Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000003

Orthogroup ID

OG0005088

Physical Location & Seq

Genomic Coordinates Reverse (-)

65031567 .. 65034801

Gene Structure 3235 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_3G00273170.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1146 bp

ATGGCTTCAATTTCGGGACCTGAAAACCAGTCGCCGAACATTTACATACCGCCAGAATGGTCCGACGCCGTCGCACACGCCTCCGTCGCTTCGCCGCCGCCCATTGTCTTAGTCTGTGGCGCCAAGAACTGTGGAAAGTCCACCTTCTCCCGCTACCTCCTCAACATTCTTCTCCACCGGTATAAGAAAGTTGGGTACTTGGATACAGATGTGGGTCAACCTGAGTTTAGTCCTCCTGGGTTTCTATCTCTTACTGTAGTAGATGAAGTTACTCCAGATTTGACAATCCCACATTTGAAGACGGCGGAGAGATGTTTGTTCTTTGGCGATGTTTCTTCGAAAAGGAATCCGACAACATACTTAAATTGTATATTTGCTTTATATGATTACTATCGGAAGGAGTACTGCAACAGTGATAACTCTCATAATATTGGATTGCCTCTCGTTGTGAATACACCTGGATGGGTGAAAGGTATTGGTTATGATCTTTTGGTGGATATGTTGAAGTATATTTCCCCTACCCATGTTGTTAAAATAAACATATCTGCTCAGAGTAAGAATCTACCAGACGGACGATTCTGGTTAGATGAGGATTATGATGGTATGGTAAATCTAACAGAGATCAGTTCAGCTCGTCAGGACTCTTTGAATAGATCGGTTCTAGTCCAAAAGGATGCACGGCTGCTGCGCGATATACGTTTAATGGCTTATTTCAGGCAGTGCTTTTCAAGTAACTTGAACATTTCTACAATCAAAGAACTTGCTAATGCTTTGGCATCTCACCCTCCTTATGAAGTTCCAATATCAAGCATTAAGATTAGACATCTCCATTGTCAGGTCCCAGGTACTGAGATCTTCTATAGTTTGAATGGAAGCATTGTTGGCTTGGCAGTTAGCTCTGAAGGCTCAAAAGATTTACCATGGTGTGTTGGTCTTGGAATTGTGAGGAGCATTGACACACTCAAAGGCTTGCTATATGTGATAACACCTGTTCCACAAGGCACGCTGGAAAATGTTGATCTTCTGCTGCAGGGTTTTATCCAAATTCCTACTAGTTTGTTGCAGTTTCCATTACATCAAATGAATTTTCAGGTCCAGGGGAGCAGATCGCCTTATATGTCTGCAAATGTTTTGTCTTCAAGCTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000448 GO:0000460 GO:0000463 GO:0000466 GO:0000469 GO:0000470 GO:0000478 GO:0000479 GO:0003674 GO:0003824 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0006139 GO:0006364 GO:0006396 GO:0006725 GO:0006793 GO:0006796 GO:0006807 GO:0008150 GO:0008152 GO:0009987 GO:0010467 GO:0016070 GO:0016072 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0016773 GO:0019205 GO:0022613 GO:0034470 GO:0034641 GO:0034660 GO:0042254 GO:0042273 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044085 GO:0044237 GO:0044238 GO:0044424 GO:0044464 GO:0046483 GO:0051731 GO:0071704 GO:0071840 GO:0090304 GO:0090305 GO:0090501 GO:0090502 GO:1901360

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

CLP1_P

Protein Analysis

381

Amino Acids

42.21

Weight (kDa)

6.5

Isoelectric Point (pI)

45.14

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
CLP1_P	PF16575	40 - 238	2.8e-37	mRNA cleavage and polyadenylation factor CLP1 P-loop
NOL9_C	PF25467	260 - 350	2.8e-32	NOL9-like, C-terminal domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

Font Size (px)

Line Width

Align Labels (Cladogram)

