Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5C

Orthogroup ID

OG0012459

Physical Location & Seq

Genomic Coordinates Forward (+)

20848150 .. 20850537

Gene Structure 2388 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5CG206800.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1443 bp

ATGATAGGGAAGGGCCAAAAGCCTGATGTGGGCCAAGCAACTCAGCTCTTGTATGATCTGTGCAAGGCGAGTAAGATGAGGAAAGCGGTGAGAGTGATCGAAATGATGGTTGCTTCAGGCATTATACCTGATGCAGCTTCATATACCTTCTTGGTGAACTATTTGTGTAAAAGAGGGAATATTGGTTATGCAATGCAGTTGGTTGAGAAGATGGAGGAGTATGGATATCCGACTAATACTGTTACCTATAATTCACTTGTTAGAGGGCTTTGTGTGCGTGGAAATTTGAATCAAAGCTTGCAGCTTTTGGATAAGCTGATACGGAAGGGGCTGGTCCCGAATGTTTATACTTACTCTTTCTTGCTTGAAGCGGCTTATAAGGAAAGAGGGGTCAACGAAGCGATGAAGCTCCTGGAGGATATCATTGCTAAAGGTGGAAAGCCTAATTTGGTTAGTTACAATGTTTTGTTGACTGGTTTGTGCAAGGAAGGTAGGAGTGATGAGGCAATGAAGTTTTTTAGGAGTTTGCCTTCGATGGGATTCAGACCGAATGTTGTGAGCTATAACATTGTGCTGAGGAACTTGTGTTATGAGGGTAGGTGGGAAGAGGCGAATGTGCTTTTAGCTGAGATGGATGGTGAGGATCGGACACCCTCCATAGTTACATATAACATCTTAATCAGTTCTCTTGCCCTTCATGGTAGAACAGAACATGCTCTTGAAGTTTTGGATGAAATGGTTAAGGGTCGGTTCAAGCCTACTGCTGCAAGCTACAATCCGATAATTGCTCGTCTCTGCAAAGAGGGGAAAGTGGATCATGTGGTGAAGTGTCTAGACCAAATGATGTTCCGGCGATGTAATCCAAATGAGGGAACATTCAATGCCATTGCTGTGCTATGTGAGCAAGGTATGTTGCAAGAAGCATACTCCATCATTCAAAGCCTCGGAAATAAACAGAAATGCTCCACGAATGAGTTCTACAGAAATGTAATCACAAGCTTGTGCAGGAAAGGGAATACATATCCAGCATTTCAGATGTTATATGAAATGACCAAGTATGGTTTTACTCCAGATTCTTATACCTATTCATCTTTGATCAGAGGGTTGTGTCTGGAGGGTATGCTAAATGAAGCAATGGAGATTTTCAAGGTCATGGAGGAAAACAACCAAAGGCCTGATACTGAGAATTTCAATGCCCTTATACTTGGATTTTGCAAATGTCGAAGAACAGATCTATCCTTGCAGGTTTTCGAGATGATGATTGAGAAAAGGCTAATGCCTAATGAAATGACATATACAATTCTCGTGGAAGGGCTTGCACATGAAAACGAAACGGAGCTGGCAGCTGAGGTTTTGAGGGAGTTGCAGGGGAGACGGGTTATGAGTCCAAATACAGTGGAAAGACTTGTTATGCAGTATGACCTTGAGGAAATACCATTGTAG

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

480

Amino Acids

54.58

Weight (kDa)

6.52

Isoelectric Point (pI)

