Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000003

Orthogroup ID

OG0002831

Physical Location & Seq

Genomic Coordinates Forward (+)

7398180 .. 7399824

Gene Structure 1645 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_3G00224300.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1389 bp

ATGGTTTCAGAGCAAAAGGGTTTCAACCACAATAATGCCACCTATGCAACTATCCTCAATAAGCTTGCTCAGTCCAAGAAGTTCAAGGCTGTTGATGCAGTTCTCTATCAAATGAAGTACGATGCCTGCAAATATCATGAGGGTATATTCCTTAATCTCATGAAGCATTTTTCAAATTCATCTATGCATGAAAGAGTGCTTGAAATGTTCTATGCTATCCAGCCAATAGTTCGGGAAAAGCCGTCTCTCAAATGCATTAGTACTTGTCTAAATCTACTGATTGAAGCGAATCAGGTTGATTTGGCCCAACAGTTTCTCATGCATTTGAAGAAAAGTCTTAACTTGAAGCTGAATACATGCATTGTCAACATCTTGGTTAAGCACCATTGCAAAAATGGGGATCTTGAATCTGCCTTTGAGGTTGTAAAGGAAATGAAAAAGTCTAAGCTTTCCTATCCTAATTTGATTACTTACTCGACTCTAATTGATGGTTTATGTCAAAGTGGAAGACTGACAGAAGCAATGGACCTGTTTGAGGAAATGATCTCAAAGGATCAGATATTGCCTGATGTGCTAACGTACAACATTTTGATTAACGGTTTTTGCCGTGGTGGGAAAGTTGATAGGGCAAGGAAGATATTGGATTTTATGAAGAGCAAAGGATGCAACCCAAATGTATTCAATTACTCAGCTCTGATGAATGGCTTCTGTAAGGAGGAAAGGTTGGAAGAGGCCAAGGAGCTTTTGGATGAAATGAAGAGCTTTGGTATCAAACCAGATACAGTTGTCTACACTACTTTAATTGATTGCTACTTTAGGACTGGGAGAGTTGATGAAGCGATAGAGTTGCTCAAAGAGATGAAAGAAAGACGGTGCAAAGCTGATACTGTGACTTTCAACGTGATACTTGGAGGACTATGTAGAGAAGGTAGAATTGAGGATGCGCTTGAGATGCTGGACAAACTTCCTTATGAGGGTATCTATCTGAATAAGGGAAGCTACAGGATTGTGTTGAATTCATTGTGTCAGAAAGGCGAACTAAACAAAGCTAAAGAGTTGTTGAGATTGATGATGGGTAGGGGGTTTGTACCACATTATGCAACTTCAAACGAGTTGCTAGTTAGCCTTTGTGAGGCTGGAATGGCAGATGATGCAATTATGGCTTTATTTGGATTGGTGGAGATGGGATTCAAGCCACTGCCTGATTCCTGGACTCTTTTTGTTGAATCAATTTGCAGAGAAAGAAAGCTGCTGCCTGCATTTGAACTGCTCGATGAATTAGTTAATGAAGAAGAAGTAGAGAATGAAGCGAAAGAAACACTGGCATTCATGAGAGGTCATTTTAAGCCAGTTTTGGAGGTTAAGCTTGATGTTGTTGGCAAGGAATGA

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

462

Amino Acids

52.75

Weight (kDa)

6.22

Isoelectric Point (pI)