Image

Tree File

Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready

iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0005088)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G11010 AT5G11010 AT5G11010 AT5G11010
fragaria_vesca	FvH4_5g16020 FvH4_5g16020 FvH4_5g16020 FvH4_5g16020
malus_domestica	MD06G1183600.v1.1 MD14G1057100.v1.1 MD14G1189700.v1.1
prunus_persica	Prupe.5G161200_v2.0.a1 Prupe.5G182300_v2.0.a1 Prupe.5G182300_v2.0.a1
pyrus_communis	pycom06g16270 pycom14g15720
rosa_chinensis	RchiOBHm_Chr7g0180051
rosa_laevigata	RLG00000005299
rosa_multiflora	Rmu_co8044072.1_g000001 Rmu_sc0002219.1_g000023 Rmu_sc0017616.1_g000001 Rmu_ssc0000119.1_g000025
rosa_roxburghii	Rroxscaffold_3G00273170
rosa_rugosa	Rorug06G0430200 Rorug06G0430200
rosa_samantha	Rh7AG030400 Rh7BG030300 Rh7CG032100 Rh7DG031100
rosa_wichuraiana	Rw7G002530

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	1 cut(s)	119
AccII	CGCG	1 cut(s)	690
AciI	CCGC	5 cut(s)	50, 95, 98, 151, 305
AcsI	RAATTY	2 cut(s)	1044, 1084
AcuI	CTGAAG	1 cut(s)	921
AcyI	GRCGYC	2 cut(s)	66, 120
AfaI	GTAC	3 cut(s)	197, 404, 847
AfiI	CCNNNNNNNGG	1 cut(s)	835
AgeI	ACCGGT	1 cut(s)	177
AgsI	TTSAA	8 cut(s)	9, 298, 505, 649, 729, 739, 868, 1140
AhlI	ACTAGT	1 cut(s)	1052
AjnI	CCWGG	4 cut(s)	235, 457, 841, 1095
AluBI	AGCT	3 cut(s)	632, 897, 1143
AluI	AGCT	3 cut(s)	632, 897, 1143
AlwNI	CAGNNNCTG	1 cut(s)	848
ApeKI	GCWGC	3 cut(s)	682, 685, 1027
ApoI	RAATTY	2 cut(s)	1044, 1084
ArsI	GACNNNNNNTTYG	1 cut(s)	1118
AsiGI	ACCGGT	1 cut(s)	177
AspLEI	GCGC	2 cut(s)	122, 690
AspS9I	GGNCC	4 cut(s)	17, 60, 838, 1093
AsuHPI	GGTGA	2 cut(s)	478, 773
AsuII	TTCGAA	1 cut(s)	338
AvaII	GGWCC	4 cut(s)	17, 60, 838, 1093
BaeI	ACNNNNGTAYC	2 cut(s)	195, 228
BanI	GGYRCC	1 cut(s)	119
BbsI	GAAGAC	2 cut(s)	305, 1128
BbvI	GCAGC	3 cut(s)	669, 672, 1014
BccI	CCATC	2 cut(s)	456, 593
BceAI	ACGGC	3 cut(s)	53, 318, 695
BciT130I	CCWGG	4 cut(s)	237, 459, 843, 1097
BciVI	GTATCC	1 cut(s)	196
BcuI	ACTAGT	1 cut(s)	1052
BfaI	CTAG	3 cut(s)	662, 1053, 1144
BfmI	CTRYAG	3 cut(s)	255, 859, 1028
