Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4B

Orthogroup ID

OG0005755

Physical Location & Seq

Genomic Coordinates Reverse (-)

55885014 .. 55886654

Gene Structure 1641 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4BG409400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1641 bp

ATGATCAGACAAACCCTCAAATTCTTCGCTCGCTTGCGAAGAACCTCAAAGCCCCAGTGTCCTTTGACCTACAACAAGCTCCTCCATGATCTCAATAGGTCCAACTGCGGTGACCTCTCTCTCAAAATCCTCTCTGATTTGGTCTCCAAAGGGTACAATCCTCACCCCTCTTCATTCAATTCAGTTATCTCCTTTTTGTGTAAACTGGGTCATGTTAACTCGGCCCAGAAGCTCACAATTTCAATGCCGATTTTCGGGTGCCGGCCCGATATTGTAACATACAATTGTTTGATTAATGGCTACTGTAAACTCTGTGATATTGATGAGGCTTGTTTAGTGATGAAGAGGATAAGGGTAGGAGGGTGTAGGCCTGATTTGGTTACTTTTAATACATTGTTTAGTGGGTTTTGTAAGGTTAAGATGAGGAAAGATGTGTTTGTGTATATGGGTTTGATGTGGAAGTGTTTTGAACCGAATGTGATTAGTTATAGTACATTGATAGATATGTTTTGCAAGATGGGGGATTTGGATTTGGGATATAGGGTTTATGGTTATATGGTGAAGGATAAGGTGTCGCCGAATTTGTTTGCTTTTACTTGTTTGATTGATGGGTATAGTAAGGCTGGTAATTTGGAGGTTGCGATTGAATTGCTTGAGGGAATGAAGAAATCGTTAGTTTTACCGAATGTGGTGACTTACGGTGCTTTGATTGATGGGCTGTGCAAGAATGGGAAGTTGGAAAGAGCTGAGCGTTTGTTTTGTGAAATGGTGGAAGATGGGGTTCGGCCTAGTTCAGCGGTTTACACTTCAATGATAGATGGGCATTTCAAGAAAGGAAATGTAGGTGAGGCCATGAAGTATATGAGTAAAATGCAGGATGGAAGGGTTAGTCTTGATGCCGCTGCATATGGAGTGGTGATCTCAGGCCTCTGTAATAATGGTCAGTTTGATAATGCAATGCGGGTTGTTACAGATTTTGCCACGAGTGGTTTTTCTCCAGATAAGATGTTGTTGACGACCATTATGGATGCATGTTTCAAAGCTGGCAATTTGAAAGCAGGTTTGGGTGTCTACAGATTGTTAGCAAAGGGTTTTGAACCAGATGCTGTGGTGCTTTCAGCTTTGATGGACGGCTTATGCAAGCATGGGCGTTTGGAGGAGGCAAGAGGCTACTTTTGCAAGGAAAAGGCTAATGAAATTTCATATACTGTGATCATTGATGGGATGTGTAAGGAAGCAAACTTTAGTGAAGTTGAGATGATCTTCAGTGAGATGTCCGAGATGGGGTTTACTCCAGACAAATATGTATACACTTCTTGGATTGCTGGGCTATGCAGACAGGGTAATCTGGTCGAGGCTTTTAGACTCAAGAATAAAATGGTTAAAGAGGGCATCAGACCTGATCTGTTTACTTATAGCTCACTTATTTTTGGTTTAGCAAGTAAGGGACTCATGGTTGAAGCACAACAGGTTTTCGATGATATGTTGAAAAGAGGAATTACTCCTGACCGTCACGTCTTTGGTATTCTGATGAGAGGGTATTGTGATGAGGGTAATGATGTTGCCATTTTAGGTTTGCACGATGAAATGAGAAAGAGAGGGCTTGTAGTCACAGGAGGTAAAGGAGATGGAGAGCATTGA

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

546

Amino Acids

60.81

Weight (kDa)

8.49

Isoelectric Point (pI)

