Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4D

Orthogroup ID

OG0005755

Physical Location & Seq

Genomic Coordinates Reverse (-)

61899550 .. 61915406

Gene Structure 15857 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4DG404200.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1209 bp

ATGATCAGACAAACCCTCAAATTCTTCGCTCGCTTGCGAAGAACCTCAAAGCCCCAATGTCCTTTGACCTGCAACAAGCTCCTCCATAACCTCAATAGGTCCAACTGCGGTGACCTCTCTCTCAAAATCCTCTCTGATTTGGTCTCCAAAGGGTACAATCCTCACCCCTCTTCATTCAATTCAGTTATCTCCTTTTTGTGTAAACTGGGTCATGTCAACTCGGCCCAGAAGCTCACAATTTCAATGCCGATTTTCGGGTGCCGGCCCGATATTGTAACATACAATTCTTTGATTAATGGGTACTGTAAACTCTGTGATATTGATGAGGCTTGTTTAGTGATGAAGATGATAAGGGTAGGAGGGTGTAGGCCTGATTTGGTTACTTTTAATACATTGTTTAGTGGGTTCTGTAAGGTTAAGATGAGGAAAGAAGTGTTTGTGTATATGGGTTTGATGTGGAAGTGTTTTGAACCGAATGTGATTAGTTATAGTACACTGATAGATATGTTTTGCAAGATGGGGGATTTGGATTTGGGATATAGGGTTTATGGTTATATGGTGAAGGATAAGGTGTCGCCGAATTTGTTTGCTTTTACTTGTTTGATTGATGGGTATAGTAAGGCTGGTAATTTGGAGGTTGCGATTGAATTGCTTGAGGGAATGAAGAAATCGTTAGTTTTACCGAATGTGGTGACTTATGGTGCTTTGATTGATGGGCTGTGCAAGAATGGGAAGTTGGAAAGAGCTGAGCGTTTGTTTTGTGAAATGGTGGAAGATGGGGTTCGGCCTAGTTCAGCGGTTTACACTTCAATGATAGATGGGCATTTCAAGAAAGGAAATGTAGGTGAGGCCATGAAGTATATGAGTAAAATGCAGGATGGAAGGGTTAGTCTTGATGCTGCTGCATATGGAGTGGTGATCTCAGGCCTCTGTAATAATGGTCAGTTCGATAATGCGATGCGAGTTGTTACAGATTTTGCCACGAGTGGTTTTTCTCCAGATAAGATGTTGTTGACGACCATTATGGATGCATGTTTCAAAGCTGGCGATTTGAAAGCAGCTTTGGGTGTCTACAGACTGTTAGCAAAGGTTTTTGAACCAGATGCTGTGGTGCTTTCAGCTTTGATGGATGGCTTATGCAAGCATGGGCATTTGGAGGAGGCAAGAGGCTACTTTTGGCTAATGAATTTCATATACTGTGCTCATTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0003676 GO:0003723 GO:0003824 GO:0004518 GO:0004519 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0006139 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009451 GO:0009987 GO:0016070 GO:0016787 GO:0016788 GO:0034641 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043412 GO:0044237 GO:0044238 GO:0044424 GO:0044464 GO:0046483 GO:0071704 GO:0090304 GO:0090305 GO:0097159 GO:1901360 GO:1901363

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

PPR PPR_1 PPR_2 PPR_3

Protein Analysis

402

Amino Acids

44.77

Weight (kDa)

8.73

Isoelectric Point (pI)

