Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4A

Orthogroup ID

OG0008613

Physical Location & Seq

Genomic Coordinates Forward (+)

58080048 .. 58081793

Gene Structure 1746 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4AG264900.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1605 bp

ATGATTGAGAAGCTTGGGAGCCAATGTGAAATGGATGGTGTGCAGTACTTGATGCACCAAATGAAATTGGAGGGGGTTGGTTGCTCTGAGGAGTTGTTTATAACTGTGGTGAAGTCTTATAGGCGAGCTGGGTTGGCTGAGCAGGCATTGAAGATGTTCTATAGGATAAACGAATTCGGGTGCAAACCCACTGTGAAGATTTACAATCACTTGTTGGATGCATTGCTTTGCGAGAATAGGTTTCAGATGATAAATCCCATATATGGTAACATGAAGAAAGATGGGGTGGAGCCGAATGTGTTTACGTATAACATTCTGTTGAAGGCATTGTGTAAGAATGATAGGGTGGATGGTGCACACAAGTTGCTTGTGGAAATGTCTAAGAAGGGATGTTGTCCTGACTCGGTGAGCTATACGACTGTAGTGTCTGCATTGTGTAGGCTTGGGAAGGTAGATGAAGCGAGGGAGCTTGCTTGTAGATTCGAACCCAATGTGGCTGTTTATAATGCTTTGGTAAATGGGTTGTGCAAGGAGTTCAAATTTGAAGAGGCATTGGCATTGCTGGTTGAAATGGCGGGTAAGGGAATAGACCCTAATGTCATTACATACTCGACGATTATTAGTTCTTTTTCTGATATGAGGAATGTTGAGTCTGCTCTTGCAGTTTTGGCGAAAATGTTTGTGAGGGGATATAGGCCTAACATTCACACCTTTACTTCCTTGATAAAGGGTTATTTTATTGAAGGCAGAGTTAGTGAAGCTCTTGACTTGTGGAACCGCATGGTTTGTGAGGGATTTGAGCCCAATGTTGTTGCATATACAACTGTTATACATGGTCTCTGCTCTGTTGGGAATATGCGTGAAGCTGTATCTGTTTTACATGAGATGGAGATAAAAGGTTGCTCTCCAAATGTGAGCACATATAGCACTCTTATTGATGGGTTTGCAAAAGCTGGCAACCTTGTTGGTGCATCGGAGACTTGGAACAATATGATGAGCCGTGGTTGCCGTCCTAATGTCATAGCATATACGTGCATGGTGGATGTTCTGTGCAGGAAATATATGTTTCATCGAGCTCAATGTCTTTTAGAAAATATGACTGCCGAAGGCTGTCCACCAAATACAGTTACATTTAACACATTTATCAAAGGGTTGTGTGAAGATGGAGAAGTAGATTGGGCTGTTAAGGTGCTGAACAAGATGAGAGAAAATGGGTGTTTGCCCAACATTACGACATATAATGAGTTATTGGATGGTCTGTTCAAGGTGAACAGATTCGAAGAAGCATTTGGACTTGTCAGGGAGATAGATGAAAAGGGACTGAAACTGAATTTGCAAGGCAGGATAAAGACTGCTATTCAGTTTTTCAACAGTACTGGTGCAGCAAAGGAGTGGTGCCCTGATGTAATAGCTTACACTAGTCTTCTATGGGGGATTTGTAACTCGGTAGGTCTAGATGAGGCCATGGTTCATCTTGATAAGATGATAAGGAAAGGTATCTGCCCCAACATTGGCACATGGGATGTGTTGGTGCGGTGTTTCTTTAGCAGCTTAGGTCATTTGGGGCCAATCTACATACTGGATGATATTCTTCGTGAAGGATAA

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 PPR_long

Protein Analysis

534

Amino Acids

59.79

Weight (kDa)

6.21

Isoelectric Point (pI)