23.91

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_2	PF13041	58 - 103	2.2e-12	PPR repeat family
PPR_3	PF13812	84 - 134	2.9e-07	Pentatricopeptide repeat domain
PPR_1	PF12854	86 - 115	1.6e-09	PPR repeat
PPR_2	PF13041	89 - 138	2.7e-16	PPR repeat family
PPR	PF01535	92 - 122	5.9e-06	PPR repeat
PPR_1	PF12854	154 - 186	2.9e-08	PPR repeat
PPR_3	PF13812	156 - 202	2e-06	Pentatricopeptide repeat domain
PPR_2	PF13041	158 - 204	2e-11	PPR repeat family
PPR_long	PF17177	174 - 249	3.5e-06	Pentacotripeptide-repeat region of PRORP
PPR_1	PF12854	191 - 222	1.5e-07	PPR repeat
PPR_2	PF13041	193 - 242	5.3e-15	PPR repeat family
PPR_3	PF13812	197 - 238	8.1e-07	Pentatricopeptide repeat domain
PPR	PF01535	197 - 223	9.3e-06	PPR repeat
PPR_1	PF12854	227 - 257	1.6e-13	PPR repeat
PPR_2	PF13041	228 - 276	2.9e-16	PPR repeat family
PPR	PF01535	231 - 261	2.4e-10	PPR repeat
TPR_24	PF23276	232 - 322	4.1e-06	Fungal tetratrico peptide repeats
PPR_long	PF17177	246 - 362	3.7e-07	Pentacotripeptide-repeat region of PRORP
PPR_2	PF13041	263 - 312	1.8e-10	PPR repeat family
PPR_1	PF12854	363 - 388	1.9e-06	PPR repeat
PPR_2	PF13041	398 - 446	1.6e-11	PPR repeat family
PPR_3	PF13812	421 - 476	4.5e-08	Pentatricopeptide repeat domain
PPR_1	PF12854	428 - 461	6.7e-08	PPR repeat
PPR	PF01535	436 - 465	8.5e-06	PPR repeat
PPR_2	PF13041	436 - 480	8.2e-13	PPR repeat family
PPR_1	PF12854	464 - 495	8.5e-09	PPR repeat
PPR	PF01535	470 - 500	1.6e-06	PPR repeat
PPR_2	PF13041	475 - 516	4e-09	PPR repeat family

