Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000002

Orthogroup ID

OG0003670

Physical Location & Seq

Genomic Coordinates Forward (+)

23228245 .. 23231597

Gene Structure 3353 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_2G00101230.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1233 bp

ATGGATTCGGACACAGAAGAAACCAGGTCCCAAGTGACCGCAACCAAGGCAGAGCCATCAAAGCCATCGCGCAAGCACAAGAAGAGGAAGAAACTCGCAGCAGAAGCCAACCCAGAGAATCCCAAATCAGTGCAAGCCACCATCAAGGTCATCCCGGGAAACCCAGAGAGAATCCCACCTCTGGTGGGCTATTTCCCATCTGGGTTCGACCCGACCCAGAACCCAGACCCGGATTCGACCAAAGTTGGGGTCTTTAGGCACAAGGAGAGAGGTGGGACTAGGCTTCAGGTTGTGGTGACCCCAAATAAGGAGGCTAAGGTTGATTTTGTTGGGACTAGCTATGCTGGTGAGGCTCAGGCTGGGGAGCTCTGCTCTTATGGACTTGGGATTCTTGATAAGGACACCCAGACTTTGAAGATTGTGCCTATTGCTAGCAACAAGATATTTAGATTGGAGCCAAAAATTCAAGGCCTTCACTTCTCTGGTAAGGAGCCTGCAAGTTCCGCGATGGCAGAACTTTCTGCACATGAGAAGGCAGAAAAACGTATAGACCTTCATAATCGTTATGGAACAAAGAAGTCAATACGGCAGAATAAAAAAATGCAGACCTTGAAGCAAGAAGATGATCCGGATTCTCAAAATGATATGGATGCAATCAAACAAGGTATGACAAACAGGGAGGATACTGAAGCTTCTGAAGGCCATACAGACCGCAATACCCCACCATTTAATGCTTCTGCCATCACTCCCCAGGAGGCTTATCCACTGGATAAAATCATCACCACAGGGAGTGGAAATTCCTCCAAGATATTAATAAGCTTTTGGAAGGATGAAGACAAGAAGTATAAGCTATCTTGCATTTTCTCATATATTACGCATCTTATAAAGTTCAAAGATCTCCACTCCATGGATGGGTTTTCCTCGGCAAAGGCCCACAGATTCCCAGGCATTATAAGGGATAAATTTTCAAGCATGTTTGATGCAGTGTCGAAGAGGCTATCAACTGAGAAAAGTAATCTTCTCATTAGTTATGTCTTGGTGCTCACTCTTTTTGCGGATGAATTCCAAACAAGTATGACAGACATAGCGAAGGATCTGAGAATGGGGACTGCAACTTTGAGGACGCATTATGAGAAGTTGGGTTGCAAGGTGTCTAAGAAGAATGGCGTATCAACGGTTACCCTTCCTGTCCCCCTCCAATTTCCAACAGTGAGGCGCAAGCGACGCAATTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0003674 GO:0003824 GO:0003899 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005730 GO:0005736 GO:0006139 GO:0006351 GO:0006360 GO:0006725 GO:0006807 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:0032774 GO:0032991 GO:0034062 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044452 GO:0044464 GO:0046483 GO:0055029 GO:0061695 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 map00230 map00240 map01100 map03020

Pfam Domains

Protein Families

RNA_pol_I_A49

Protein Analysis

410

Amino Acids

45.73

Weight (kDa)

9.5

Isoelectric Point (pI)

34.39

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_I_A49	PF06870	77 - 263	1.7e-20	A49-like RNA polymerase I associated factor
RNA_pol_I_A49	PF06870	272 - 402	9e-20	A49-like RNA polymerase I associated factor