24.87

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_2	PF13041	58 - 103	1.4e-12	PPR repeat family
PPR_3	PF13812	83 - 134	3.1e-07	Pentatricopeptide repeat domain
PPR_1	PF12854	86 - 114	7.4e-10	PPR repeat
PPR_2	PF13041	89 - 138	6.1e-16	PPR repeat family
PPR	PF01535	92 - 122	3.7e-06	PPR repeat
PPR_1	PF12854	154 - 186	1.9e-08	PPR repeat
PPR_3	PF13812	156 - 202	1.3e-06	Pentatricopeptide repeat domain
PPR_2	PF13041	158 - 204	1.3e-11	PPR repeat family
PPR_long	PF17177	174 - 249	2.1e-06	Pentacotripeptide-repeat region of PRORP
PPR_1	PF12854	191 - 222	1e-07	PPR repeat
PPR_2	PF13041	193 - 242	3.5e-15	PPR repeat family
PPR_3	PF13812	193 - 238	8.2e-08	Pentatricopeptide repeat domain
PPR	PF01535	197 - 223	6.4e-06	PPR repeat
PPR_1	PF12854	227 - 257	1.1e-13	PPR repeat
PPR_2	PF13041	228 - 274	5.1e-16	PPR repeat family
PPR	PF01535	231 - 261	1.6e-10	PPR repeat
TPR_24	PF23276	232 - 322	2.6e-06	Fungal tetratrico peptide repeats
PPR_long	PF17177	246 - 364	3.8e-08	Pentacotripeptide-repeat region of PRORP
PPR_2	PF13041	263 - 312	1.2e-10	PPR repeat family
TPR_24	PF23276	268 - 359	3.7e-06	Fungal tetratrico peptide repeats

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: OG0005755)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT2G01740
prunus_persica	Prupe.1G333800_v2.0.a1 Prupe.1G333800_v2.0.a1 Prupe.1G333800_v2.0.a1
rosa_chinensis	RchiOBHm_Chr2g0123271 RchiOBHm_Chr4g0442881 RchiOBHm_Chr4g0442961 RchiOBHm_Chr4g0443001
rosa_laevigata	RLG00000005963 RLG00000005969 RLG00000005972 RLG00000005974 RLG00000010013
rosa_multiflora	Rmu_sc0001917.1_g000006 Rmu_sc0005806.1_g000015 Rmu_sc0007295.1_g000001 Rmu_sc0014119.1_g000001 Rmu_ssc0000204.1_g000003 Rmu_ssc0000204.1_g000010
rosa_roxburghii	Rroxscaffold_5G00383640
rosa_samantha	Rh2BG311500 Rh4AG397900 Rh4BG409100 Rh4BG409400 Rh4CG424900 Rh4DG403700 Rh4DG404200
rosa_wichuraiana	Rw4G034270

