Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4A

Orthogroup ID

OG0005755

Physical Location & Seq

Genomic Coordinates Reverse (-)

70234511 .. 70236151

Gene Structure 1641 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4AG397900.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1641 bp

ATGATCAGACAAACCCTCAAATTCTTCGCTCGCTTGCGAAGAACCTCAAAGCCCCAATGTCCTTTGACCTGCAACAAGCTCCTCCATAACCTCAATAGGTCCAACTGCGGTGACCTCTCTCTCAAAATCCTCTCTGATTTGGTCTCCAAAGGGTACAATCCTCACCCCTCTTCATTCAATTCAGTTATCTCCTTTTTGTGTAAACTGGGTCATGTCAACTCGGCCCAGAAGCTCACAATTTCAATGCCGATTTTCGGGTGCCGGCCCGATATTGTAACATACAATTCTTTGATTAATGGGTACTGTAAACTCTGTGATATTGATGAGGCTTGTTTAGTGATGAAGATGATAAGGGTAGGAGGGTGTAGGCCTGATTTGGTTACTTTTAATACATTGTTTAGTGGGTTCTGTAAGGTTAAGATGAGGAAAGAAGTGTTTGTGTATATGGGTTTGATGTGGAAGTGTTTTGAACCGAATGTGATTAGTTATAGTACACTGATAGATATGTTTTGCAAGATGGGGGATTTGGATTTGGGATATAGGGTTTATGGTTATATGGTGAAGGATAAGGTGTCGCCGAATTTGTTTGCTTTTACTTGTTTGATTGATGGGTATAGTAAGGCTGGTAATTTGGAGGTTGCGATTGAATTGCTTGAGGGAATGAAGAAATCGTTAGTTTTACCGAATGTGGTGACTTATGGTGCTTTGATTGATGGGCTGTGCAAGAATGGGAAGTTGGAAAGAGCTGAGCGTTTGTTTTGTGAAATGGTGGAAGATGGGGTTCGGCCTAGTTCAGCGGTTTACACTTCAATGATAGATGGGCATTTCAAGAAAGGAAATGTAGGTGAGGCCATGAAGTATATGAGTAAAATGCAGGATGGAAGGGTTAGTCTTGATGCTGCTGCATATGGAGTGGTGATCTCAGGCCTCTGTAATAATGGTCAGTTCGATAATGCGATGCGAGTTGTTACAGATTTTGCCACGAGTGGTTTTTCTCCAGATAAGATGTTGTTGACGACCATTATGGATGCATGTTTCAAAGCTGGCGATTTGAAAGCAGCTTTGGGTGTCTACAGACTGTTAGCAAAGGTTTTTGAACCAGATGCTGTGGTGCTTTCAGCTTTGATGGATGGCTTATGCAAGCATGGGCATTTGGAGGAGGCAAGAGGCTACTTTTGTAAGGAAAAGGCTAATGAAATTTCATATACTGTGATCATTGATGGGATGTGTAAGGAAGCAAACTTTAGTGAAGTTGAGATGATCTTCAGTGAGATGTCCGAGATGGGGTTTACTCCAGACAAATATGTATACACTTCTTGGATTGCTGAGCTATGCAGACAGGGTAATCTGGTCGAGACTTTTAGACTTAAGAATAAAATGGTTAAAGAGGGCATCAGACCTGATCTGTTTACTTATAGCTCACTTATTTTTGGTTTAGCAAGTAAGGGACTCATGGTTGAAGCACAACAGGTTTTCGATGATATGTTGAAAAGAGGAATTACTCCTGACCGTCACGTCTTTGGTATTCTGATGAGAGGGTATTGTGATGAGGGTAATGATGTTGCCATTTTAGGTTTGCACGATGAAATGAGAAAGAGAGGGCTTGTAGTCACAGGAGGTAAAGGAGATGGAGAGCATTGA

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

60.86

Weight (kDa)

8.22

Isoelectric Point (pI)