26.51

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_2	PF13041	63 - 112	2.5e-14	PPR repeat family
PPR_3	PF13812	67 - 112	5e-09	Pentatricopeptide repeat domain
PPR_1	PF12854	94 - 127	4.5e-12	PPR repeat
PPR	PF01535	101 - 131	2.4e-07	PPR repeat
PPR_2	PF13041	106 - 147	4.7e-12	PPR repeat family
PPR_1	PF12854	129 - 157	5.6e-10	PPR repeat
PPR_long	PF17177	161 - 243	3.3e-07	Pentacotripeptide-repeat region of PRORP
PPR_3	PF13812	161 - 212	1.2e-06	Pentatricopeptide repeat domain
PPR_1	PF12854	161 - 191	1.1e-07	PPR repeat
PPR_2	PF13041	163 - 210	1.8e-14	PPR repeat family
PPR	PF01535	167 - 196	6e-06	PPR repeat
PPR_3	PF13812	187 - 245	2.7e-09	Pentatricopeptide repeat domain
PPR_1	PF12854	194 - 226	2.3e-06	PPR repeat
PPR_2	PF13041	198 - 245	1.4e-11	PPR repeat family
PPR_1	PF12854	229 - 262	6.9e-08	PPR repeat
PPR_2	PF13041	237 - 281	6e-14	PPR repeat family
PPR	PF01535	237 - 266	1.1e-06	PPR repeat
PPR_long	PF17177	252 - 347	3.8e-07	Pentacotripeptide-repeat region of PRORP
PPR_3	PF13812	259 - 313	1.2e-12	Pentatricopeptide repeat domain
PPR_1	PF12854	265 - 297	2e-11	PPR repeat
PPR_2	PF13041	268 - 317	4.4e-19	PPR repeat family
PPR	PF01535	271 - 301	1.8e-07	PPR repeat
PPR_3	PF13812	291 - 349	5.9e-11	Pentatricopeptide repeat domain
PPR_1	PF12854	299 - 331	1.6e-09	PPR repeat
PPR	PF01535	306 - 336	1e-05	PPR repeat
PPR_2	PF13041	310 - 352	3.4e-10	PPR repeat family
PPR_2	PF13041	338 - 386	2.1e-13	PPR repeat family
PPR_3	PF13812	362 - 417	4.8e-11	Pentatricopeptide repeat domain
PPR_1	PF12854	370 - 402	3.6e-14	PPR repeat
PPR_2	PF13041	373 - 422	4.1e-16	PPR repeat family
PPR	PF01535	376 - 406	2.5e-07	PPR repeat
PPR_1	PF12854	404 - 435	2.7e-06	PPR repeat
PPR_2	PF13041	408 - 444	1.7e-06	PPR repeat family
PPR_2	PF13041	467 - 514	3.4e-07	PPR repeat family

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

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Genomic Context

Gene Family Tree

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Orthologous Genes (Group: OG0008613)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G48810
fragaria_vesca	FvH4_4g20630
malus_domestica	MD13G1149200.v1.1
prunus_persica	Prupe.1G113200_v2.0.a1
pyrus_communis	pycom13g12840
rosa_chinensis	RchiOBHm_Chr4g0425991 RchiOBHm_Chr4g0426031
rosa_laevigata	RLG00000007323 RLG00000007325
rosa_multiflora	Rmu_ssc0000281.1_g000016 Rmu_ssc0000281.1_g000018 Rmu_ssc0000281.1_g000020
rosa_roxburghii	Rroxscaffold_5G00368000
rosa_rugosa	Rorug04G0207900 Rorug04G0208100
rosa_samantha	Rh4AG264900 Rh4BG270800 Rh4BG271100 Rh4CG283400 Rh4CG283700 Rh4CG283900 Rh4DG267400
rosa_wichuraiana	Rw4G022880