28.39

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_3	PF13812	112 - 163	8.9e-07	Pentatricopeptide repeat domain
PPR_long	PF17177	112 - 185	1.5e-06	Pentacotripeptide-repeat region of PRORP
PPR_1	PF12854	114 - 146	5.6e-07	PPR repeat
PPR_2	PF13041	118 - 167	4.5e-14	PPR repeat family
PPR_2	PF13041	153 - 203	2e-17	PPR repeat family
PPR_1	PF12854	153 - 181	3.2e-13	PPR repeat
PPR	PF01535	156 - 184	1.8e-09	PPR repeat
PPR_long	PF17177	167 - 322	1.6e-10	Pentacotripeptide-repeat region of PRORP
PPR_3	PF13812	178 - 236	1.3e-11	Pentatricopeptide repeat domain
PPR_1	PF12854	187 - 218	3.1e-13	PPR repeat
PPR_2	PF13041	189 - 238	1.3e-17	PPR repeat family
PPR	PF01535	193 - 222	1.2e-08	PPR repeat
PPR_1	PF12854	220 - 253	6.8e-13	PPR repeat
PPR_2	PF13041	224 - 269	4.1e-14	PPR repeat family
TPR_24	PF23276	228 - 318	3.4e-08	Fungal tetratrico peptide repeats
PPR	PF01535	229 - 257	2.9e-08	PPR repeat
PPR_long	PF17177	242 - 354	5.8e-06	Pentacotripeptide-repeat region of PRORP
PPR_3	PF13812	248 - 304	2.3e-13	Pentatricopeptide repeat domain
PPR_1	PF12854	256 - 288	5.5e-13	PPR repeat
PPR_2	PF13041	259 - 308	2.3e-18	PPR repeat family
PPR	PF01535	262 - 292	6.2e-10	PPR repeat
PPR_1	PF12854	291 - 321	7.9e-10	PPR repeat
PPR_2	PF13041	295 - 343	4.2e-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: OG0002831)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G18475
fragaria_vesca	FvH4_5g35730 FvH4_5g35730 FvH4_5g35730 FvH4_5g35730 FvH4_5g35730
prunus_persica	Prupe.1G528200_v2.0.a1
pyrus_communis	pycom08g16680
rosa_chinensis	RchiOBHm_Chr4g0424581 RchiOBHm_Chr7g0237351
rosa_laevigata	RLG00000001010 RLG00000007454
rosa_multiflora	Rmu_co8091050.1_g000001 Rmu_sc0000281.1_g000013 Rmu_sc0000820.1_g000045 Rmu_sc0002603.1_g000021 Rmu_sc0002923.1_g000038 Rmu_sc0006438.1_g000010
rosa_roxburghii	Rroxscaffold_3G00224290 Rroxscaffold_3G00224300 Rroxscaffold_5G00366500
rosa_rugosa	Rorug04G0198000 Rorug07G0302800 Rorug07G0302800
rosa_samantha	Rh1CG247200 Rh1DG083900 Rh4AG254700 Rh4BG260200 Rh4CG271700 Rh4DG254900 Rh5AG212800 Rh6DG464200 Rh7AG460000 Rh7BG429900 Rh7CG477300 Rh7DG446600
rosa_wichuraiana	Rw1G023340 Rw4G022020 Rw7G038100

