	CCNNNNNNNGG	1 cut(s)	488
BseMII	CTCAG	6 cut(s)	84, 99, 174, 464, 705, 741
BseNI	ACTGG	1 cut(s)	348
BseRI	GAGGAG	1 cut(s)	15
BseXI	GCAGC	8 cut(s)	126, 211, 300, 520, 570, 703, 853, 893
BshFI	GGCC	1 cut(s)	915
BshNI	GGYRCC	1 cut(s)	256
BsiHKCI	CYCGRG	1 cut(s)	578
BsiSI	CCGG	2 cut(s)	31, 834
BslI	CCNNNNNNNGG	1 cut(s)	488
BsmAI	GTCTC	1 cut(s)	486
BsnI	GGCC	1 cut(s)	915
Bso31I	GGTCTC	1 cut(s)	486
BsoBI	CYCGRG	1 cut(s)	578
Bsp143I	GATC	2 cut(s)	277, 316
Bsp1720I	GCTNAGC	1 cut(s)	691
BspACI	CCGC	2 cut(s)	389, 729
BspANI	GGCC	1 cut(s)	915
BspCNI	CTCAG	6 cut(s)	85, 100, 175, 465, 704, 742
BspLI	GGNNCC	1 cut(s)	258
BspMAI	CTGCAG	1 cut(s)	883
BspT107I	GGYRCC	1 cut(s)	256
BspTNI	GGTCTC	1 cut(s)	486
BsrI	ACTGG	1 cut(s)	348
BssECI	CCNNGG	1 cut(s)	129
BssMI	GATC	2 cut(s)	277, 316
BssT1I	CCWWGG	1 cut(s)	129
Bst2UI	CCWGG	2 cut(s)	152, 219
Bst4CI	ACNGT	3 cut(s)	82, 199, 819
Bst6I	CTCTTC	2 cut(s)	471, 735
BstC8I	GCNNGC	1 cut(s)	917
BstDEI	CTNAG	7 cut(s)	93, 108, 183, 292, 473, 691, 750
BstF5I	GGATG	3 cut(s)	227, 397, 535
BstHHI	GCGC	1 cut(s)	175
BstKTI	GATC	2 cut(s)	280, 319
BstMAI	GTCTC	1 cut(s)	486
BstMBI	GATC	2 cut(s)	277, 316
BstMWI	GCNNNNNNNGC	4 cut(s)	170, 179, 589, 916
BstNI	CCWGG	2 cut(s)	152, 219
BstSCI	CCNGG	3 cut(s)	150, 217, 832
BstSFI	CTRYAG	1 cut(s)	879
BstV1I	GCAGC	8 cut(s)	126, 211, 300, 520, 570, 703, 853, 893
BsuRI	GGCC	1 cut(s)	915
BtrI	CACGTC	1 cut(s)	170
BtsCI	GGATG	3 cut(s)	227, 397, 535
BtsI	GCAGTG	1 cut(s)	876
BtsIMutI	CAGTG	4 cut(s)	78, 355, 815, 876
Cac8I	GCNNGC	1 cut(s)	917
CaiI	CAGNNNCTG	1 cut(s)	224
CfoI	GCGC	1 cut(s)	175
Cfr13I	GGNCC	1 cut(s)	215
CseI	GACGC	1 cut(s)	965
Csp6I	GTAC	2 cut(s)	257, 555
CviQI	GTAC	2 cut(s)	257, 555
DdeI	CTNAG	7 cut(s)	93, 108, 183, 292, 473, 691, 750
DpnI	GATC	2 cut(s)	279, 318
DpnII	GATC	2 cut(s)	277, 316
EaeI	YGGCCR	1 cut(s)	913
Eam1104I	CTCTTC	2 cut(s)	471, 735
EarI	CTCTTC	2 cut(s)	471, 735
Eco130I	CCWWGG	1 cut(s)	129
Eco31I	GGTCTC	1 cut(s)	486
Eco47I	GGWCC	1 cut(s)	215
Eco57I	CTGAAG	1 cut(s)	555