BfoI	RGCGCY	1 cut(s)	123
BfuI	GTATCC	1 cut(s)	196
BglII	AGATCT	1 cut(s)	852
BisI	GCNGC	5 cut(s)	95, 98, 683, 686, 1028
BlsI	GCNGC	5 cut(s)	96, 99, 684, 687, 1029
BmcAI	AGTACT	1 cut(s)	404
Bme1390I	CCNGG	4 cut(s)	237, 459, 843, 1097
Bme18I	GGWCC	4 cut(s)	17, 60, 838, 1093
BmgT120I	GGNCC	4 cut(s)	17, 60, 838, 1093
BmiI	GGNNCC	3 cut(s)	18, 121, 840
BmrFI	CCNGG	4 cut(s)	237, 459, 843, 1097
BmsI	GCATC	2 cut(s)	664, 785
BpiI	GAAGAC	2 cut(s)	305, 1128
BpmI	CTGGAG	1 cut(s)	258
Bpu14I	TTCGAA	1 cut(s)	338
BsaBI	GATNNNNATC	1 cut(s)	390
BsaHI	GRCGYC	2 cut(s)	66, 120
BsaJI	CCNNGG	4 cut(s)	236, 841, 920, 1096
BsaWI	WCCGGW	1 cut(s)	177
Bsc4I	CCNNNNNNNGG	1 cut(s)	835
Bse118I	RCCGGY	1 cut(s)	177
Bse1I	ACTGG	1 cut(s)	28
Bse8I	GATNNNNATC	1 cut(s)	390
BseBI	CCWGG	4 cut(s)	237, 459, 843, 1097
BseDI	CCNNGG	4 cut(s)	236, 841, 920, 1096
BseGI	GGATG	2 cut(s)	467, 679
BseJI	GATNNNNATC	1 cut(s)	390
BseLI	CCNNNNNNNGG	1 cut(s)	835
BseMII	CTCAG	3 cut(s)	213, 563, 840
BseNI	ACTGG	1 cut(s)	28
BseRI	GAGGAG	2 cut(s)	149, 961
BseXI	GCAGC	3 cut(s)	669, 672, 1014
Bsh1236I	CGCG	1 cut(s)	690
BshNI	GGYRCC	1 cut(s)	119
BshTI	ACCGGT	1 cut(s)	177
BsiSI	CCGG	1 cut(s)	178
BslFI	GGGAC	2 cut(s)	30, 824
BslI	CCNNNNNNNGG	1 cut(s)	835
BsmFI	GGGAC	2 cut(s)	30, 824
Bsp119I	TTCGAA	1 cut(s)	338
Bsp143I	GATC	6 cut(s)	484, 621, 653, 852, 1018, 1106
Bsp19I	CCATGG	1 cut(s)	920
BspACI	CCGC	5 cut(s)	50, 95, 98, 151, 305
BspCNI	CTCAG	3 cut(s)	214, 562, 841
BspFNI	CGCG	1 cut(s)	690
BspLI	GGNNCC	3 cut(s)	18, 121, 840
BspMAI	CTGCAG	1 cut(s)	1032
BspT104I	TTCGAA	1 cut(s)	338
BspT107I	GGYRCC	1 cut(s)	119
BsrFI	RCCGGY	1 cut(s)	177
BsrI	ACTGG	1 cut(s)	28
BssAI	RCCGGY	1 cut(s)	177
BssECI	CCNNGG	4 cut(s)	236, 841, 920, 1096
BssMI	GATC	6 cut(s)	484, 621, 653, 852, 1018, 1106
BssNI	GRCGYC	2 cut(s)	66, 120
BssT1I	CCWWGG	1 cut(s)	920
Bst2UI	CCWGG	4 cut(s)	237, 459, 843, 1097
Bst4CI	ACNGT	3 cut(s)	131, 256, 413
BstACI	GRCGYC	2 cut(s)	66, 120
BstBI	TTCGAA	1 cut(s)	338
BstC8I	GCNNGC	2 cut(s)	971, 1004
BstDEI	CTNAG	4 cut(s)	109, 222, 549, 849