34.96

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_2	PF13041	16 - 57	3.9e-07	PPR repeat family
PPR_long	PF17177	25 - 126	2e-07	Pentacotripeptide-repeat region of PRORP
PPR_1	PF12854	40 - 72	5.7e-07	PPR repeat
PPR_2	PF13041	43 - 91	4.4e-12	PPR repeat family
TPR_24	PF23276	59 - 175	6.5e-07	Fungal tetratrico peptide repeats
PPR_3	PF13812	67 - 124	8.5e-08	Pentatricopeptide repeat domain
PPR_1	PF12854	76 - 105	2.5e-06	PPR repeat
PPR_2	PF13041	79 - 124	8.7e-12	PPR repeat family
PPR_2	PF13041	121 - 162	1.4e-07	PPR repeat family
PPR_3	PF13812	136 - 192	2.3e-07	Pentatricopeptide repeat domain
PPR_1	PF12854	144 - 174	3.2e-10	PPR repeat
PPR_2	PF13041	148 - 196	4.6e-15	PPR repeat family
PPR	PF01535	151 - 181	7.3e-07	PPR repeat
PPR_1	PF12854	179 - 211	2.3e-06	PPR repeat
PPR_2	PF13041	183 - 231	9.4e-13	PPR repeat family
PPR_3	PF13812	207 - 263	4.7e-09	Pentatricopeptide repeat domain
PPR_1	PF12854	218 - 247	1.6e-08	PPR repeat
PPR_2	PF13041	218 - 259	1.1e-09	PPR repeat family
PPR	PF01535	221 - 248	4.1e-07	PPR repeat
PPR_2	PF13041	253 - 296	9.3e-09	PPR repeat family
PPR_2	PF13041	327 - 370	1e-11	PPR repeat family
PPR_3	PF13812	347 - 401	5.6e-08	Pentatricopeptide repeat domain
PPR_1	PF12854	354 - 386	1.7e-11	PPR repeat
PPR	PF01535	360 - 389	1.9e-07	PPR repeat
PPR_2	PF13041	392 - 441	3.5e-11	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: OG0012459)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G79080
fragaria_vesca	FvH4_3g15990
malus_domestica	MD05G1216400.v1.1 MD10G1198700.v1.1
prunus_persica	Prupe.4G143000_v2.0.a1
pyrus_communis	pycom05g19870 pycom10g17140
rosa_chinensis	RchiOBHm_Chr5g0026921
rosa_laevigata	RLG00000032970
rosa_multiflora	Rmu_co8463079.1_g000001 Rmu_sc0004223.1_g000006 Rmu_sc0008732.1_g000003
rosa_roxburghii	Rroxscaffold_1G00052550
rosa_rugosa	Rorug05G0095900
rosa_samantha	Rh5AG189500 Rh5BG187100 Rh5CG206800 Rh5DG188800
rosa_wichuraiana	Rw5G017240