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc36I	ACCTGC	1 cut(s)	77
AccB1I	GGYRCC	1 cut(s)	258
AccI	GTMKAC	1 cut(s)	1071
AciI	CCGC	2 cut(s)	108, 797
AcsI	RAATTY	3 cut(s)	20, 580, 1186
AfaI	GTAC	3 cut(s)	155, 302, 493
AfiI	CCNNNNNNNGG	1 cut(s)	254
AgsI	TTSAA	9 cut(s)	178, 243, 470, 647, 810, 829, 1039, 1054, 1097
AjuI	GAANNNNNNNTTGG	4 cut(s)	719, 751, 1046, 1078
AluBI	AGCT	6 cut(s)	79, 232, 746, 1043, 1061, 1121
AluI	AGCT	6 cut(s)	79, 232, 746, 1043, 1061, 1121
Alw21I	GWGCWC	1 cut(s)	1204
Alw26I	GTCTC	1 cut(s)	148
AlwNI	CAGNNNCTG	1 cut(s)	1106
AoxI	GGCC	6 cut(s)	222, 263, 368, 785, 849, 925
ApeKI	GCWGC	3 cut(s)	899, 902, 1058
ApoI	RAATTY	3 cut(s)	20, 580, 1186
AseI	ATTAAT	1 cut(s)	294
AspS9I	GGNCC	3 cut(s)	99, 223, 264
AsuHPI	GGTGA	6 cut(s)	122, 155, 571, 703, 857, 928
AvaII	GGWCC	1 cut(s)	99
BanI	GGYRCC	1 cut(s)	258
BauI	CACGAG	1 cut(s)	982
Bbv12I	GWGCWC	1 cut(s)	1204
BbvI	GCAGC	3 cut(s)	886, 889, 1070
BccI	CCATC	8 cut(s)	511, 602, 707, 770, 812, 872, 1120, 1124
BcgI	CGANNNNNNTGC	2 cut(s)	631, 665
BclI	TGATCA	1 cut(s)	3
BcoDI	GTCTC	1 cut(s)	148
BfaI	CTAG	1 cut(s)	789
BfmI	CTRYAG	1 cut(s)	1072
BfuAI	ACCTGC	1 cut(s)	77
BisI	GCNGC	3 cut(s)	900, 903, 1059
BlpI	GCTNAGC	1 cut(s)	747
BlsI	GCNGC	3 cut(s)	901, 904, 1060
Bme18I	GGWCC	1 cut(s)	99
BmgT120I	GGNCC	3 cut(s)	99, 223, 264
BmiI	GGNNCC	1 cut(s)	260
BmrI	ACTGGG	1 cut(s)	215
BmsI	GCATC	4 cut(s)	886, 948, 1018, 1093
BmuI	ACTGGG	1 cut(s)	215
BpmI	CTGGAG	1 cut(s)	981
Bpu1102I	GCTNAGC	1 cut(s)	747
BpuEI	CTTGAG	1 cut(s)	674
BsaI	GGTCTC	1 cut(s)	148
Bsc4I	CCNNNNNNNGG	1 cut(s)	254
Bse118I	RCCGGY	1 cut(s)	261
Bse1I	ACTGG	1 cut(s)	210
BseGI	GGATG	3 cut(s)	883, 1033, 1135
BseLI	CCNNNNNNNGG	1 cut(s)	254
BseMII	CTCAG	2 cut(s)	738, 936
BseNI	ACTGG	1 cut(s)	210
BseRI	GAGGAG	2 cut(s)	71, 1172
BseXI	GCAGC	3 cut(s)	886, 889, 1070
BshFI	GGCC	6 cut(s)	224, 265, 370, 787, 851, 927
BshNI	GGYRCC	1 cut(s)	258
BsiHKAI	GWGCWC	1 cut(s)	1204
BsiSI	CCGG	1 cut(s)	262
BslI	CCNNNNNNNGG	1 cut(s)	254
BsmAI	GTCTC	1 cut(s)	148
BsnI	GGCC	6 cut(s)	224, 265, 370, 787, 851, 927
Bso31I	GGTCTC	1 cut(s)	148
Bsp1286I	GDGCHC	1 cut(s)	1204
Bsp143I	GATC	2 cut(s)	3, 918
Bsp1720I	GCTNAGC	1 cut(s)	747
BspACI	CCGC	2 cut(s)	108, 797
BspANI	GGCC	6 cut(s)	224, 265, 370, 787, 851, 927
BspCNI	CTCAG	2 cut(s)	739, 935
BspLI	GGNNCC	1 cut(s)	260
BspMI	ACCTGC	1 cut(s)	77
BspT107I	GGYRCC	1 cut(s)	258
BspTNI	GGTCTC	1 cut(s)	148