BstDSI	CCRYGG	1 cut(s)	920
BstF5I	GGATG	2 cut(s)	467, 679
BstFNI	CGCG	1 cut(s)	690
BstH2I	RGCGCY	1 cut(s)	123
BstHHI	GCGC	2 cut(s)	122, 690
BstKTI	GATC	6 cut(s)	487, 624, 656, 855, 1021, 1109
BstMBI	GATC	6 cut(s)	484, 621, 653, 852, 1018, 1106
BstMWI	GCNNNNNNNGC	3 cut(s)	86, 882, 903
BstNI	CCWGG	4 cut(s)	237, 459, 843, 1097
BstSCI	CCNGG	4 cut(s)	235, 457, 841, 1095
BstSFI	CTRYAG	3 cut(s)	255, 859, 1028
BstUI	CGCG	1 cut(s)	690
BstV1I	GCAGC	3 cut(s)	669, 672, 1014
BstV2I	GAAGAC	2 cut(s)	305, 1128
BstX2I	RGATCY	1 cut(s)	852
BstYI	RGATCY	1 cut(s)	852
BsuI	GTATCC	1 cut(s)	196
BtgI	CCRYGG	1 cut(s)	920
BtgZI	GCGATG	1 cut(s)	342
BtsCI	GGATG	2 cut(s)	467, 679
BtsI	GCAGTG	1 cut(s)	725
BtsIMutI	CAGTG	2 cut(s)	418, 725
Cac8I	GCNNGC	2 cut(s)	971, 1004
CaiI	CAGNNNCTG	1 cut(s)	848
CfoI	GCGC	2 cut(s)	122, 690
Cfr10I	RCCGGY	1 cut(s)	177
Cfr13I	GGNCC	4 cut(s)	17, 60, 838, 1093
CseI	GACGC	1 cut(s)	74
Csp6I	GTAC	3 cut(s)	196, 403, 846
CspAI	ACCGGT	1 cut(s)	177
CspCI	CAANNNNNGTGG	2 cut(s)	112, 147
CviAII	CATG	2 cut(s)	524, 921
CviJI	RGCY	9 cut(s)	5, 632, 682, 707, 885, 897, 906, 969, 1143
CviKI_1	RGCY	9 cut(s)	5, 632, 682, 707, 885, 897, 906, 969, 1143
CviQI	GTAC	3 cut(s)	196, 403, 846
DdeI	CTNAG	4 cut(s)	109, 222, 549, 849
DinI	GGCGCC	1 cut(s)	121
DpnI	GATC	6 cut(s)	486, 623, 655, 854, 1020, 1108
DpnII	GATC	6 cut(s)	484, 621, 653, 852, 1018, 1106
EciI	GGCGGA	1 cut(s)	320
Eco130I	CCWWGG	1 cut(s)	920
Eco47I	GGWCC	4 cut(s)	17, 60, 838, 1093
Eco57I	CTGAAG	1 cut(s)	921
EcoO109I	RGGNCCY	2 cut(s)	17, 838
EcoRII	CCWGG	4 cut(s)	235, 457, 841, 1095
EcoT14I	CCWWGG	1 cut(s)	920
EgeI	GGCGCC	1 cut(s)	121
EheI	GGCGCC	1 cut(s)	121
ErhI	CCWWGG	1 cut(s)	920
FaeI	CATG	2 cut(s)	527, 924
FalI	AAGNNNNNCTT	2 cut(s)	128, 160
FaqI	GGGAC	2 cut(s)	30, 824
FatI	CATG	2 cut(s)	523, 920
FauI	CCCGC	1 cut(s)	158
Fnu4HI	GCNGC	5 cut(s)	95, 98, 683, 686, 1028
FokI	GGATG	2 cut(s)	474, 686
Fsp4HI	GCNGC	5 cut(s)	95, 98, 683, 686, 1028
FspBI	CTAG	3 cut(s)	662, 1053, 1144
GlaI	GCGC	2 cut(s)	121, 689
GluI	GCNGC	5 cut(s)	95, 98, 683, 686, 1028