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	378
Acc36I	ACCTGC	1 cut(s)	1234
AciI	CCGC	2 cut(s)	86, 371
AclWI	GGATC	2 cut(s)	651, 822
AcsI	RAATTY	2 cut(s)	283, 1186
AcuI	CTGAAG	1 cut(s)	99
AfiI	CCNNNNNNNGG	3 cut(s)	29, 536, 869
AgsI	TTSAA	8 cut(s)	289, 368, 722, 754, 880, 938, 1147, 1192
AjnI	CCWGG	1 cut(s)	411
Alw26I	GTCTC	2 cut(s)	797, 1366
AlwI	GGATC	2 cut(s)	651, 822
AoxI	GGCC	3 cut(s)	13, 31, 1172
ApeKI	GCWGC	4 cut(s)	134, 301, 764, 1343
ApoI	RAATTY	2 cut(s)	283, 1186
Asp700I	GAANNNNTTC	1 cut(s)	974
AspS9I	GGNCC	3 cut(s)	13, 31, 334
AsuHPI	GGTGA	4 cut(s)	100, 166, 650, 835
AvaII	GGWCC	1 cut(s)	334
BauI	CACGAG	1 cut(s)	1304
BbvCI	CCTCAGC	2 cut(s)	575, 1347
BbvI	GCAGC	4 cut(s)	146, 313, 751, 1355
BccI	CCATC	6 cut(s)	100, 205, 529, 625, 629, 938
BciT130I	CCWGG	1 cut(s)	413
BclI	TGATCA	1 cut(s)	1095
BcoDI	GTCTC	2 cut(s)	797, 1366
BfaI	CTAG	1 cut(s)	833
BfmI	CTRYAG	1 cut(s)	979
BfuAI	ACCTGC	1 cut(s)	1234
BglII	AGATCT	1 cut(s)	1231
BisI	GCNGC	5 cut(s)	135, 302, 372, 765, 1344
BlsI	GCNGC	5 cut(s)	136, 303, 373, 766, 1345
Bme1390I	CCNGG	1 cut(s)	413
Bme18I	GGWCC	1 cut(s)	334
BmgT120I	GGNCC	3 cut(s)	13, 31, 334
BmiI	GGNNCC	1 cut(s)	336
BmrFI	CCNGG	1 cut(s)	413
BmsI	GCATC	1 cut(s)	121
BpmI	CTGGAG	3 cut(s)	434, 1053, 1133
Bpu10I	CCTNAGC	2 cut(s)	575, 1347
BsaJI	CCNNGG	1 cut(s)	943
Bsc4I	CCNNNNNNNGG	3 cut(s)	29, 536, 869
Bse1I	ACTGG	1 cut(s)	478
Bse3DI	GCAATG	5 cut(s)	198, 423, 513, 885, 1140
BseBI	CCWGG	1 cut(s)	413
BseDI	CCNNGG	1 cut(s)	943
BseGI	GGATG	2 cut(s)	640, 736
BseLI	CCNNNNNNNGG	3 cut(s)	29, 536, 869
BseMI	GCAATG	5 cut(s)	198, 423, 513, 885, 1140
BseMII	CTCAG	5 cut(s)	56, 566, 618, 1173, 1338
BseNI	ACTGG	1 cut(s)	478
BseRI	GAGGAG	1 cut(s)	230
BseXI	GCAGC	4 cut(s)	146, 313, 751, 1355
BsgI	GTGCAG	1 cut(s)	1024
BshFI	GGCC	3 cut(s)	15, 33, 1174
BsiSI	CCGG	1 cut(s)	850
BslFI	GGGAC	1 cut(s)	320
BslI	CCNNNNNNNGG	3 cut(s)	29, 536, 869
BsmAI	GTCTC	2 cut(s)	797, 1366
BsmBI	CGTCTC	2 cut(s)	797, 1366
BsmFI	GGGAC	1 cut(s)	320
BsnI	GGCC	3 cut(s)	15, 33, 1174
Bsp143I	GATC	6 cut(s)	55, 96, 643, 814, 1095, 1231
BspACI	CCGC	2 cut(s)	86, 371
BspANI	GGCC	3 cut(s)	15, 33, 1174
BspCNI	CTCAG	5 cut(s)	55, 567, 619, 1174, 1339
BspLI	GGNNCC	1 cut(s)	336
BspMI	ACCTGC	1 cut(s)	1234
BspPI	GGATC	2 cut(s)	651, 822
BsrDI	GCAATG	5 cut(s)	198, 423, 513, 885, 1140
BsrI	ACTGG	1 cut(s)	478
BssECI	CCNNGG	1 cut(s)	943
BssMI	GATC	6 cut(s)	55, 96, 643, 814, 1095, 1231
BssSI	CACGAG	1 cut(s)	1304
Bst2BI	CACGAG	1 cut(s)	1304