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccI	GTMKAC	1 cut(s)	789
AclWI	GGATC	2 cut(s)	408, 561
AcsI	RAATTY	2 cut(s)	175, 1015
AfaI	GTAC	4 cut(s)	119, 262, 581, 1089
AfiI	CCNNNNNNNGG	3 cut(s)	535, 974, 1132
AjnI	CCWGG	1 cut(s)	1208
Alw26I	GTCTC	1 cut(s)	249
AlwI	GGATC	2 cut(s)	408, 561
AoxI	GGCC	2 cut(s)	303, 732
ApeKI	GCWGC	2 cut(s)	1249, 1252
ApoI	RAATTY	2 cut(s)	175, 1015
Asp700I	GAANNNNTTC	1 cut(s)	704
AspLEI	GCGC	1 cut(s)	946
AspS9I	GGNCC	2 cut(s)	304, 526
AvaII	GGWCC	1 cut(s)	526
BaeI	ACNNNNGTAYC	2 cut(s)	771, 804
BbsI	GAAGAC	1 cut(s)	514
BbvI	GCAGC	2 cut(s)	1236, 1239
BccI	CCATC	3 cut(s)	482, 1066, 1177
BceAI	ACGGC	2 cut(s)	226, 591
BcgI	CGANNNNNNTGC	2 cut(s)	829, 863
BciT130I	CCWGG	1 cut(s)	1210
BcoDI	GTCTC	1 cut(s)	249
BfaI	CTAG	1 cut(s)	1118
BfmI	CTRYAG	1 cut(s)	1000
BisI	GCNGC	2 cut(s)	1250, 1253
BlsI	GCNGC	2 cut(s)	1251, 1254
BmcAI	AGTACT	1 cut(s)	262
Bme1390I	CCNGG	1 cut(s)	1210
Bme18I	GGWCC	1 cut(s)	526
BmgT120I	GGNCC	2 cut(s)	304, 526
BmrFI	CCNGG	1 cut(s)	1210
BmrI	ACTGGG	1 cut(s)	831
BmsI	GCATC	6 cut(s)	85, 112, 653, 931, 942, 1141
BmuI	ACTGGG	1 cut(s)	831
BpiI	GAAGAC	1 cut(s)	514
BpuEI	CTTGAG	1 cut(s)	968
BsaJI	CCNNGG	2 cut(s)	607, 735
BsaXI	ACNNNNNCTCC	2 cut(s)	707, 737
Bsc4I	CCNNNNNNNGG	3 cut(s)	535, 974, 1132
Bse1I	ACTGG	3 cut(s)	826, 1326, 1349
Bse3DI	GCAATG	2 cut(s)	385, 528
BseBI	CCWGG	1 cut(s)	1210
BseDI	CCNNGG	2 cut(s)	607, 735
BseGI	GGATG	3 cut(s)	668, 754, 946
BseLI	CCNNNNNNNGG	3 cut(s)	535, 974, 1132
BseMI	GCAATG	2 cut(s)	385, 528
BseMII	CTCAG	2 cut(s)	83, 702
BseNI	ACTGG	3 cut(s)	826, 1326, 1349
BseXI	GCAGC	2 cut(s)	1236, 1239
BshFI	GGCC	2 cut(s)	305, 734
BslI	CCNNNNNNNGG	3 cut(s)	535, 974, 1132
BsmAI	GTCTC	1 cut(s)	249
BsmBI	CGTCTC	1 cut(s)	249
BsmI	GAATGC	1 cut(s)	1325
BsnI	GGCC	2 cut(s)	305, 734
Bsp143I	GATC	3 cut(s)	400, 543, 553
BspANI	GGCC	2 cut(s)	305, 734
BspCNI	CTCAG	2 cut(s)	82, 701
BspHI	TCATGA	3 cut(s)	136, 159, 1329
BspPI	GGATC	2 cut(s)	408, 561
BspQI	GCTCTTC	2 cut(s)	647, 752
BsrDI	GCAATG	2 cut(s)	385, 528
BsrI	ACTGG	3 cut(s)	826, 1326, 1349
BssECI	CCNNGG	2 cut(s)	607, 735
BssMI	GATC	3 cut(s)	400, 543, 553
BssT1I	CCWWGG	1 cut(s)	735
Bst2UI	CCWGG	1 cut(s)	1210
Bst4CI	ACNGT	5 cut(s)	312, 599, 784, 873, 889
Bst6I	CTCTTC	3 cut(s)	647, 723, 752
BstAPI	GCANNNNNTGC	2 cut(s)	663, 1151
BstC8I	GCNNGC	3 cut(s)	66, 127, 1257
BstDEI	CTNAG	3 cut(s)	69, 444, 688
BstDSI	CCRYGG	1 cut(s)	607
BstENI	CCTNNNNNAGG	2 cut(s)	533, 1130
BstF5I	GGATG	3 cut(s)	668, 754, 946
BstHHI	GCGC	1 cut(s)	946
BstKTI	GATC	3 cut(s)	403, 546, 556
BstMAI	GTCTC	1 cut(s)	249