Eco88I	CYCGRG	1 cut(s)	578
EcoRII	CCWGG	2 cut(s)	150, 217
EcoT14I	CCWWGG	1 cut(s)	129
EcoT22I	ATGCAT	1 cut(s)	397
ErhI	CCWWGG	1 cut(s)	129
FalI	AAGNNNNNCTT	2 cut(s)	599, 631
FauNDI	CATATG	1 cut(s)	250
FbaI	TGATCA	2 cut(s)	277, 316
Fnu4HI	GCNGC	8 cut(s)	140, 225, 289, 534, 584, 717, 867, 882
FokI	GGATG	3 cut(s)	214, 404, 542
Fsp4HI	GCNGC	8 cut(s)	140, 225, 289, 534, 584, 717, 867, 882
FspBI	CTAG	4 cut(s)	165, 660, 806, 953
GlaI	GCGC	1 cut(s)	174
GluI	GCNGC	8 cut(s)	140, 225, 289, 534, 584, 717, 867, 882
GsuI	CTGGAG	2 cut(s)	510, 608
HaeIII	GGCC	1 cut(s)	915
HapII	CCGG	2 cut(s)	31, 834
HgaI	GACGC	1 cut(s)	965
HhaI	GCGC	1 cut(s)	175
Hin6I	GCGC	1 cut(s)	173
HinP1I	GCGC	1 cut(s)	173
HinfI	GANTC	3 cut(s)	14, 415, 944
HpaII	CCGG	2 cut(s)	31, 834
HphI	GGTGA	3 cut(s)	321, 327, 822
Hpy166II	GTNNAC	1 cut(s)	778
Hpy188I	TCNGA	8 cut(s)	310, 474, 513, 574, 686, 703, 751, 841
Hpy188III	TCNNGA	5 cut(s)	275, 412, 489, 857, 935
Hpy8I	GTNNAC	1 cut(s)	778
HpyAV	CCTTC	6 cut(s)	28, 33, 256, 342, 700, 718
HpyCH4III	ACNGT	3 cut(s)	82, 199, 819
HpyCH4IV	ACGT	1 cut(s)	169
HpyF10VI	GCNNNNNNNGC	4 cut(s)	170, 179, 589, 916
HpyF3I	CTNAG	7 cut(s)	93, 108, 183, 292, 473, 691, 750
HpySE526I	ACGT	1 cut(s)	169
HspAI	GCGC	1 cut(s)	173
KpnI	GGTACC	1 cut(s)	260
Ksp22I	TGATCA	2 cut(s)	277, 316
Kzo9I	GATC	2 cut(s)	277, 316
LmnI	GCTCC	7 cut(s)	28, 221, 242, 285, 353, 589, 788
Lsp1109I	GCAGC	8 cut(s)	126, 211, 300, 520, 570, 703, 853, 893
LweI	GCATC	8 cut(s)	94, 236, 355, 382, 404, 520, 759, 802
MaeI	CTAG	4 cut(s)	165, 660, 806, 953
MaeII	ACGT	1 cut(s)	169
MaeIII	GTNAC	1 cut(s)	327
MalI	GATC	2 cut(s)	279, 318
MboI	GATC	2 cut(s)	277, 316
MboII	GAAGA	5 cut(s)	113, 128, 458, 752, 778
MlsI	TGGCCA	1 cut(s)	915
MluCI	AATT	4 cut(s)	321, 399, 518, 562
MluNI	TGGCCA	1 cut(s)	915
MlyI	GAGTC	1 cut(s)	23
MmeI	TCCRAC	2 cut(s)	664, 951
Mox20I	TGGCCA	1 cut(s)	915
Mph1103I	ATGCAT	1 cut(s)	397
MscI	TGGCCA	1 cut(s)	915
MseI	TTAA	2 cut(s)	507, 561
Msp20I	TGGCCA	1 cut(s)	915
MspI	CCGG	2 cut(s)	31, 834