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: OG0003670)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G13940
fragaria_vesca	FvH4_2g14600 FvH4_2g14600 FvH4_2g14600 FvH4_6g34180 FvH4_6g47280
malus_domestica	MD09G1187900.v1.1 MD17G1172300.v1.1
prunus_persica	Prupe.3G044800_v2.0.a1
pyrus_communis	pycom09g10420 pycom09g10430 pycom17g16990 pycom17g17000
rosa_chinensis	RchiOBHm_Chr2g0144531 RchiOBHm_Chr2g0166351
rosa_laevigata	RLG00000020086 RLG00000021613
rosa_multiflora	Rmu_sc0005789.1_g000005 Rmu_sc0007974.1_g000004 Rmu_sc0029020.1_g000001 Rmu_sc0029020.1_g000002
rosa_roxburghii	Rroxscaffold_2G00084950 Rroxscaffold_2G00101230
rosa_rugosa	Rorug02G0387600 Rorug02G0522400
rosa_samantha	Rh2AG439600 Rh2AG588500 Rh2BG449700 Rh2BG600500 Rh2CG426600 Rh2CG571300 Rh2DG459600 Rh2DG610700
rosa_wichuraiana	Rw2G035960 Rw2G049040

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	2 cut(s)	884, 953
AccB7I	CCANNNNNTGG	1 cut(s)	907
AccII	CGCG	2 cut(s)	70, 506
AccIII	TCCGGA	1 cut(s)	628
AciI	CCGC	4 cut(s)	39, 504, 712, 1055
AclWI	GGATC	2 cut(s)	620, 1101
AcsI	RAATTY	4 cut(s)	462, 796, 962, 1061
AcuI	CTGAAG	3 cut(s)	269, 708, 717
AfiI	CCNNNNNNNGG	7 cut(s)	181, 185, 229, 246, 307, 907, 912
AgsI	TTSAA	5 cut(s)	415, 467, 613, 892, 969
AjnI	CCWGG	3 cut(s)	23, 750, 943
AluBI	AGCT	5 cut(s)	339, 367, 692, 819, 850
AluI	AGCT	5 cut(s)	339, 367, 692, 819, 850
Alw21I	GWGCWC	2 cut(s)	369, 1044
AlwI	GGATC	2 cut(s)	620, 1101
Ama87I	CYCGRG	1 cut(s)	154
Aor13HI	TCCGGA	1 cut(s)	628
AoxI	GGCC	3 cut(s)	469, 700, 930
ApeKI	GCWGC	1 cut(s)	98
ApoI	RAATTY	4 cut(s)	462, 796, 962, 1061
ArsI	GACNNNNNNTTYG	4 cut(s)	234, 266, 1099, 1131
AseI	ATTAAT	1 cut(s)	812
AspLEI	GCGC	2 cut(s)	72, 1218
AspS9I	GGNCC	2 cut(s)	27, 931
AsuC2I	CCSGG	3 cut(s)	155, 156, 230
AsuHPI	GGTGA	3 cut(s)	307, 359, 772
AsuNHI	GCTAGC	1 cut(s)	431
AvaI	CYCGRG	1 cut(s)	154
AvaII	GGWCC	1 cut(s)	27
BanII	GRGCYC	1 cut(s)	369
BbsI	GAAGAC	1 cut(s)	840
Bbv12I	GWGCWC	2 cut(s)	369, 1044
BbvI	GCAGC	1 cut(s)	110
BccI	CCATC	7 cut(s)	64, 73, 149, 205, 502, 749, 905
BceAI	ACGGC	1 cut(s)	602