BstMBI	GATC	3 cut(s)	400, 543, 553
BstMWI	GCNNNNNNNGC	8 cut(s)	44, 95, 571, 663, 952, 1142, 1151, 1160
BstNI	CCWGG	1 cut(s)	1210
BstNSI	RCATGY	1 cut(s)	360
BstSCI	CCNGG	1 cut(s)	1208
BstSFI	CTRYAG	1 cut(s)	1000
BstV1I	GCAGC	2 cut(s)	1236, 1239
BstV2I	GAAGAC	1 cut(s)	514
BstX2I	RGATCY	1 cut(s)	400
BstYI	RGATCY	1 cut(s)	400
BsuRI	GGCC	2 cut(s)	305, 734
BtgI	CCRYGG	1 cut(s)	607
BtsCI	GGATG	3 cut(s)	668, 754, 946
BtsI	GCAGTG	1 cut(s)	1196
BtsIMutI	CAGTG	2 cut(s)	1196, 1319
Cac8I	GCNNGC	3 cut(s)	66, 127, 1257
CciI	TCATGA	3 cut(s)	136, 159, 1329
CfoI	GCGC	1 cut(s)	946
Cfr13I	GGNCC	2 cut(s)	304, 526
Csp6I	GTAC	4 cut(s)	118, 261, 580, 1088
CviAII	CATG	6 cut(s)	137, 160, 188, 319, 357, 1330
CviQI	GTAC	4 cut(s)	118, 261, 580, 1088
DdeI	CTNAG	3 cut(s)	69, 444, 688
DpnI	GATC	3 cut(s)	402, 545, 555
DpnII	GATC	3 cut(s)	400, 543, 553
Eam1104I	CTCTTC	3 cut(s)	647, 723, 752
EarI	CTCTTC	3 cut(s)	647, 723, 752
Eco130I	CCWWGG	1 cut(s)	735
Eco47I	GGWCC	1 cut(s)	526
EcoNI	CCTNNNNNAGG	2 cut(s)	533, 1130
EcoRI	GAATTC	1 cut(s)	1015
EcoRII	CCWGG	1 cut(s)	1208
EcoT14I	CCWWGG	1 cut(s)	735
EcoT22I	ATGCAT	4 cut(s)	189, 257, 324, 362
ErhI	CCWWGG	1 cut(s)	735
Esp3I	CGTCTC	1 cut(s)	249
FaeI	CATG	6 cut(s)	140, 163, 191, 322, 360, 1333
FatI	CATG	6 cut(s)	136, 159, 187, 318, 356, 1329
FblI	GTMKAC	1 cut(s)	789
Fnu4HI	GCNGC	2 cut(s)	1250, 1253
FokI	GGATG	3 cut(s)	675, 761, 953
Fsp4HI	GCNGC	2 cut(s)	1250, 1253
FspBI	CTAG	1 cut(s)	1118
GlaI	GCGC	1 cut(s)	945
GluI	GCNGC	2 cut(s)	1250, 1253
HaeIII	GGCC	2 cut(s)	305, 734
HhaI	GCGC	1 cut(s)	946
Hin1II	CATG	6 cut(s)	140, 163, 191, 322, 360, 1333
Hin6I	GCGC	1 cut(s)	944
HinP1I	GCGC	1 cut(s)	944
HincII	GTYRAC	1 cut(s)	367
HindII	GTYRAC	1 cut(s)	367
HindIII	AAGCTT	3 cut(s)	62, 446, 1364
HinfI	GANTC	7 cut(s)	289, 407, 478, 1188, 1205, 1213, 1226
Hpy166II	GTNNAC	2 cut(s)	367, 790
Hpy188I	TCNGA	5 cut(s)	10, 558, 696, 987, 1029
Hpy188III	TCNNGA	5 cut(s)	137, 160, 233, 404, 1330
Hpy8I	GTNNAC	2 cut(s)	367, 790
HpyAV	CCTTC	1 cut(s)	920
HpyCH4III	ACNGT	5 cut(s)	312, 599, 784, 873, 889
HpyCH4IV	ACGT	2 cut(s)	578, 900
HpyF10VI	GCNNNNNNNGC	8 cut(s)	44, 95, 571, 663, 952, 1142, 1151, 1160
HpyF3I	CTNAG	3 cut(s)	69, 444, 688
HpySE526I	ACGT	2 cut(s)	578, 900
Hsp92II	CATG	6 cut(s)	140, 163, 191, 322, 360, 1333
HspAI	GCGC	1 cut(s)	944
Kzo9I	GATC	3 cut(s)	400, 543, 553
LguI	GCTCTTC	2 cut(s)	647, 752
LmnI	GCTCC	1 cut(s)	739
Lsp1109I	GCAGC	2 cut(s)	1236, 1239
LweI	GCATC	6 cut(s)	85, 112, 653, 931, 942, 1141
MaeI	CTAG	1 cut(s)	1118
MaeII	ACGT	2 cut(s)	578, 900
MaeIII	GTNAC	1 cut(s)	889