24.43

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	4.8e-07	Pentatricopeptide repeat domain
PPR_1	PF12854	86 - 114	1.1e-09	PPR repeat
PPR_2	PF13041	89 - 138	9.2e-16	PPR repeat family
PPR	PF01535	92 - 122	5.5e-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 - 205	7e-12	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	194 - 238	3.2e-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 - 274	7.8e-16	PPR repeat family
PPR	PF01535	231 - 261	2.4e-10	PPR repeat
TPR_24	PF23276	232 - 321	7.9e-06	Fungal tetratrico peptide repeats
PPR_long	PF17177	246 - 364	6.5e-08	Pentacotripeptide-repeat region of PRORP
PPR_2	PF13041	263 - 312	1.8e-10	PPR repeat family
TPR_24	PF23276	268 - 359	6.9e-06	Fungal tetratrico peptide repeats
PPR_2	PF13041	398 - 446	1.7e-10	PPR repeat family
PPR_3	PF13812	421 - 476	1.5e-06	Pentatricopeptide repeat domain
PPR_2	PF13041	436 - 480	1.3e-10	PPR repeat family
PPR_3	PF13812	455 - 514	5.6e-08	Pentatricopeptide repeat domain
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)	77
AccB1I	GGYRCC	1 cut(s)	258
AccI	GTMKAC	2 cut(s)	1071, 1308
AciI	CCGC	2 cut(s)	108, 797
AcsI	RAATTY	3 cut(s)	20, 580, 1197
AcuI	CTGAAG	1 cut(s)	1249
AfaI	GTAC	3 cut(s)	155, 302, 493
AfiI	CCNNNNNNNGG	2 cut(s)	254, 1284
AflII	CTTAAG	1 cut(s)	1367
AjiI	CACGTC	1 cut(s)	1516
AjuI	GAANNNNNNNTTGG	4 cut(s)	719, 751, 1046, 1078
AluBI	AGCT	8 cut(s)	79, 232, 746, 1043, 1061, 1121, 1330, 1419
AluI	AGCT	8 cut(s)	79, 232, 746, 1043, 1061, 1121, 1330, 1419
Alw26I	GTCTC	2 cut(s)	148, 1349
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, 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	3 cut(s)	886, 889, 1070
BcgI	CGANNNNNNTGC	2 cut(s)	631, 665
BclI	TGATCA	2 cut(s)	3, 1212
BcoDI	GTCTC	2 cut(s)	148, 1349
BfaI	CTAG	1 cut(s)	789
BfmI	CTRYAG	1 cut(s)	1072
BfrI	CTTAAG	1 cut(s)	1367
BfuAI	ACCTGC	1 cut(s)	77
BisI	GCNGC	3 cut(s)	900, 903, 1059
BlpI	GCTNAGC	2 cut(s)	747, 1326
BlsI	GCNGC	3 cut(s)	901, 904, 1060
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	1 cut(s)	215
BmsI	GCATC	5 cut(s)	886, 948, 1018, 1093, 1401
BmuI	ACTGGG	1 cut(s)	215
BpmI	CTGGAG	2 cut(s)	981, 1278
Bpu1102I	GCTNAGC	2 cut(s)	747, 1326
BpuEI	CTTGAG	1 cut(s)	674
BsaI	GGTCTC	1 cut(s)	148
Bsc4I	CCNNNNNNNGG	2 cut(s)	254, 1284
Bse118I	RCCGGY	1 cut(s)	261
Bse1I	ACTGG	1 cut(s)	210
BseGI	GGATG	4 cut(s)	883, 1033, 1135, 1230
BseLI	CCNNNNNNNGG	2 cut(s)	254, 1284
BseMII	CTCAG	3 cut(s)	738, 936, 1317
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
BsiSI	CCGG	1 cut(s)	262
BslFI	GGGAC	1 cut(s)	1461
BslI	CCNNNNNNNGG	2 cut(s)	254, 1284
BsmAI	GTCTC	2 cut(s)	148, 1349
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	5 cut(s)	3, 918, 1212, 1260, 1402
Bsp1720I	GCTNAGC	2 cut(s)	747, 1326
BspACI	CCGC	2 cut(s)	108, 797
BspANI	GGCC	6 cut(s)	224, 265, 370, 787, 851, 927
BspCNI	CTCAG	3 cut(s)	739, 935, 1318
BspLI	GGNNCC	1 cut(s)	260
BspMI	ACCTGC	1 cut(s)	77
BspT107I	GGYRCC	1 cut(s)	258
BspTI	CTTAAG	1 cut(s)	1367
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	5 cut(s)	3, 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, 1080, 1210, 1511
Bst6I	CTCTTC	1 cut(s)	175
BstAFI	CTTAAG	1 cut(s)	1367
BstC8I	GCNNGC	5 cut(s)	31, 35, 263, 1045, 1142
BstDEI	CTNAG	3 cut(s)	747, 922, 1326
BstEII	GGTNACC	1 cut(s)	110
BstF5I	GGATG	4 cut(s)	883, 1033, 1135, 1230
BstKTI	GATC	5 cut(s)	6, 921, 1215, 1263, 1405
BstMAI	GTCTC	2 cut(s)	148, 1349
BstMBI	GATC	5 cut(s)	3, 918, 1212, 1260, 1402
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
BstZ17I	GTATAC	1 cut(s)	1309
BsuRI	GGCC	6 cut(s)	224, 265, 370, 787, 851, 927