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	2 cut(s)	101, 504
AasI	GACNNNNNNGTC	2 cut(s)	424, 596
AccB1I	GGYRCC	1 cut(s)	1395
AciI	CCGC	3 cut(s)	575, 778, 1534
AcsI	RAATTY	3 cut(s)	173, 539, 1330
AfaI	GTAC	2 cut(s)	47, 1375
AfiI	CCNNNNNNNGG	2 cut(s)	263, 1511
AgsI	TTSAA	8 cut(s)	151, 322, 538, 545, 569, 743, 1264, 1369
AhlI	ACTAGT	1 cut(s)	1418
AjuI	GAANNNNNNNTTGG	2 cut(s)	1272, 1304
AloI	GAACNNNNNNTCC	2 cut(s)	1244, 1276
Alw21I	GWGCWC	3 cut(s)	358, 920, 1078
Alw26I	GTCTC	2 cut(s)	842, 971
Alw44I	GTGCAC	1 cut(s)	354
AoxI	GGCC	3 cut(s)	695, 1461, 1565
ApaLI	GTGCAC	1 cut(s)	354
ApeKI	GCWGC	2 cut(s)	1382, 1548
ApoI	RAATTY	3 cut(s)	173, 539, 1330
Asp700I	GAANNNNTTC	2 cut(s)	155, 1274
AspS9I	GGNCC	1 cut(s)	1565
AsuHPI	GGTGA	3 cut(s)	121, 418, 1279
AsuII	TTCGAA	2 cut(s)	483, 1278
BaeGI	GKGCMC	2 cut(s)	358, 1400
BanI	GGYRCC	1 cut(s)	1395
BanII	GRGCYC	2 cut(s)	804, 1078
BbsI	GAAGAC	1 cut(s)	1415
Bbv12I	GWGCWC	3 cut(s)	358, 920, 1078
BbvI	GCAGC	2 cut(s)	1394, 1560
BccI	CCATC	7 cut(s)	29, 275, 344, 880, 932, 1157, 1247
BceAI	ACGGC	2 cut(s)	984, 993
BcoDI	GTCTC	2 cut(s)	842, 971
BcuI	ACTAGT	1 cut(s)	1418
BfaI	CTAG	2 cut(s)	1419, 1454
BfmI	CTRYAG	2 cut(s)	160, 420
BisI	GCNGC	2 cut(s)	1383, 1549
BlpI	GCTNAGC	1 cut(s)	138
BlsI	GCNGC	2 cut(s)	1384, 1550
BmcAI	AGTACT	2 cut(s)	47, 1375
BmgT120I	GGNCC	1 cut(s)	1565
BmiI	GGNNCC	5 cut(s)	20, 291, 776, 1397, 1566
BmsI	GCATC	3 cut(s)	42, 208, 980
BpiI	GAAGAC	1 cut(s)	1415
Bpu10I	CCTNAGC	1 cut(s)	1552
Bpu1102I	GCTNAGC	1 cut(s)	138
Bpu14I	TTCGAA	2 cut(s)	483, 1278
BsaAI	YACGTR	2 cut(s)	306, 1032
BsaI	GGTCTC	1 cut(s)	842
BsaJI	CCNNGG	2 cut(s)	1000, 1464
BsaXI	ACNNNNNCTCC	2 cut(s)	10, 40
Bsc4I	CCNNNNNNNGG	2 cut(s)	263, 1511
Bse1I	ACTGG	2 cut(s)	1381, 1584
Bse3DI	GCAATG	2 cut(s)	221, 557
BseDI	CCNNGG	2 cut(s)	1000, 1464
BseGI	GGATG	8 cut(s)	40, 223, 355, 395, 1048, 1258, 1528, 1588
BseLI	CCNNNNNNNGG	2 cut(s)	263, 1511
BseMI	GCAATG	2 cut(s)	221, 557
BseMII	CTCAG	2 cut(s)	78, 129
BseNI	ACTGG	2 cut(s)	1381, 1584
BseRI	GAGGAG	1 cut(s)	104