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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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)
AasI	GACNNNNNNGTC	1 cut(s)	1514
Acc36I	ACCTGC	1 cut(s)	1049
AccB1I	GGYRCC	1 cut(s)	258
AccI	GTMKAC	2 cut(s)	1071, 1308
AciI	CCGC	4 cut(s)	108, 797, 900, 961
AcsI	RAATTY	3 cut(s)	20, 580, 1197
AcuI	CTGAAG	1 cut(s)	1249
AfaI	GTAC	2 cut(s)	155, 493
AfiI	CCNNNNNNNGG	2 cut(s)	254, 1284
AjiI	CACGTC	1 cut(s)	1516
AjuI	GAANNNNNNNTTGG	4 cut(s)	719, 751, 1046, 1078
AluBI	AGCT	6 cut(s)	79, 232, 746, 1043, 1121, 1419
AluI	AGCT	6 cut(s)	79, 232, 746, 1043, 1121, 1419
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	1 cut(s)	902
ApoI	RAATTY	3 cut(s)	20, 580, 1197
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
BbvI	GCAGC	1 cut(s)	889
BceAI	ACGGC	1 cut(s)	1147
BcgI	CGANNNNNNTGC	2 cut(s)	631, 665
BclI	TGATCA	2 cut(s)	3, 1212
BcoDI	GTCTC	1 cut(s)	148
BfaI	CTAG	1 cut(s)	789
BfmI	CTRYAG	1 cut(s)	1072
BfuAI	ACCTGC	1 cut(s)	1049
BisI	GCNGC	2 cut(s)	900, 903
BlpI	GCTNAGC	1 cut(s)	747
BlsI	GCNGC	2 cut(s)	901, 904
Bme18I	GGWCC	1 cut(s)	99
BmgBI	CACGTC	1 cut(s)	1516
BmgT120I	GGNCC	3 cut(s)	99, 223, 264
BmiI	GGNNCC	1 cut(s)	260
BmrI	ACTGGG	2 cut(s)	49, 215
BmsI	GCATC	4 cut(s)	886, 1018, 1093, 1401
BmuI	ACTGGG	2 cut(s)	49, 215
BpmI	CTGGAG	2 cut(s)	981, 1278
Bpu1102I	GCTNAGC	1 cut(s)	747
BpuEI	CTTGAG	2 cut(s)	674, 1352
BsaI	GGTCTC	1 cut(s)	148
Bsc4I	CCNNNNNNNGG	2 cut(s)	254, 1284
Bse118I	RCCGGY	1 cut(s)	261
Bse1I	ACTGG	2 cut(s)	55, 210
Bse3DI	GCAATG	1 cut(s)	963
BseGI	GGATG	3 cut(s)	883, 1033, 1230
BseLI	CCNNNNNNNGG	2 cut(s)	254, 1284
BseMI	GCAATG	1 cut(s)	963
BseMII	CTCAG	2 cut(s)	738, 936
BseNI	ACTGG	2 cut(s)	55, 210
BseRI	GAGGAG	2 cut(s)	71, 1172
BseXI	GCAGC	1 cut(s)	889
BseYI	CCCAGC	1 cut(s)	1325
BshFI	GGCC	6 cut(s)	224, 265, 370, 787, 851, 927
BshNI	GGYRCC	1 cut(s)	258
BsiSI	CCGG	1 cut(s)	262
BslFI	GGGAC	1 cut(s)	1461
BslI	CCNNNNNNNGG	2 cut(s)	254, 1284
BsmAI	GTCTC	1 cut(s)	148
BsmFI	GGGAC	1 cut(s)	1461
BsnI	GGCC	6 cut(s)	224, 265, 370, 787, 851, 927
Bso31I	GGTCTC	1 cut(s)	148
Bsp143I	GATC	6 cut(s)	3, 88, 918, 1212, 1260, 1402
Bsp1720I	GCTNAGC	1 cut(s)	747
BspACI	CCGC	4 cut(s)	108, 797, 900, 961
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)	1049
BspT107I	GGYRCC	1 cut(s)	258
BspTNI	GGTCTC	1 cut(s)	148
BsrDI	GCAATG	1 cut(s)	963
BsrFI	RCCGGY	1 cut(s)	261
BsrI	ACTGG	2 cut(s)	55, 210
BssAI	RCCGGY	1 cut(s)	261
BssMI	GATC	6 cut(s)	3, 88, 918, 1212, 1260, 1402
BssNAI	GTATAC	1 cut(s)	1309
BssSI	CACGAG	1 cut(s)	982
Bst1107I	GTATAC	1 cut(s)	1309
Bst2BI	CACGAG	1 cut(s)	982