MalI	GATC	3 cut(s)	402, 545, 555
MboI	GATC	3 cut(s)	400, 543, 553
MboII	GAAGA	8 cut(s)	340, 519, 646, 664, 740, 769, 1301, 1304
MflI	RGATCY	1 cut(s)	400
MlyI	GAGTC	2 cut(s)	472, 1207
MmeI	TCCRAC	1 cut(s)	705
Mph1103I	ATGCAT	4 cut(s)	189, 257, 324, 362
MroXI	GAANNNNTTC	1 cut(s)	704
MseI	TTAA	8 cut(s)	153, 339, 378, 594, 800, 1284, 1344, 1362
MslI	CAYNNNNRTG	1 cut(s)	33
MspR9I	CCNGG	1 cut(s)	1210
Mva1269I	GAATGC	1 cut(s)	1325
MvaI	CCWGG	1 cut(s)	1210
MwoI	GCNNNNNNNGC	8 cut(s)	44, 95, 571, 663, 952, 1142, 1151, 1160
NdeII	GATC	3 cut(s)	400, 543, 553
NlaIII	CATG	6 cut(s)	140, 163, 191, 322, 360, 1333
NmuCI	GTSAC	1 cut(s)	889
NsiI	ATGCAT	4 cut(s)	189, 257, 324, 362
NspI	RCATGY	1 cut(s)	360
PagI	TCATGA	3 cut(s)	136, 159, 1329
PciSI	GCTCTTC	2 cut(s)	647, 752
PctI	GAATGC	1 cut(s)	1325
PdmI	GAANNNNTTC	1 cut(s)	704
PfeI	GAWTC	5 cut(s)	289, 407, 1188, 1205, 1226
PfoI	TCCNGGA	1 cut(s)	1208
PkrI	GCNGC	2 cut(s)	1251, 1254
PleI	GAGTC	2 cut(s)	472, 1207
PpsI	GAGTC	2 cut(s)	472, 1207
Psp6I	CCWGG	1 cut(s)	1208
PspGI	CCWGG	1 cut(s)	1208
PspPI	GGNCC	2 cut(s)	304, 526
PsuI	RGATCY	1 cut(s)	400
RsaI	GTAC	4 cut(s)	119, 262, 581, 1089
RsaNI	GTAC	4 cut(s)	118, 261, 580, 1088
RseI	CAYNNNNRTG	1 cut(s)	33
SapI	GCTCTTC	2 cut(s)	647, 752
SaqAI	TTAA	8 cut(s)	153, 339, 378, 594, 800, 1284, 1344, 1362
SatI	GCNGC	2 cut(s)	1250, 1253
Sau3AI	GATC	3 cut(s)	400, 543, 553
Sau96I	GGNCC	2 cut(s)	304, 526
ScaI	AGTACT	1 cut(s)	262
SchI	GAGTC	2 cut(s)	472, 1207
ScrFI	CCNGG	1 cut(s)	1210
SfaNI	GCATC	6 cut(s)	85, 112, 653, 931, 942, 1141
SfcI	CTRYAG	1 cut(s)	1000
SinI	GGWCC	1 cut(s)	526
SmiMI	CAYNNNNRTG	1 cut(s)	33
SmlI	CTYRAG	1 cut(s)	947
SmoI	CTYRAG	1 cut(s)	947
SspMI	CTAG	1 cut(s)	1118
StyD4I	CCNGG	1 cut(s)	1208
StyI	CCWWGG	1 cut(s)	735
TaaI	ACNGT	5 cut(s)	312, 599, 784, 873, 889
TaiI	ACGT	2 cut(s)	581, 903
TaqI	TCGA	2 cut(s)	476, 1272
TatI	WGTACW	1 cut(s)	260
TfiI	GAWTC	5 cut(s)	289, 407, 1188, 1205, 1226
Tru1I	TTAA	8 cut(s)	153, 339, 378, 594, 800, 1284, 1344, 1362
Tru9I	TTAA	8 cut(s)	153, 339, 378, 594, 800, 1284, 1344, 1362
TscAI	CASTG	2 cut(s)	1203, 1326
TseFI	GTSAC	1 cut(s)	889
TseI	GCWGC	2 cut(s)	1249, 1252
Tsp45I	GTSAC	1 cut(s)	889
TspRI	CASTG	2 cut(s)	1203, 1326
VpaK11BI	GGWCC	1 cut(s)	526
XagI	CCTNNNNNAGG	2 cut(s)	533, 1130
XapI	RAATTY	2 cut(s)	175, 1015
XceI	RCATGY	1 cut(s)	360
XcmI	CCANNNNNNNNNTGG	2 cut(s)	392, 742
XmiI	GTMKAC	1 cut(s)	789
XmnI	GAANNNNTTC	1 cut(s)	704
XspI	CTAG	1 cut(s)	1118
ZrmI	AGTACT	1 cut(s)	262
Zsp2I	ATGCAT	4 cut(s)	189, 257, 324, 362

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