BseSI	GKGCMC	2 cut(s)	358, 1400
BseXI	GCAGC	2 cut(s)	1394, 1560
BseYI	CCCAGC	1 cut(s)	128
BsgI	GTGCAG	3 cut(s)	62, 1072, 1401
BshFI	GGCC	3 cut(s)	697, 1463, 1567
BshNI	GGYRCC	1 cut(s)	1395
BsiHKAI	GWGCWC	3 cut(s)	358, 920, 1078
BslFI	GGGAC	1 cut(s)	1332
BslI	CCNNNNNNNGG	2 cut(s)	263, 1511
BsmAI	GTCTC	2 cut(s)	842, 971
BsmFI	GGGAC	1 cut(s)	1332
BsnI	GGCC	3 cut(s)	697, 1463, 1567
Bso31I	GGTCTC	1 cut(s)	842
Bsp119I	TTCGAA	2 cut(s)	483, 1278
Bsp1286I	GDGCHC	5 cut(s)	358, 804, 920, 1078, 1400
Bsp1720I	GCTNAGC	1 cut(s)	138
Bsp19I	CCATGG	1 cut(s)	1464
BspACI	CCGC	3 cut(s)	575, 778, 1534
BspANI	GGCC	3 cut(s)	697, 1463, 1567
BspCNI	CTCAG	2 cut(s)	79, 130
BspLI	GGNNCC	5 cut(s)	20, 291, 776, 1397, 1566
BspT104I	TTCGAA	2 cut(s)	483, 1278
BspT107I	GGYRCC	1 cut(s)	1395
BspTNI	GGTCTC	1 cut(s)	842
BsrDI	GCAATG	2 cut(s)	221, 557
BsrI	ACTGG	2 cut(s)	1381, 1584
BssECI	CCNNGG	2 cut(s)	1000, 1464
BssT1I	CCWWGG	1 cut(s)	1464
Bst4CI	ACNGT	6 cut(s)	106, 193, 421, 826, 1126, 1373
Bst6I	CTCTTC	1 cut(s)	540
BstBAI	YACGTR	2 cut(s)	306, 1032
BstBI	TTCGAA	2 cut(s)	483, 1278
BstC8I	GCNNGC	4 cut(s)	126, 144, 471, 955
BstDEI	CTNAG	4 cut(s)	87, 138, 381, 1552
BstDSI	CCRYGG	2 cut(s)	1000, 1464
BstF5I	GGATG	8 cut(s)	40, 223, 355, 395, 1048, 1258, 1528, 1588
BstMAI	GTCTC	2 cut(s)	842, 971
BstMWI	GCNNNNNNNGC	5 cut(s)	134, 143, 668, 924, 1005
BstSFI	CTRYAG	2 cut(s)	160, 420
BstSLI	GKGCMC	2 cut(s)	358, 1400
BstSNI	TACGTA	1 cut(s)	306
BstV1I	GCAGC	2 cut(s)	1394, 1560
BstV2I	GAAGAC	1 cut(s)	1415
BsuRI	GGCC	3 cut(s)	697, 1463, 1567
BtgI	CCRYGG	2 cut(s)	1000, 1464
BtsCI	GGATG	8 cut(s)	40, 223, 355, 395, 1048, 1258, 1528, 1588
BtsIMutI	CAGTG	1 cut(s)	189
Cac8I	GCNNGC	4 cut(s)	126, 144, 471, 955
Cfr13I	GGNCC	1 cut(s)	1565
Csp6I	GTAC	2 cut(s)	46, 1374
CviAII	CATG	7 cut(s)	271, 781, 833, 881, 1036, 1465, 1518
CviQI	GTAC	2 cut(s)	46, 1374
DdeI	CTNAG	4 cut(s)	87, 138, 381, 1552
DrdI	GACNNNNNNGTC	2 cut(s)	424, 596
DseDI	GACNNNNNNGTC	2 cut(s)	424, 596
Eam1104I	CTCTTC	1 cut(s)	540
EarI	CTCTTC	1 cut(s)	540
Ecl136II	GAGCTC	1 cut(s)	1076
Eco105I	TACGTA	1 cut(s)	306