BciT130I	CCWGG	3 cut(s)	25, 752, 945
BciVI	GTATCC	1 cut(s)	676
BcnI	CCSGG	3 cut(s)	155, 156, 230
BfaI	CTAG	3 cut(s)	279, 336, 432
BfuI	GTATCC	1 cut(s)	676
BglII	AGATCT	1 cut(s)	895
BisI	GCNGC	1 cut(s)	99
BlsI	GCNGC	1 cut(s)	100
Bme1390I	CCNGG	6 cut(s)	25, 155, 156, 230, 752, 945
Bme18I	GGWCC	1 cut(s)	27
BmeT110I	CYCGRG	1 cut(s)	154
BmgT120I	GGNCC	2 cut(s)	27, 931
BmiI	GGNNCC	3 cut(s)	29, 456, 492
BmrFI	CCNGG	6 cut(s)	25, 155, 156, 230, 752, 945
BmsI	GCATC	3 cut(s)	640, 886, 970
BmtI	GCTAGC	1 cut(s)	435
BpiI	GAAGAC	1 cut(s)	840
BplI	GAGNNNNNCTC	2 cut(s)	356, 388
Bpu10I	CCTNAGC	2 cut(s)	315, 354
BpuMI	CCSGG	3 cut(s)	155, 156, 230
BsaJI	CCNNGG	6 cut(s)	45, 154, 750, 906, 921, 943
BsaWI	WCCGGW	1 cut(s)	628
Bsc4I	CCNNNNNNNGG	7 cut(s)	181, 185, 229, 246, 307, 907, 912
Bse1I	ACTGG	1 cut(s)	771
BseAI	TCCGGA	1 cut(s)	628
BseBI	CCWGG	3 cut(s)	25, 752, 945
BseDI	CCNNGG	6 cut(s)	45, 154, 750, 906, 921, 943
BseGI	GGATG	5 cut(s)	150, 655, 835, 916, 1063
BseLI	CCNNNNNNNGG	7 cut(s)	181, 185, 229, 246, 307, 907, 912
BseMII	CTCAG	3 cut(s)	368, 996, 1088
BseNI	ACTGG	1 cut(s)	771
BseXI	GCAGC	1 cut(s)	110
BseYI	CCCAGC	1 cut(s)	359
BsgI	GTGCAG	1 cut(s)	507
Bsh1236I	CGCG	2 cut(s)	70, 506
BshFI	GGCC	3 cut(s)	471, 702, 932
BsiHKAI	GWGCWC	2 cut(s)	369, 1044
BsiHKCI	CYCGRG	1 cut(s)	154
BsiSI	CCGG	3 cut(s)	155, 230, 629
BslFI	GGGAC	5 cut(s)	13, 289, 346, 1120, 1175
BslI	CCNNNNNNNGG	7 cut(s)	181, 185, 229, 246, 307, 907, 912
BsmFI	GGGAC	5 cut(s)	13, 289, 346, 1120, 1175
BsnI	GGCC	3 cut(s)	471, 702, 932
BsoBI	CYCGRG	1 cut(s)	154
Bsp1286I	GDGCHC	2 cut(s)	369, 1044
Bsp13I	TCCGGA	1 cut(s)	628
Bsp143I	GATC	3 cut(s)	625, 895, 1093
Bsp19I	CCATGG	1 cut(s)	906
BspACI	CCGC	4 cut(s)	39, 504, 712, 1055
BspANI	GGCC	3 cut(s)	471, 702, 932
BspCNI	CTCAG	3 cut(s)	367, 997, 1089
BspEI	TCCGGA	1 cut(s)	628
BspFNI	CGCG	2 cut(s)	70, 506
BspLI	GGNNCC	3 cut(s)	29, 456, 492
BspOI	GCTAGC	1 cut(s)	435
BspPI	GGATC	2 cut(s)	620, 1101
BsrI	ACTGG	1 cut(s)	771
BssECI	CCNNGG	6 cut(s)	45, 154, 750, 906, 921, 943
BssMI	GATC	3 cut(s)	625, 895, 1093
BssT1I	CCWWGG	2 cut(s)	45, 906