Bst4CI	ACNGT	4 cut(s)	305, 701, 1210, 1511
Bst6I	CTCTTC	2 cut(s)	175, 338
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, 1230
BstKTI	GATC	6 cut(s)	6, 91, 921, 1215, 1263, 1405
BstMAI	GTCTC	1 cut(s)	148
BstMBI	GATC	6 cut(s)	3, 88, 918, 1212, 1260, 1402
BstMWI	GCNNNNNNNGC	1 cut(s)	1176
BstNSI	RCATGY	1 cut(s)	1035
BstPI	GGTNACC	1 cut(s)	110
BstSFI	CTRYAG	1 cut(s)	1072
BstV1I	GCAGC	1 cut(s)	889
BstZ17I	GTATAC	1 cut(s)	1309
BsuRI	GGCC	6 cut(s)	224, 265, 370, 787, 851, 927
BtrI	CACGTC	1 cut(s)	1516
BtsCI	GGATG	3 cut(s)	883, 1033, 1230
BtsIMutI	CAGTG	2 cut(s)	62, 1273
BveI	ACCTGC	1 cut(s)	1049
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	2 cut(s)	154, 492
CviAII	CATG	6 cut(s)	86, 212, 853, 1032, 1145, 1453
CviQI	GTAC	2 cut(s)	154, 492
DdeI	CTNAG	2 cut(s)	747, 922
DpnI	GATC	6 cut(s)	5, 90, 920, 1214, 1262, 1404
DpnII	GATC	6 cut(s)	3, 88, 918, 1212, 1260, 1402
DrdI	GACNNNNNNGTC	1 cut(s)	1514
DseDI	GACNNNNNNGTC	1 cut(s)	1514
Eam1104I	CTCTTC	2 cut(s)	175, 338
EarI	CTCTTC	2 cut(s)	175, 338
Eco147I	AGGCCT	2 cut(s)	370, 927
Eco31I	GGTCTC	1 cut(s)	148
Eco47I	GGWCC	1 cut(s)	99
Eco57I	CTGAAG	1 cut(s)	1249
Eco91I	GGTNACC	1 cut(s)	110
EcoO65I	GGTNACC	1 cut(s)	110
EcoT22I	ATGCAT	1 cut(s)	1033
FaeI	CATG	6 cut(s)	89, 215, 856, 1035, 1148, 1456
FaqI	GGGAC	1 cut(s)	1461
FatI	CATG	6 cut(s)	85, 211, 852, 1031, 1144, 1452
FauI	CCCGC	1 cut(s)	954
FauNDI	CATATG	1 cut(s)	907
FbaI	TGATCA	2 cut(s)	3, 1212
FblI	GTMKAC	2 cut(s)	1071, 1308
Fnu4HI	GCNGC	2 cut(s)	900, 903
FokI	GGATG	3 cut(s)	890, 1040, 1237
Fsp4HI	GCNGC	2 cut(s)	900, 903
FspBI	CTAG	1 cut(s)	789
GluI	GCNGC	2 cut(s)	900, 903
GsaI	CCCAGC	1 cut(s)	1329
GsuI	CTGGAG	2 cut(s)	981, 1278
HaeIII	GGCC	6 cut(s)	224, 265, 370, 787, 851, 927
HapII	CCGG	1 cut(s)	262
Hin1II	CATG	6 cut(s)	89, 215, 856, 1035, 1148, 1456
HincII	GTYRAC	2 cut(s)	217, 1014
HindII	GTYRAC	2 cut(s)	217, 1014
HinfI	GANTC	2 cut(s)	1365, 1449
HpaI	GTTAAC	1 cut(s)	217
HpaII	CCGG	1 cut(s)	262
HphI	GGTGA	6 cut(s)	122, 155, 571, 703, 857, 928
Hpy166II	GTNNAC	9 cut(s)	203, 217, 308, 802, 1014, 1072, 1290, 1309, 1410
Hpy188I	TCNGA	5 cut(s)	8, 136, 1279, 1397, 1530
Hpy188III	TCNNGA	6 cut(s)	829, 893, 998, 1295, 1369, 1505
Hpy8I	GTNNAC	9 cut(s)	203, 217, 308, 802, 1014, 1072, 1290, 1309, 1410
HpyAV	CCTTC	2 cut(s)	556, 876
HpyCH4III	ACNGT	4 cut(s)	305, 701, 1210, 1511
HpyCH4IV	ACGT	1 cut(s)	1515
HpyF10VI	GCNNNNNNNGC	1 cut(s)	1176
HpyF3I	CTNAG	2 cut(s)	747, 922
HpySE526I	ACGT	1 cut(s)	1515
Hsp92II	CATG	6 cut(s)	89, 215, 856, 1035, 1148, 1456
KroI	GCCGGC	1 cut(s)	261
KroNI	GCCGGC	1 cut(s)	263
Ksp22I	TGATCA	2 cut(s)	3, 1212
KspAI	GTTAAC	1 cut(s)	217