Eco130I	CCWWGG	1 cut(s)	1464
Eco147I	AGGCCT	1 cut(s)	697
Eco24I	GRGCYC	2 cut(s)	804, 1078
Eco31I	GGTCTC	1 cut(s)	842
Eco53kI	GAGCTC	1 cut(s)	1076
EcoICRI	GAGCTC	1 cut(s)	1076
EcoRI	GAATTC	1 cut(s)	173
EcoT14I	CCWWGG	1 cut(s)	1464
EcoT22I	ATGCAT	1 cut(s)	223
EcoT38I	GRGCYC	2 cut(s)	804, 1078
ErhI	CCWWGG	1 cut(s)	1464
FaeI	CATG	7 cut(s)	274, 784, 836, 884, 1039, 1468, 1521
FaqI	GGGAC	1 cut(s)	1332
FatI	CATG	7 cut(s)	270, 780, 832, 880, 1035, 1464, 1517
FauI	CCCGC	1 cut(s)	568
Fnu4HI	GCNGC	2 cut(s)	1383, 1549
FokI	GGATG	8 cut(s)	47, 230, 362, 402, 1055, 1265, 1535, 1595
FriOI	GRGCYC	2 cut(s)	804, 1078
Fsp4HI	GCNGC	2 cut(s)	1383, 1549
FspBI	CTAG	2 cut(s)	1419, 1454
GluI	GCNGC	2 cut(s)	1383, 1549
GsaI	CCCAGC	1 cut(s)	132
HaeIII	GGCC	3 cut(s)	697, 1463, 1567
Hin1II	CATG	7 cut(s)	274, 784, 836, 884, 1039, 1468, 1521
HindIII	AAGCTT	1 cut(s)	11
HinfI	GANTC	4 cut(s)	401, 480, 650, 1275
HphI	GGTGA	3 cut(s)	121, 418, 1279
Hpy166II	GTNNAC	4 cut(s)	303, 356, 1115, 1270
Hpy188I	TCNGA	4 cut(s)	88, 246, 634, 976
Hpy188III	TCNNGA	5 cut(s)	398, 764, 1454, 1475, 1595
Hpy8I	GTNNAC	4 cut(s)	303, 356, 1115, 1270
Hpy99I	CGWCG	1 cut(s)	616
HpyAV	CCTTC	6 cut(s)	316, 379, 442, 737, 1100, 1592
HpyCH4III	ACNGT	6 cut(s)	106, 193, 421, 826, 1126, 1373
HpyCH4IV	ACGT	2 cut(s)	305, 1031
HpyF10VI	GCNNNNNNNGC	5 cut(s)	134, 143, 668, 924, 1005
HpyF3I	CTNAG	4 cut(s)	87, 138, 381, 1552
HpySE526I	ACGT	2 cut(s)	305, 1031
Hsp92II	CATG	7 cut(s)	274, 784, 836, 884, 1039, 1468, 1521
LmnI	GCTCC	3 cut(s)	18, 289, 466
Lsp1109I	GCAGC	2 cut(s)	1394, 1560
LweI	GCATC	3 cut(s)	42, 208, 980
MaeI	CTAG	2 cut(s)	1419, 1454
MaeII	ACGT	2 cut(s)	305, 1031
MaeIII	GTNAC	3 cut(s)	266, 1126, 1439
MboII	GAAGA	8 cut(s)	163, 208, 286, 557, 1172, 1292, 1415, 1583
MhlI	GDGCHC	5 cut(s)	358, 804, 920, 1078, 1400
MluCI	AATT	4 cut(s)	65, 173, 539, 1330
MlyI	GAGTC	2 cut(s)	395, 659
MmeI	TCCRAC	1 cut(s)	195
MnlI	CCTC	8 cut(s)	64, 82, 456, 541, 633, 678, 784, 1453
Mph1103I	ATGCAT	1 cut(s)	223
MroXI	GAANNNNTTC	2 cut(s)	155, 1274
MseI	TTAA	2 cut(s)	1134, 1185