Bst2UI	CCWGG	3 cut(s)	25, 752, 945
Bst4CI	ACNGT	2 cut(s)	1177, 1210
Bst6I	CTCTTC	2 cut(s)	77, 986
BstC8I	GCNNGC	5 cut(s)	74, 135, 433, 495, 1220
BstDEI	CTNAG	5 cut(s)	315, 354, 1005, 1097, 1155
BstDSI	CCRYGG	1 cut(s)	906
BstEII	GGTNACC	2 cut(s)	295, 1177
BstF5I	GGATG	5 cut(s)	150, 655, 835, 916, 1063
BstFNI	CGCG	2 cut(s)	70, 506
BstHHI	GCGC	2 cut(s)	72, 1218
BstKTI	GATC	3 cut(s)	628, 898, 1096
BstMBI	GATC	3 cut(s)	625, 895, 1093
BstMWI	GCNNNNNNNGC	6 cut(s)	47, 61, 104, 350, 503, 1224
BstNI	CCWGG	3 cut(s)	25, 752, 945
BstNSI	RCATGY	1 cut(s)	976
BstPI	GGTNACC	2 cut(s)	295, 1177
BstSCI	CCNGG	6 cut(s)	23, 153, 154, 228, 750, 943
BstUI	CGCG	2 cut(s)	70, 506
BstV1I	GCAGC	1 cut(s)	110
BstV2I	GAAGAC	1 cut(s)	840
BstX2I	RGATCY	2 cut(s)	895, 1093
BstYI	RGATCY	2 cut(s)	895, 1093
BsuI	GTATCC	1 cut(s)	676
BsuRI	GGCC	3 cut(s)	471, 702, 932
BtgI	CCRYGG	1 cut(s)	906
BtgZI	GCGATG	2 cut(s)	51, 521
BtsCI	GGATG	5 cut(s)	150, 655, 835, 916, 1063
BtsI	GCAGTG	1 cut(s)	990
BtsIMutI	CAGTG	4 cut(s)	135, 764, 990, 1215
Cac8I	GCNNGC	5 cut(s)	74, 135, 433, 495, 1220
CfoI	GCGC	2 cut(s)	72, 1218
Cfr13I	GGNCC	2 cut(s)	27, 931
Cfr9I	CCCGGG	1 cut(s)	154
CseI	GACGC	1 cut(s)	1132
CsiI	ACCWGGT	1 cut(s)	23
CviAII	CATG	3 cut(s)	527, 907, 973
DdeI	CTNAG	5 cut(s)	315, 354, 1005, 1097, 1155
DpnI	GATC	3 cut(s)	627, 897, 1095
DpnII	GATC	3 cut(s)	625, 895, 1093
Eam1104I	CTCTTC	2 cut(s)	77, 986
EarI	CTCTTC	2 cut(s)	77, 986
Ecl136II	GAGCTC	1 cut(s)	367
Eco130I	CCWWGG	2 cut(s)	45, 906
Eco147I	AGGCCT	1 cut(s)	471
Eco24I	GRGCYC	1 cut(s)	369
Eco47I	GGWCC	1 cut(s)	27
Eco53kI	GAGCTC	1 cut(s)	367
Eco57I	CTGAAG	3 cut(s)	269, 708, 717
Eco88I	CYCGRG	1 cut(s)	154
Eco91I	GGTNACC	2 cut(s)	295, 1177
EcoICRI	GAGCTC	1 cut(s)	367
EcoO109I	RGGNCCY	1 cut(s)	27
EcoO65I	GGTNACC	2 cut(s)	295, 1177
EcoRI	GAATTC	1 cut(s)	1061
EcoRII	CCWGG	3 cut(s)	23, 750, 943
EcoT14I	CCWWGG	2 cut(s)	45, 906
EcoT38I	GRGCYC	1 cut(s)	369
ErhI	CCWWGG	2 cut(s)	45, 906
FaeI	CATG	3 cut(s)	530, 910, 976
FaqI	GGGAC	5 cut(s)	13, 289, 346, 1120, 1175
FatI	CATG	3 cut(s)	526, 906, 972
Fnu4HI	GCNGC	1 cut(s)	99