Kzo9I	GATC	6 cut(s)	3, 88, 918, 1212, 1260, 1402
LmnI	GCTCC	1 cut(s)	84
Lsp1109I	GCAGC	1 cut(s)	889
LweI	GCATC	4 cut(s)	886, 1018, 1093, 1401
MaeI	CTAG	1 cut(s)	789
MaeII	ACGT	1 cut(s)	1515
MaeIII	GTNAC	7 cut(s)	110, 274, 379, 691, 967, 1511, 1609
MalI	GATC	6 cut(s)	5, 90, 920, 1214, 1262, 1404
MboI	GATC	6 cut(s)	3, 88, 918, 1212, 1260, 1402
MboII	GAAGA	7 cut(s)	16, 51, 162, 355, 676, 785, 1255
MfeI	CAATTG	1 cut(s)	283
MlyI	GAGTC	2 cut(s)	1359, 1443
MmeI	TCCRAC	2 cut(s)	126, 717
Mph1103I	ATGCAT	1 cut(s)	1033
MroNI	GCCGGC	1 cut(s)	261
MseI	TTAA	5 cut(s)	216, 294, 387, 417, 1383
MslI	CAYNNNNRTG	1 cut(s)	809
MspA1I	CMGCKG	2 cut(s)	797, 902
MspI	CCGG	1 cut(s)	262
MunI	CAATTG	1 cut(s)	283
MwoI	GCNNNNNNNGC	1 cut(s)	1176
NaeI	GCCGGC	1 cut(s)	263
NdeI	CATATG	1 cut(s)	907
NdeII	GATC	6 cut(s)	3, 88, 918, 1212, 1260, 1402
NgoMIV	GCCGGC	1 cut(s)	261
NlaIII	CATG	6 cut(s)	89, 215, 856, 1035, 1148, 1456
NlaIV	GGNNCC	1 cut(s)	260
NmeAIII	GCCGAG	1 cut(s)	200
NmuCI	GTSAC	4 cut(s)	110, 691, 1511, 1609
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	2 cut(s)	901, 904
PleI	GAGTC	2 cut(s)	1359, 1443
PpsI	GAGTC	2 cut(s)	1359, 1443
PshBI	ATTAAT	1 cut(s)	294
PspEI	GGTNACC	1 cut(s)	110
PspFI	CCCAGC	1 cut(s)	1325
PspN4I	GGNNCC	1 cut(s)	260
PspPI	GGNCC	3 cut(s)	99, 223, 264
PstNI	CAGNNNCTG	1 cut(s)	1106
RsaI	GTAC	2 cut(s)	155, 493
RsaNI	GTAC	2 cut(s)	154, 492
RseI	CAYNNNNRTG	1 cut(s)	809
SaqAI	TTAA	5 cut(s)	216, 294, 387, 417, 1383
SatI	GCNGC	2 cut(s)	900, 903
Sau3AI	GATC	6 cut(s)	3, 88, 918, 1212, 1260, 1402
Sau96I	GGNCC	3 cut(s)	99, 223, 264
SchI	GAGTC	2 cut(s)	1359, 1443
SfaNI	GCATC	4 cut(s)	886, 1018, 1093, 1401
SfcI	CTRYAG	1 cut(s)	1072
SinI	GGWCC	1 cut(s)	99
SmiMI	CAYNNNNRTG	1 cut(s)	809
SmlI	CTYRAG	2 cut(s)	653, 1367
SmoI	CTYRAG	2 cut(s)	653, 1367
SseBI	AGGCCT	2 cut(s)	370, 927
SsiI	CCGC	4 cut(s)	108, 797, 900, 961
SspMI	CTAG	1 cut(s)	789
StuI	AGGCCT	2 cut(s)	370, 927
TaaI	ACNGT	4 cut(s)	305, 701, 1210, 1511
TaiI	ACGT	1 cut(s)	1518
TaqI	TCGA	2 cut(s)	1353, 1476
TatI	WGTACW	1 cut(s)	491
TauI	GCSGC	1 cut(s)	902
Tru1I	TTAA	5 cut(s)	216, 294, 387, 417, 1383
Tru9I	TTAA	5 cut(s)	216, 294, 387, 417, 1383
TscAI	CASTG	2 cut(s)	62, 1273
TseFI	GTSAC	4 cut(s)	110, 691, 1511, 1609
TseI	GCWGC	1 cut(s)	902
Tsp45I	GTSAC	4 cut(s)	110, 691, 1511, 1609
TspDTI	ATGAA	7 cut(s)	162, 356, 677, 869, 1191, 1209, 1599
TspRI	CASTG	2 cut(s)	62, 1273
VpaK11BI	GGWCC	1 cut(s)	99
VspI	ATTAAT	1 cut(s)	294
XapI	RAATTY	3 cut(s)	20, 580, 1197
XceI	RCATGY	1 cut(s)	1035
XmiI	GTMKAC	2 cut(s)	1071, 1308
XspI	CTAG	1 cut(s)	789
Zsp2I	ATGCAT	1 cut(s)	1033

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