BsrFI	RCCGGY	1 cut(s)	261
BsrI	ACTGG	1 cut(s)	210
BssAI	RCCGGY	1 cut(s)	261
BssMI	GATC	2 cut(s)	3, 918
BssSI	CACGAG	1 cut(s)	982
Bst2BI	CACGAG	1 cut(s)	982
Bst4CI	ACNGT	3 cut(s)	305, 1080, 1199
Bst6I	CTCTTC	1 cut(s)	175
BstC8I	GCNNGC	5 cut(s)	31, 35, 263, 1045, 1142
BstDEI	CTNAG	2 cut(s)	747, 922
BstEII	GGTNACC	1 cut(s)	110
BstF5I	GGATG	3 cut(s)	883, 1033, 1135
BstKTI	GATC	2 cut(s)	6, 921
BstMAI	GTCTC	1 cut(s)	148
BstMBI	GATC	2 cut(s)	3, 918
BstNSI	RCATGY	1 cut(s)	1035
BstPI	GGTNACC	1 cut(s)	110
BstSFI	CTRYAG	1 cut(s)	1072
BstV1I	GCAGC	3 cut(s)	886, 889, 1070
BsuRI	GGCC	6 cut(s)	224, 265, 370, 787, 851, 927
BtgZI	GCGATG	1 cut(s)	971
BtsCI	GGATG	3 cut(s)	883, 1033, 1135
BtsIMutI	CAGTG	1 cut(s)	494
BveI	ACCTGC	1 cut(s)	77
Cac8I	GCNNGC	5 cut(s)	31, 35, 263, 1045, 1142
CaiI	CAGNNNCTG	1 cut(s)	1106
Cfr10I	RCCGGY	1 cut(s)	261
Cfr13I	GGNCC	3 cut(s)	99, 223, 264
Csp6I	GTAC	3 cut(s)	154, 301, 492
CviAII	CATG	4 cut(s)	212, 853, 1032, 1145
CviQI	GTAC	3 cut(s)	154, 301, 492
DdeI	CTNAG	2 cut(s)	747, 922
DpnI	GATC	2 cut(s)	5, 920
DpnII	GATC	2 cut(s)	3, 918
Eam1104I	CTCTTC	1 cut(s)	175
EarI	CTCTTC	1 cut(s)	175
Eco147I	AGGCCT	2 cut(s)	370, 927
Eco31I	GGTCTC	1 cut(s)	148
Eco47I	GGWCC	1 cut(s)	99
Eco91I	GGTNACC	1 cut(s)	110
EcoO65I	GGTNACC	1 cut(s)	110
EcoT22I	ATGCAT	1 cut(s)	1033
FaeI	CATG	4 cut(s)	215, 856, 1035, 1148
FatI	CATG	4 cut(s)	211, 852, 1031, 1144
FauNDI	CATATG	1 cut(s)	907
FbaI	TGATCA	1 cut(s)	3
FblI	GTMKAC	1 cut(s)	1071
Fnu4HI	GCNGC	3 cut(s)	900, 903, 1059
FokI	GGATG	3 cut(s)	890, 1040, 1142
Fsp4HI	GCNGC	3 cut(s)	900, 903, 1059
FspBI	CTAG	1 cut(s)	789
GluI	GCNGC	3 cut(s)	900, 903, 1059
GsuI	CTGGAG	1 cut(s)	981
HaeIII	GGCC	6 cut(s)	224, 265, 370, 787, 851, 927
HapII	CCGG	1 cut(s)	262
Hin1II	CATG	4 cut(s)	215, 856, 1035, 1148
HincII	GTYRAC	2 cut(s)	217, 1014
HindII	GTYRAC	2 cut(s)	217, 1014
HpaII	CCGG	1 cut(s)	262
HphI	GGTGA	6 cut(s)	122, 155, 571, 703, 857, 928
Hpy166II	GTNNAC	7 cut(s)	203, 217, 308, 494, 802, 1014, 1072
Hpy188I	TCNGA	2 cut(s)	8, 136
Hpy188III	TCNNGA	3 cut(s)	829, 893, 998
Hpy8I	GTNNAC	7 cut(s)	203, 217, 308, 494, 802, 1014, 1072
HpyAV	CCTTC	2 cut(s)	556, 876
HpyCH4III	ACNGT	3 cut(s)	305, 1080, 1199
HpyCH4V	TGCA	7 cut(s)	72, 513, 723, 874, 905, 1031, 1140
HpyF3I	CTNAG	2 cut(s)	747, 922
Hsp92II	CATG	4 cut(s)	215, 856, 1035, 1148
KroI	GCCGGC	1 cut(s)	261
KroNI	GCCGGC	1 cut(s)	263
Ksp22I	TGATCA	1 cut(s)	3