MspR9I	CCNGG	3 cut(s)	152, 219, 834
MvaI	CCWGG	2 cut(s)	152, 219
MwoI	GCNNNNNNNGC	4 cut(s)	170, 179, 589, 916
NciI	CCSGG	1 cut(s)	834
NdeI	CATATG	1 cut(s)	250
NdeII	GATC	2 cut(s)	277, 316
NlaIV	GGNNCC	1 cut(s)	258
NmuCI	GTSAC	1 cut(s)	327
NsiI	ATGCAT	1 cut(s)	397
PfeI	GAWTC	2 cut(s)	415, 944
PflMI	CCANNNNNTGG	1 cut(s)	488
PfoI	TCCNGGA	2 cut(s)	150, 217
PkrI	GCNGC	8 cut(s)	141, 226, 290, 535, 585, 718, 868, 883
PleI	GAGTC	1 cut(s)	22
PpsI	GAGTC	1 cut(s)	22
PshBI	ATTAAT	1 cut(s)	561
PsiI	TTATAA	1 cut(s)	929
Psp6I	CCWGG	2 cut(s)	150, 217
PspGI	CCWGG	2 cut(s)	150, 217
PspN4I	GGNNCC	1 cut(s)	258
PspPI	GGNCC	1 cut(s)	215
PstI	CTGCAG	1 cut(s)	883
PstNI	CAGNNNCTG	1 cut(s)	224
RsaI	GTAC	2 cut(s)	258, 556
RsaNI	GTAC	2 cut(s)	257, 555
SaqAI	TTAA	2 cut(s)	507, 561
SatI	GCNGC	8 cut(s)	140, 225, 289, 534, 584, 717, 867, 882
Sau3AI	GATC	2 cut(s)	277, 316
Sau96I	GGNCC	1 cut(s)	215
ScaI	AGTACT	1 cut(s)	556
SchI	GAGTC	1 cut(s)	23
ScrFI	CCNGG	3 cut(s)	152, 219, 834
SfaNI	GCATC	8 cut(s)	94, 236, 355, 382, 404, 520, 759, 802
SfcI	CTRYAG	1 cut(s)	879
SinI	GGWCC	1 cut(s)	215
SmlI	CTYRAG	3 cut(s)	232, 241, 855
SmoI	CTYRAG	3 cut(s)	232, 241, 855
SpeI	ACTAGT	1 cut(s)	659
Sse9I	AATT	4 cut(s)	321, 399, 518, 562
SsiI	CCGC	2 cut(s)	389, 729
SspMI	CTAG	4 cut(s)	165, 660, 806, 953
StyD4I	CCNGG	3 cut(s)	150, 217, 832
StyI	CCWWGG	1 cut(s)	129
TaaI	ACNGT	3 cut(s)	82, 199, 819
TaiI	ACGT	1 cut(s)	172
TasI	AATT	4 cut(s)	321, 399, 518, 562
TatI	WGTACW	1 cut(s)	554
TfiI	GAWTC	2 cut(s)	415, 944
Tru1I	TTAA	2 cut(s)	507, 561
Tru9I	TTAA	2 cut(s)	507, 561
TscAI	CASTG	4 cut(s)	85, 355, 822, 883
TseFI	GTSAC	1 cut(s)	327
TseI	GCWGC	8 cut(s)	139, 224, 288, 533, 583, 716, 866, 881
Tsp45I	GTSAC	1 cut(s)	327
TspRI	CASTG	4 cut(s)	85, 355, 822, 883
Van91I	CCANNNNNTGG	1 cut(s)	488
VpaK11BI	GGWCC	1 cut(s)	215
VspI	ATTAAT	1 cut(s)	561
XapI	RAATTY	2 cut(s)	321, 518
XspI	CTAG	4 cut(s)	165, 660, 806, 953
ZrmI	AGTACT	1 cut(s)	556
Zsp2I	ATGCAT	1 cut(s)	397

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