FokI	GGATG	5 cut(s)	137, 662, 842, 923, 1070
FriOI	GRGCYC	1 cut(s)	369
Fsp4HI	GCNGC	1 cut(s)	99
FspBI	CTAG	3 cut(s)	279, 336, 432
GlaI	GCGC	2 cut(s)	71, 1217
GluI	GCNGC	1 cut(s)	99
GsaI	CCCAGC	1 cut(s)	363
HaeIII	GGCC	3 cut(s)	471, 702, 932
HapII	CCGG	3 cut(s)	155, 230, 629
HgaI	GACGC	1 cut(s)	1132
HhaI	GCGC	2 cut(s)	72, 1218
Hin1II	CATG	3 cut(s)	530, 910, 976
Hin6I	GCGC	2 cut(s)	70, 1216
HinP1I	GCGC	2 cut(s)	70, 1216
HindIII	AAGCTT	2 cut(s)	690, 817
HinfI	GANTC	7 cut(s)	5, 118, 171, 233, 388, 632, 939
HpaII	CCGG	3 cut(s)	155, 230, 629
HphI	GGTGA	3 cut(s)	307, 359, 772
Hpy188I	TCNGA	3 cut(s)	10, 697, 1098
Hpy188III	TCNNGA	2 cut(s)	392, 629
Hpy99I	CGWCG	1 cut(s)	1227
HpyAV	CCTTC	7 cut(s)	482, 526, 563, 692, 820, 1084, 1193
HpyCH4III	ACNGT	2 cut(s)	1177, 1210
HpyCH4IV	ACGT	1 cut(s)	544
HpyCH4V	TGCA	9 cut(s)	133, 497, 524, 604, 653, 858, 983, 1112, 1146
HpyF10VI	GCNNNNNNNGC	6 cut(s)	47, 61, 104, 350, 503, 1224
HpyF3I	CTNAG	5 cut(s)	315, 354, 1005, 1097, 1155
HpySE526I	ACGT	1 cut(s)	544
Hsp92II	CATG	3 cut(s)	530, 910, 976
HspAI	GCGC	2 cut(s)	70, 1216
Kpn2I	TCCGGA	1 cut(s)	628
Kzo9I	GATC	3 cut(s)	625, 895, 1093
LmnI	GCTCC	3 cut(s)	364, 454, 490
Lsp1109I	GCAGC	1 cut(s)	110
LweI	GCATC	3 cut(s)	640, 886, 970
MabI	ACCWGGT	1 cut(s)	23
MaeI	CTAG	3 cut(s)	279, 336, 432
MaeII	ACGT	1 cut(s)	544
MaeIII	GTNAC	3 cut(s)	34, 295, 1177
MalI	GATC	3 cut(s)	627, 897, 1095
MboI	GATC	3 cut(s)	625, 895, 1093
MboII	GAAGA	9 cut(s)	29, 94, 100, 427, 632, 845, 1003, 1010, 1171
MfeI	CAATTG	1 cut(s)	1228
MflI	RGATCY	2 cut(s)	895, 1093
MhlI	GDGCHC	2 cut(s)	369, 1044
MluCI	AATT	6 cut(s)	462, 796, 962, 1061, 1199, 1228
MmeI	TCCRAC	1 cut(s)	1229
MroI	TCCGGA	1 cut(s)	628
MseI	TTAA	2 cut(s)	729, 812
MspI	CCGG	3 cut(s)	155, 230, 629
MspR9I	CCNGG	6 cut(s)	25, 155, 156, 230, 752, 945
MunI	CAATTG	1 cut(s)	1228
MvaI	CCWGG	3 cut(s)	25, 752, 945
MvnI	CGCG	2 cut(s)	70, 506
MwoI	GCNNNNNNNGC	6 cut(s)	47, 61, 104, 350, 503, 1224
NciI	CCSGG	3 cut(s)	155, 156, 230
NcoI	CCATGG	1 cut(s)	906
NdeII	GATC	3 cut(s)	625, 895, 1093
NheI	GCTAGC	1 cut(s)	431