GsuI	CTGGAG	1 cut(s)	258
HaeII	RGCGCY	1 cut(s)	123
HapII	CCGG	1 cut(s)	178
HgaI	GACGC	1 cut(s)	74
HhaI	GCGC	2 cut(s)	122, 690
Hin1I	GRCGYC	2 cut(s)	66, 120
Hin1II	CATG	2 cut(s)	527, 924
Hin6I	GCGC	2 cut(s)	120, 688
HinP1I	GCGC	2 cut(s)	120, 688
HincII	GTYRAC	1 cut(s)	218
HindII	GTYRAC	1 cut(s)	218
HinfI	GANTC	4 cut(s)	346, 559, 576, 641
HpaII	CCGG	1 cut(s)	178
HphI	GGTGA	2 cut(s)	478, 773
Hpy166II	GTNNAC	2 cut(s)	141, 218
Hpy188I	TCNGA	5 cut(s)	64, 351, 396, 552, 901
Hpy188III	TCNNGA	3 cut(s)	15, 275, 638
Hpy8I	GTNNAC	2 cut(s)	141, 218
Hpy99I	CGWCG	3 cut(s)	68, 74, 89
HpyAV	CCTTC	3 cut(s)	154, 391, 896
HpyCH4III	ACNGT	3 cut(s)	131, 256, 413
HpyCH4IV	ACGT	1 cut(s)	697
HpyCH4V	TGCA	5 cut(s)	408, 677, 1030, 1063, 1124
HpyF10VI	GCNNNNNNNGC	3 cut(s)	86, 882, 903
HpyF3I	CTNAG	4 cut(s)	109, 222, 549, 849
HpySE526I	ACGT	1 cut(s)	697
Hsp92I	GRCGYC	2 cut(s)	66, 120
Hsp92II	CATG	2 cut(s)	527, 924
HspAI	GCGC	2 cut(s)	120, 688
KasI	GGCGCC	1 cut(s)	119
Kzo9I	GATC	6 cut(s)	484, 621, 653, 852, 1018, 1106
LmnI	GCTCC	2 cut(s)	948, 1101
Lsp1109I	GCAGC	3 cut(s)	669, 672, 1014
LweI	GCATC	2 cut(s)	664, 785
MaeI	CTAG	3 cut(s)	662, 1053, 1144
MaeII	ACGT	1 cut(s)	697
MaeIII	GTNAC	2 cut(s)	268, 731
MalI	GATC	6 cut(s)	486, 623, 655, 854, 1020, 1108
MboI	GATC	6 cut(s)	484, 621, 653, 852, 1018, 1106
MboII	GAAGA	6 cut(s)	161, 310, 327, 847, 1013, 1128
MflI	RGATCY	1 cut(s)	852
MluCI	AATT	5 cut(s)	9, 364, 939, 1044, 1084
Mly113I	GGCGCC	1 cut(s)	120
MlyI	GAGTC	1 cut(s)	635
MmeI	TCCRAC	2 cut(s)	87, 374
MnlI	CCTC	8 cut(s)	91, 167, 170, 243, 450, 583, 795, 939
MseI	TTAA	4 cut(s)	362, 531, 701, 813
MslI	CAYNNNNRTG	1 cut(s)	460
MspI	CCGG	1 cut(s)	178
MspR9I	CCNGG	4 cut(s)	237, 459, 843, 1097
MvaI	CCWGG	4 cut(s)	237, 459, 843, 1097
MvnI	CGCG	1 cut(s)	690
MwoI	GCNNNNNNNGC	3 cut(s)	86, 882, 903
NarI	GGCGCC	1 cut(s)	120
NcoI	CCATGG	1 cut(s)	920
NdeII	GATC	6 cut(s)	484, 621, 653, 852, 1018, 1106
NlaIII	CATG	2 cut(s)	527, 924
NlaIV	GGNNCC	3 cut(s)	18, 121, 840
NspV	TTCGAA	1 cut(s)	338
PfeI	GAWTC	3 cut(s)	346, 559, 576