Bst2UI	CCWGG	1 cut(s)	413
Bst4CI	ACNGT	2 cut(s)	241, 1396
Bst6I	CTCTTC	1 cut(s)	600
BstC8I	GCNNGC	4 cut(s)	299, 769, 1317, 1341
BstDEI	CTNAG	5 cut(s)	42, 575, 627, 1182, 1347
BstF5I	GGATG	2 cut(s)	640, 736
BstKTI	GATC	6 cut(s)	58, 99, 646, 817, 1098, 1234
BstMAI	GTCTC	2 cut(s)	797, 1366
BstMBI	GATC	6 cut(s)	55, 96, 643, 814, 1095, 1231
BstMWI	GCNNNNNNNGC	2 cut(s)	274, 901
BstNI	CCWGG	1 cut(s)	413
BstNSI	RCATGY	1 cut(s)	716
BstSCI	CCNGG	1 cut(s)	411
BstSFI	CTRYAG	1 cut(s)	979
BstV1I	GCAGC	4 cut(s)	146, 313, 751, 1355
BstX2I	RGATCY	1 cut(s)	1231
BstYI	RGATCY	1 cut(s)	1231
BsuRI	GGCC	3 cut(s)	15, 33, 1174
BtgZI	GCGATG	2 cut(s)	416, 868
BtsCI	GGATG	2 cut(s)	640, 736
BtsIMutI	CAGTG	1 cut(s)	1401
BveI	ACCTGC	1 cut(s)	1234
Cac8I	GCNNGC	4 cut(s)	299, 769, 1317, 1341
Cfr13I	GGNCC	3 cut(s)	13, 31, 334
CspCI	CAANNNNNGTGG	4 cut(s)	1287, 1322, 1377, 1412
CviAII	CATG	5 cut(s)	698, 713, 818, 1153, 1322
DdeI	CTNAG	5 cut(s)	42, 575, 627, 1182, 1347
DpnI	GATC	6 cut(s)	57, 98, 645, 816, 1097, 1233
DpnII	GATC	6 cut(s)	55, 96, 643, 814, 1095, 1231
Eam1104I	CTCTTC	1 cut(s)	600
EarI	CTCTTC	1 cut(s)	600
Eco147I	AGGCCT	1 cut(s)	1174
Eco32I	GATATC	2 cut(s)	227, 421
Eco47I	GGWCC	1 cut(s)	334
Eco57I	CTGAAG	1 cut(s)	99
EcoRII	CCWGG	1 cut(s)	411
EcoRV	GATATC	2 cut(s)	227, 421
Esp3I	CGTCTC	2 cut(s)	797, 1366
FaeI	CATG	5 cut(s)	701, 716, 821, 1156, 1325
FaqI	GGGAC	1 cut(s)	320
FatI	CATG	5 cut(s)	697, 712, 817, 1152, 1321
FbaI	TGATCA	1 cut(s)	1095
Fnu4HI	GCNGC	5 cut(s)	135, 302, 372, 765, 1344
FokI	GGATG	2 cut(s)	647, 743
Fsp4HI	GCNGC	5 cut(s)	135, 302, 372, 765, 1344
FspBI	CTAG	1 cut(s)	833
GluI	GCNGC	5 cut(s)	135, 302, 372, 765, 1344
GsuI	CTGGAG	3 cut(s)	434, 1053, 1133
HaeIII	GGCC	3 cut(s)	15, 33, 1174
HapII	CCGG	1 cut(s)	850
Hin1II	CATG	5 cut(s)	701, 716, 821, 1156, 1325
HincII	GTYRAC	2 cut(s)	394, 471
HindII	GTYRAC	2 cut(s)	394, 471
HindIII	AAGCTT	2 cut(s)	295, 997
HinfI	GANTC	4 cut(s)	289, 540, 1073, 1384
HpaII	CCGG	1 cut(s)	850
HphI	GGTGA	4 cut(s)	100, 166, 650, 835
Hpy166II	GTNNAC	3 cut(s)	157, 394, 471
Hpy188I	TCNGA	7 cut(s)	231, 545, 648, 780, 947, 1035, 1100
Hpy188III	TCNNGA	6 cut(s)	337, 719, 833, 1070, 1112, 1252
Hpy8I	GTNNAC	3 cut(s)	157, 394, 471
HpyAV	CCTTC	7 cut(s)	4, 157, 319, 482, 540, 704, 1304
HpyCH4III	ACNGT	2 cut(s)	241, 1396
HpyF10VI	GCNNNNNNNGC	2 cut(s)	274, 901
HpyF3I	CTNAG	5 cut(s)	42, 575, 627, 1182, 1347
Hsp92II	CATG	5 cut(s)	701, 716, 821, 1156, 1325
Ksp22I	TGATCA	1 cut(s)	1095