NlaIII	CATG	3 cut(s)	530, 910, 976
NlaIV	GGNNCC	3 cut(s)	29, 456, 492
NmeAIII	GCCGAG	1 cut(s)	902
NmuCI	GTSAC	2 cut(s)	34, 295
NspI	RCATGY	1 cut(s)	976
PceI	AGGCCT	1 cut(s)	471
PfeI	GAWTC	7 cut(s)	5, 118, 171, 233, 388, 632, 939
PflMI	CCANNNNNTGG	1 cut(s)	907
PkrI	GCNGC	1 cut(s)	100
PpuMI	RGGWCCY	1 cut(s)	27
PshBI	ATTAAT	1 cut(s)	812
PsiI	TTATAA	2 cut(s)	884, 953
Psp124BI	GAGCTC	1 cut(s)	369
Psp5II	RGGWCCY	1 cut(s)	27
Psp6I	CCWGG	3 cut(s)	23, 750, 943
PspEI	GGTNACC	2 cut(s)	295, 1177
PspFI	CCCAGC	1 cut(s)	359
PspGI	CCWGG	3 cut(s)	23, 750, 943
PspN4I	GGNNCC	3 cut(s)	29, 456, 492
PspPI	GGNCC	2 cut(s)	27, 931
PspPPI	RGGWCCY	1 cut(s)	27
PsuI	RGATCY	2 cut(s)	895, 1093
SacI	GAGCTC	1 cut(s)	369
SaqAI	TTAA	2 cut(s)	729, 812
SatI	GCNGC	1 cut(s)	99
Sau3AI	GATC	3 cut(s)	625, 895, 1093
Sau96I	GGNCC	2 cut(s)	27, 931
ScrFI	CCNGG	6 cut(s)	25, 155, 156, 230, 752, 945
SduI	GDGCHC	2 cut(s)	369, 1044
SexAI	ACCWGGT	1 cut(s)	23
SfaNI	GCATC	3 cut(s)	640, 886, 970
SinI	GGWCC	1 cut(s)	27
SmaI	CCCGGG	1 cut(s)	156
Sse9I	AATT	6 cut(s)	462, 796, 962, 1061, 1199, 1228
SseBI	AGGCCT	1 cut(s)	471
SsiI	CCGC	4 cut(s)	39, 504, 712, 1055
SspMI	CTAG	3 cut(s)	279, 336, 432
SstI	GAGCTC	1 cut(s)	369
StuI	AGGCCT	1 cut(s)	471
StyD4I	CCNGG	6 cut(s)	23, 153, 154, 228, 750, 943
StyI	CCWWGG	2 cut(s)	45, 906
TaaI	ACNGT	2 cut(s)	1177, 1210
TaiI	ACGT	1 cut(s)	547
TaqI	TCGA	3 cut(s)	207, 236, 989
TasI	AATT	6 cut(s)	462, 796, 962, 1061, 1199, 1228
TfiI	GAWTC	7 cut(s)	5, 118, 171, 233, 388, 632, 939
Tru1I	TTAA	2 cut(s)	729, 812
Tru9I	TTAA	2 cut(s)	729, 812
TscAI	CASTG	4 cut(s)	135, 771, 990, 1215
TseFI	GTSAC	2 cut(s)	34, 295
TseI	GCWGC	1 cut(s)	98
Tsp45I	GTSAC	2 cut(s)	34, 295
TspDTI	ATGAA	3 cut(s)	545, 846, 1074
TspMI	CCCGGG	1 cut(s)	154
TspRI	CASTG	4 cut(s)	135, 771, 990, 1215
Van91I	CCANNNNNTGG	1 cut(s)	907
VpaK11BI	GGWCC	1 cut(s)	27
VspI	ATTAAT	1 cut(s)	812
XapI	RAATTY	4 cut(s)	462, 796, 962, 1061
XceI	RCATGY	1 cut(s)	976
XcmI	CCANNNNNNNNNTGG	1 cut(s)	908
XmaI	CCCGGG	1 cut(s)	154
XspI	CTAG	3 cut(s)	279, 336, 432

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