PflFI	GACNNNGTC	1 cut(s)	68
PinAI	ACCGGT	1 cut(s)	177
PkrI	GCNGC	5 cut(s)	96, 99, 684, 687, 1029
PleI	GAGTC	1 cut(s)	635
PluTI	GGCGCC	1 cut(s)	123
PpsI	GAGTC	1 cut(s)	635
PpuMI	RGGWCCY	2 cut(s)	17, 838
Psp5II	RGGWCCY	2 cut(s)	17, 838
Psp6I	CCWGG	4 cut(s)	235, 457, 841, 1095
PspGI	CCWGG	4 cut(s)	235, 457, 841, 1095
PspN4I	GGNNCC	3 cut(s)	18, 121, 840
PspPI	GGNCC	4 cut(s)	17, 60, 838, 1093
PspPPI	RGGWCCY	2 cut(s)	17, 838
PstI	CTGCAG	1 cut(s)	1032
PstNI	CAGNNNCTG	1 cut(s)	848
PsuI	RGATCY	1 cut(s)	852
PsyI	GACNNNGTC	1 cut(s)	68
RsaI	GTAC	3 cut(s)	197, 404, 847
RsaNI	GTAC	3 cut(s)	196, 403, 846
RseI	CAYNNNNRTG	1 cut(s)	460
SaqAI	TTAA	4 cut(s)	362, 531, 701, 813
SatI	GCNGC	5 cut(s)	95, 98, 683, 686, 1028
Sau3AI	GATC	6 cut(s)	484, 621, 653, 852, 1018, 1106
Sau96I	GGNCC	4 cut(s)	17, 60, 838, 1093
ScaI	AGTACT	1 cut(s)	404
SchI	GAGTC	1 cut(s)	635
ScrFI	CCNGG	4 cut(s)	237, 459, 843, 1097
SfaNI	GCATC	2 cut(s)	664, 785
SfcI	CTRYAG	3 cut(s)	255, 859, 1028
SfoI	GGCGCC	1 cut(s)	121
SfuI	TTCGAA	1 cut(s)	338
SinI	GGWCC	4 cut(s)	17, 60, 838, 1093
SmiMI	CAYNNNNRTG	1 cut(s)	460
SpeI	ACTAGT	1 cut(s)	1052
Sse9I	AATT	5 cut(s)	9, 364, 939, 1044, 1084
SsiI	CCGC	5 cut(s)	50, 95, 98, 151, 305
SspDI	GGCGCC	1 cut(s)	119
SspI	AATATT	1 cut(s)	430
SspMI	CTAG	3 cut(s)	662, 1053, 1144
StyD4I	CCNGG	4 cut(s)	235, 457, 841, 1095
StyI	CCWWGG	1 cut(s)	920
TaaI	ACNGT	3 cut(s)	131, 256, 413
TaiI	ACGT	1 cut(s)	700
TaqI	TCGA	1 cut(s)	338
TasI	AATT	5 cut(s)	9, 364, 939, 1044, 1084
TatI	WGTACW	1 cut(s)	402
TauI	GCSGC	2 cut(s)	97, 100
TfiI	GAWTC	3 cut(s)	346, 559, 576
Tru1I	TTAA	4 cut(s)	362, 531, 701, 813
Tru9I	TTAA	4 cut(s)	362, 531, 701, 813
TscAI	CASTG	2 cut(s)	418, 725
TseI	GCWGC	3 cut(s)	682, 685, 1027
TspDTI	ATGAA	3 cut(s)	279, 807, 1097
TspGWI	ACGGA	2 cut(s)	73, 585
TspRI	CASTG	2 cut(s)	418, 725
Tth111I	GACNNNGTC	1 cut(s)	68
VpaK11BI	GGWCC	4 cut(s)	17, 60, 838, 1093
XapI	RAATTY	2 cut(s)	1044, 1084
XspI	CTAG	3 cut(s)	662, 1053, 1144
ZrmI	AGTACT	1 cut(s)	404

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