Kzo9I	GATC	2 cut(s)	3, 918
LmnI	GCTCC	1 cut(s)	84
Lsp1109I	GCAGC	3 cut(s)	886, 889, 1070
LweI	GCATC	4 cut(s)	886, 948, 1018, 1093
MaeI	CTAG	1 cut(s)	789
MaeIII	GTNAC	5 cut(s)	110, 274, 379, 691, 967
MalI	GATC	2 cut(s)	5, 920
MboI	GATC	2 cut(s)	3, 918
MboII	GAAGA	6 cut(s)	16, 51, 162, 355, 676, 785
MhlI	GDGCHC	1 cut(s)	1204
MluCI	AATT	8 cut(s)	20, 178, 237, 283, 580, 628, 647, 1186
MmeI	TCCRAC	2 cut(s)	126, 717
Mph1103I	ATGCAT	1 cut(s)	1033
MroNI	GCCGGC	1 cut(s)	261
MseI	TTAA	3 cut(s)	294, 387, 417
MslI	CAYNNNNRTG	1 cut(s)	809
MspA1I	CMGCKG	1 cut(s)	797
MspI	CCGG	1 cut(s)	262
NaeI	GCCGGC	1 cut(s)	263
NdeI	CATATG	1 cut(s)	907
NdeII	GATC	2 cut(s)	3, 918
NgoMIV	GCCGGC	1 cut(s)	261
NlaIII	CATG	4 cut(s)	215, 856, 1035, 1148
NlaIV	GGNNCC	1 cut(s)	260
NmeAIII	GCCGAG	1 cut(s)	200
NmuCI	GTSAC	2 cut(s)	110, 691
NsiI	ATGCAT	1 cut(s)	1033
NspI	RCATGY	1 cut(s)	1035
PceI	AGGCCT	2 cut(s)	370, 927
PdiI	GCCGGC	1 cut(s)	263
PkrI	GCNGC	3 cut(s)	901, 904, 1060
PshBI	ATTAAT	1 cut(s)	294
PspEI	GGTNACC	1 cut(s)	110
PspN4I	GGNNCC	1 cut(s)	260
PspPI	GGNCC	3 cut(s)	99, 223, 264
PstNI	CAGNNNCTG	1 cut(s)	1106
RsaI	GTAC	3 cut(s)	155, 302, 493
RsaNI	GTAC	3 cut(s)	154, 301, 492
RseI	CAYNNNNRTG	1 cut(s)	809
SaqAI	TTAA	3 cut(s)	294, 387, 417
SatI	GCNGC	3 cut(s)	900, 903, 1059
Sau3AI	GATC	2 cut(s)	3, 918
Sau96I	GGNCC	3 cut(s)	99, 223, 264
SduI	GDGCHC	1 cut(s)	1204
SfaNI	GCATC	4 cut(s)	886, 948, 1018, 1093
SfcI	CTRYAG	1 cut(s)	1072
SinI	GGWCC	1 cut(s)	99
SmiMI	CAYNNNNRTG	1 cut(s)	809
SmlI	CTYRAG	1 cut(s)	653
SmoI	CTYRAG	1 cut(s)	653
Sse9I	AATT	8 cut(s)	20, 178, 237, 283, 580, 628, 647, 1186
SseBI	AGGCCT	2 cut(s)	370, 927
SsiI	CCGC	2 cut(s)	108, 797
SspMI	CTAG	1 cut(s)	789
StuI	AGGCCT	2 cut(s)	370, 927
TaaI	ACNGT	3 cut(s)	305, 1080, 1199
TaqI	TCGA	1 cut(s)	948
TasI	AATT	8 cut(s)	20, 178, 237, 283, 580, 628, 647, 1186
TatI	WGTACW	1 cut(s)	491
Tru1I	TTAA	3 cut(s)	294, 387, 417
Tru9I	TTAA	3 cut(s)	294, 387, 417
TscAI	CASTG	1 cut(s)	501
TseFI	GTSAC	2 cut(s)	110, 691
TseI	GCWGC	3 cut(s)	899, 902, 1058
Tsp45I	GTSAC	2 cut(s)	110, 691
TspDTI	ATGAA	6 cut(s)	162, 356, 677, 869, 1180, 1199
TspRI	CASTG	1 cut(s)	501
VpaK11BI	GGWCC	1 cut(s)	99
VspI	ATTAAT	1 cut(s)	294
XapI	RAATTY	3 cut(s)	20, 580, 1186
XceI	RCATGY	1 cut(s)	1035
XmiI	GTMKAC	1 cut(s)	1071
XspI	CTAG	1 cut(s)	789
Zsp2I	ATGCAT	1 cut(s)	1033

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