MslI	CAYNNNNRTG	1 cut(s)	1030
MwoI	GCNNNNNNNGC	5 cut(s)	134, 143, 668, 924, 1005
NcoI	CCATGG	1 cut(s)	1464
NlaIII	CATG	7 cut(s)	274, 784, 836, 884, 1039, 1468, 1521
NlaIV	GGNNCC	5 cut(s)	20, 291, 776, 1397, 1566
NsiI	ATGCAT	1 cut(s)	223
NspV	TTCGAA	2 cut(s)	483, 1278
PceI	AGGCCT	1 cut(s)	697
PdmI	GAANNNNTTC	2 cut(s)	155, 1274
PfeI	GAWTC	2 cut(s)	480, 1275
PkrI	GCNGC	2 cut(s)	1384, 1550
PleI	GAGTC	2 cut(s)	395, 658
PpsI	GAGTC	2 cut(s)	395, 658
Ppu21I	YACGTR	2 cut(s)	306, 1032
PsiI	TTATAA	2 cut(s)	101, 504
Psp124BI	GAGCTC	1 cut(s)	1078
PspFI	CCCAGC	1 cut(s)	128
PspN4I	GGNNCC	5 cut(s)	20, 291, 776, 1397, 1566
PspPI	GGNCC	1 cut(s)	1565
RsaI	GTAC	2 cut(s)	47, 1375
RsaNI	GTAC	2 cut(s)	46, 1374
RseI	CAYNNNNRTG	1 cut(s)	1030
SacI	GAGCTC	1 cut(s)	1078
SaqAI	TTAA	2 cut(s)	1134, 1185
SatI	GCNGC	2 cut(s)	1383, 1549
Sau96I	GGNCC	1 cut(s)	1565
ScaI	AGTACT	2 cut(s)	47, 1375
SchI	GAGTC	2 cut(s)	395, 659
SduI	GDGCHC	5 cut(s)	358, 804, 920, 1078, 1400
SfaNI	GCATC	3 cut(s)	42, 208, 980
SfcI	CTRYAG	2 cut(s)	160, 420
SfuI	TTCGAA	2 cut(s)	483, 1278
SmiMI	CAYNNNNRTG	1 cut(s)	1030
SnaBI	TACGTA	1 cut(s)	306
SpeI	ACTAGT	1 cut(s)	1418
Sse9I	AATT	4 cut(s)	65, 173, 539, 1330
SseBI	AGGCCT	1 cut(s)	697
SsiI	CCGC	3 cut(s)	575, 778, 1534
SspMI	CTAG	2 cut(s)	1419, 1454
SstI	GAGCTC	1 cut(s)	1078
StuI	AGGCCT	1 cut(s)	697
StyI	CCWWGG	1 cut(s)	1464
TaaI	ACNGT	6 cut(s)	106, 193, 421, 826, 1126, 1373
TaiI	ACGT	2 cut(s)	308, 1034
TaqI	TCGA	4 cut(s)	483, 611, 1072, 1278
TasI	AATT	4 cut(s)	65, 173, 539, 1330
TatI	WGTACW	2 cut(s)	45, 1373
TfiI	GAWTC	2 cut(s)	480, 1275
Tru1I	TTAA	2 cut(s)	1134, 1185
Tru9I	TTAA	2 cut(s)	1134, 1185
TscAI	CASTG	1 cut(s)	196
TseI	GCWGC	2 cut(s)	1382, 1548
TspDTI	ATGAA	6 cut(s)	77, 287, 471, 1058, 1326, 1460
TspRI	CASTG	1 cut(s)	196
VneI	GTGCAC	1 cut(s)	354
XapI	RAATTY	3 cut(s)	173, 539, 1330
XbaI	TCTAGA	1 cut(s)	1453
XmnI	GAANNNNTTC	2 cut(s)	155, 1274
XspI	CTAG	2 cut(s)	1419, 1454
ZrmI	AGTACT	2 cut(s)	47, 1375
Zsp2I	ATGCAT	1 cut(s)	223

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