BtgZI	GCGATG	1 cut(s)	971
BtrI	CACGTC	1 cut(s)	1516
BtsCI	GGATG	4 cut(s)	883, 1033, 1135, 1230
BtsIMutI	CAGTG	2 cut(s)	494, 1273
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	5 cut(s)	212, 853, 1032, 1145, 1453
CviQI	GTAC	3 cut(s)	154, 301, 492
DdeI	CTNAG	3 cut(s)	747, 922, 1326
DpnI	GATC	5 cut(s)	5, 920, 1214, 1262, 1404
DpnII	GATC	5 cut(s)	3, 918, 1212, 1260, 1402
DrdI	GACNNNNNNGTC	1 cut(s)	1514
DseDI	GACNNNNNNGTC	1 cut(s)	1514
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
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	5 cut(s)	215, 856, 1035, 1148, 1456
FaqI	GGGAC	1 cut(s)	1461
FatI	CATG	5 cut(s)	211, 852, 1031, 1144, 1452
FauNDI	CATATG	1 cut(s)	907
FbaI	TGATCA	2 cut(s)	3, 1212
FblI	GTMKAC	2 cut(s)	1071, 1308
Fnu4HI	GCNGC	3 cut(s)	900, 903, 1059
FokI	GGATG	4 cut(s)	890, 1040, 1142, 1237
Fsp4HI	GCNGC	3 cut(s)	900, 903, 1059
FspBI	CTAG	1 cut(s)	789
GluI	GCNGC	3 cut(s)	900, 903, 1059
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	5 cut(s)	215, 856, 1035, 1148, 1456
HincII	GTYRAC	2 cut(s)	217, 1014
HindII	GTYRAC	2 cut(s)	217, 1014
HinfI	GANTC	1 cut(s)	1449
HpaII	CCGG	1 cut(s)	262
HphI	GGTGA	6 cut(s)	122, 155, 571, 703, 857, 928
Hpy188I	TCNGA	5 cut(s)	8, 136, 1279, 1397, 1530
Hpy188III	TCNNGA	6 cut(s)	829, 893, 998, 1295, 1354, 1505
HpyAV	CCTTC	2 cut(s)	556, 876
HpyCH4III	ACNGT	4 cut(s)	305, 1080, 1210, 1511
HpyCH4IV	ACGT	1 cut(s)	1515
HpyCH4V	TGCA	9 cut(s)	72, 513, 723, 874, 905, 1031, 1140, 1335, 1579
HpyF3I	CTNAG	3 cut(s)	747, 922, 1326
HpySE526I	ACGT	1 cut(s)	1515
Hsp92II	CATG	5 cut(s)	215, 856, 1035, 1148, 1456
KroI	GCCGGC	1 cut(s)	261
KroNI	GCCGGC	1 cut(s)	263
Ksp22I	TGATCA	2 cut(s)	3, 1212
Kzo9I	GATC	5 cut(s)	3, 918, 1212, 1260, 1402
LmnI	GCTCC	1 cut(s)	84
Lsp1109I	GCAGC	3 cut(s)	886, 889, 1070
LweI	GCATC	5 cut(s)	886, 948, 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	5 cut(s)	5, 920, 1214, 1262, 1404
MboI	GATC	5 cut(s)	3, 918, 1212, 1260, 1402
MboII	GAAGA	7 cut(s)	16, 51, 162, 355, 676, 785, 1255
MluCI	AATT	9 cut(s)	20, 178, 237, 283, 580, 628, 647, 1197, 1497
MlyI	GAGTC	1 cut(s)	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)	294, 387, 417, 1368, 1383
MslI	CAYNNNNRTG	1 cut(s)	809
MspA1I	CMGCKG	1 cut(s)	797
MspCI	CTTAAG	1 cut(s)	1367
MspI	CCGG	1 cut(s)	262
NaeI	GCCGGC	1 cut(s)	263
NdeI	CATATG	1 cut(s)	907
NdeII	GATC	5 cut(s)	3, 918, 1212, 1260, 1402
NgoMIV	GCCGGC	1 cut(s)	261
NlaIII	CATG	5 cut(s)	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	3 cut(s)	901, 904, 1060
PleI	GAGTC	1 cut(s)	1443
PpsI	GAGTC	1 cut(s)	1443
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	5 cut(s)	294, 387, 417, 1368, 1383
SatI	GCNGC	3 cut(s)	900, 903, 1059
Sau3AI	GATC	5 cut(s)	3, 918, 1212, 1260, 1402
Sau96I	GGNCC	3 cut(s)	99, 223, 264
SchI	GAGTC	1 cut(s)	1443
SfaNI	GCATC	5 cut(s)	886, 948, 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
Sse9I	AATT	9 cut(s)	20, 178, 237, 283, 580, 628, 647, 1197, 1497
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	4 cut(s)	305, 1080, 1210, 1511
TaiI	ACGT	1 cut(s)	1518
TaqI	TCGA	3 cut(s)	948, 1353, 1476
TasI	AATT	9 cut(s)	20, 178, 237, 283, 580, 628, 647, 1197, 1497
TatI	WGTACW	1 cut(s)	491
Tru1I	TTAA	5 cut(s)	294, 387, 417, 1368, 1383
Tru9I	TTAA	5 cut(s)	294, 387, 417, 1368, 1383
TscAI	CASTG	2 cut(s)	501, 1273
TseFI	GTSAC	4 cut(s)	110, 691, 1511, 1609
TseI	GCWGC	3 cut(s)	899, 902, 1058
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)	501, 1273
Vha464I	CTTAAG	1 cut(s)	1367
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.