Kzo9I	GATC	6 cut(s)	55, 96, 643, 814, 1095, 1231
LmnI	GCTCC	3 cut(s)	414, 968, 1336
Lsp1109I	GCAGC	4 cut(s)	146, 313, 751, 1355
LweI	GCATC	1 cut(s)	121
MaeI	CTAG	1 cut(s)	833
MaeIII	GTNAC	3 cut(s)	241, 455, 661
MalI	GATC	6 cut(s)	57, 98, 645, 816, 1097, 1233
MboI	GATC	6 cut(s)	55, 96, 643, 814, 1095, 1231
MboII	GAAGA	3 cut(s)	220, 617, 1236
MflI	RGATCY	1 cut(s)	1231
MluCI	AATT	6 cut(s)	250, 283, 445, 783, 1186, 1299
MlyI	GAGTC	1 cut(s)	1393
MmeI	TCCRAC	1 cut(s)	254
MroXI	GAANNNNTTC	1 cut(s)	974
MseI	TTAA	2 cut(s)	677, 741
MslI	CAYNNNNRTG	1 cut(s)	890
MspA1I	CMGCKG	1 cut(s)	1346
MspI	CCGG	1 cut(s)	850
MspR9I	CCNGG	1 cut(s)	413
MvaI	CCWGG	1 cut(s)	413
MwoI	GCNNNNNNNGC	2 cut(s)	274, 901
NdeII	GATC	6 cut(s)	55, 96, 643, 814, 1095, 1231
NlaIII	CATG	5 cut(s)	701, 716, 821, 1156, 1325
NlaIV	GGNNCC	1 cut(s)	336
NspI	RCATGY	1 cut(s)	716
PceI	AGGCCT	1 cut(s)	1174
PdmI	GAANNNNTTC	1 cut(s)	974
PfeI	GAWTC	3 cut(s)	289, 540, 1073
PfoI	TCCNGGA	1 cut(s)	411
PkrI	GCNGC	5 cut(s)	136, 303, 373, 766, 1345
PleI	GAGTC	1 cut(s)	1392
PpsI	GAGTC	1 cut(s)	1392
PsiI	TTATAA	1 cut(s)	378
Psp6I	CCWGG	1 cut(s)	411
PspGI	CCWGG	1 cut(s)	411
PspN4I	GGNNCC	1 cut(s)	336
PspPI	GGNCC	3 cut(s)	13, 31, 334
PsuI	RGATCY	1 cut(s)	1231
PvuII	CAGCTG	1 cut(s)	1346
RseI	CAYNNNNRTG	1 cut(s)	890
SaqAI	TTAA	2 cut(s)	677, 741
SatI	GCNGC	5 cut(s)	135, 302, 372, 765, 1344
Sau3AI	GATC	6 cut(s)	55, 96, 643, 814, 1095, 1231
Sau96I	GGNCC	3 cut(s)	13, 31, 334
SchI	GAGTC	1 cut(s)	1393
ScrFI	CCNGG	1 cut(s)	413
SfaNI	GCATC	1 cut(s)	121
SfcI	CTRYAG	1 cut(s)	979
SinI	GGWCC	1 cut(s)	334
SmiMI	CAYNNNNRTG	1 cut(s)	890
SmlI	CTYRAG	1 cut(s)	1424
SmoI	CTYRAG	1 cut(s)	1424
Sse9I	AATT	6 cut(s)	250, 283, 445, 783, 1186, 1299
SseBI	AGGCCT	1 cut(s)	1174
SsiI	CCGC	2 cut(s)	86, 371
SspI	AATATT	1 cut(s)	181
SspMI	CTAG	1 cut(s)	833
StuI	AGGCCT	1 cut(s)	1174
StyD4I	CCNGG	1 cut(s)	411
TaaI	ACNGT	2 cut(s)	241, 1396
TaqI	TCGA	4 cut(s)	99, 533, 1222, 1251
TaqII	GACCGA	1 cut(s)	562
TasI	AATT	6 cut(s)	250, 283, 445, 783, 1186, 1299
TauI	GCSGC	1 cut(s)	374
TfiI	GAWTC	3 cut(s)	289, 540, 1073
Tru1I	TTAA	2 cut(s)	677, 741
Tru9I	TTAA	2 cut(s)	677, 741
TscAI	CASTG	1 cut(s)	1401
TseI	GCWGC	4 cut(s)	134, 301, 764, 1343
TspGWI	ACGGA	2 cut(s)	337, 1349
TspRI	CASTG	1 cut(s)	1401
VpaK11BI	GGWCC	1 cut(s)	334
XapI	RAATTY	2 cut(s)	283, 1186
XbaI	TCTAGA	1 cut(s)	832
XceI	RCATGY	1 cut(s)	716
XmnI	GAANNNNTTC	1 cut(s)	974
XspI	CTAG	1 cut(s)	833

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