Basic Information

Type: gene

Biological Identity

Species

rosa_laevigata

Chromosome

Chr4

Orthogroup ID

OG0003945

Physical Location & Seq

Genomic Coordinates Reverse (-)

29507474 .. 29511397

Gene Structure 3924 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

RLM00000018415

Sequence Viewer

CDS Protein Promoter (2k)

Length: 663 bp

ATGGTGTCGTCGAGGAGAAGGACGAGGTCGCGCAATCAGATCGGGTTTCGAGGAGGCTCTAGGCTTGAGCTCCTGGAGGACGTCAGCAACATCATCCACAACCCGTGCCTCGTCGGAAGACTACTTCCGATCCCGAATTGGTCACCTGCGATACTAGGCCAGCTGGCGGACCAAGTGACCAAGGTAGCAGACGACCTAGAACCAAGCCTAGACGATCCGACCCACAGTGAGTTCGCCATCGACTTGGAGAAAATATACAGAATATTAGGCAAATTCCACTCCCGGGTCCCCAAACTAGAGCTCGCTCTACACCAATCTGGAGTCGTTTTGCACTCCAACTTAACCGAGCGAGTGCTGTCTCGGTGCCTGCTCTATATTGTGGGGTATAACAATTTGCTTGGTGGGTATGCTCAGGCTGAGAAGATGGTTGATGCGTATGAGCTGTTGAAGGAGATGAAGAGGAAGGGTTGTAAGCCCAATGCGGGTTCGTATACGACTATGATTCAGGCACTTTGCGGGCAAGAGAAGATGGAGGAGGCGATGAGGGTGTTTGTGGAGATGGAGAGGAGTGGTTATGAGATTATGTTGGCTCATGAGAAGAAGGAAGACTTGGAGGAGTGCATAATTGATGGGGCAGATGAGGAAGATTGGTTGCATGCCTGA

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

221

Amino Acids

24.94

Weight (kDa)

5.56

Isoelectric Point (pI)

47.95

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_2	PF13041	126 - 172	8.1e-17	PPR repeat family
PPR_3	PF13812	126 - 171	2.6e-08	Pentatricopeptide repeat domain
PPR	PF01535	129 - 157	2.6e-07	PPR repeat
PPR_1	PF12854	155 - 188	7.6e-10	PPR repeat
PPR_2	PF13041	161 - 193	1.1e-07	PPR repeat family
PPR	PF01535	163 - 191	1.9e-07	PPR repeat

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0003945)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_4g05081
malus_domestica	MD10G1101700.v1.1
pyrus_communis	pycom09g04910 pycom15g38900
rosa_chinensis	RchiOBHm_Chr2g0123831 RchiOBHm_Chr4g0385181 RchiOBHm_Chr5g0064611
rosa_laevigata	RLG00000008165 RLG00000018415 RLG00000019614
rosa_multiflora	Rmu_sc0000571.1_g000023 Rmu_sc0001609.1_g000009 Rmu_sc0002893.1_g000021 Rmu_sc0003314.1_g000036 Rmu_sc0004010.1_g000014 Rmu_sc0008955.1_g000004 Rmu_sc0026245.1_g000002 Rmu_sc0027612.1_g000001
rosa_roxburghii	Rroxscaffold_5G00379810 Rroxscaffold_7G00189080
rosa_rugosa	Rorug03G0223000 Rorug06G0045100
rosa_samantha	Rh1CG355700 Rh1DG373200 Rh2BG315600 Rh3BG307100 Rh3CG368600 Rh3DG369600 Rh6BG404300 Rh6DG233700 Rh6DG396800 Rh6DG396900 Rh7AG211300 Rh7CG234500

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	154
AatII	GACGTC	1 cut(s)	84
Acc36I	ACCTGC	1 cut(s)	154
AccB1I	GGYRCC	1 cut(s)	363
AccI	GTMKAC	1 cut(s)	491
AccII	CGCG	1 cut(s)	31
AciI	CCGC	3 cut(s)	167, 482, 516
AclWI	GGATC	2 cut(s)	124, 209
AcsI	RAATTY	1 cut(s)	272
AcyI	GRCGYC	1 cut(s)	81
AfiI	CCNNNNNNNGG	3 cut(s)	166, 283, 482
AgsI	TTSAA	1 cut(s)	448
AjnI	CCWGG	1 cut(s)	72
AjuI	GAANNNNNNNTTGG	2 cut(s)	593, 625
AluBI	AGCT	4 cut(s)	70, 163, 301, 442
AluI	AGCT	4 cut(s)	70, 163, 301, 442
Alw21I	GWGCWC	2 cut(s)	72, 303
Alw26I	GTCTC	1 cut(s)	363
AlwI	GGATC	2 cut(s)	124, 209
Ama87I	CYCGRG	1 cut(s)	282
AoxI	GGCC	1 cut(s)	157
ApoI	RAATTY	1 cut(s)	272
AspLEI	GCGC	1 cut(s)	33
AspS9I	GGNCC	2 cut(s)	169, 286
AsuC2I	CCSGG	2 cut(s)	283, 284
AsuHPI	GGTGA	1 cut(s)	135
AvaI	CYCGRG	1 cut(s)	282
AvaII	GGWCC	2 cut(s)	169, 286
BanI	GGYRCC	1 cut(s)	363
BanII	GRGCYC	2 cut(s)	72, 303
BbsI	GAAGAC	2 cut(s)	124, 612
Bbv12I	GWGCWC	2 cut(s)	72, 303
BccI	CCATC	5 cut(s)	245, 418, 523, 553, 623
BcgI	CGANNNNNNTGC	2 cut(s)	22, 56
BciT130I	CCWGG	1 cut(s)	74
BcnI	CCSGG	2 cut(s)	283, 284
BcoDI	GTCTC	1 cut(s)	363
BfaI	CTAG	5 cut(s)	60, 155, 197, 209, 296
BfuAI	ACCTGC	1 cut(s)	154
Bme1390I	CCNGG	3 cut(s)	74, 283, 284
Bme18I	GGWCC	2 cut(s)	169, 286
BmeT110I	CYCGRG	1 cut(s)	282
BmgT120I	GGNCC	2 cut(s)	169, 286
BmiI	GGNNCC	3 cut(s)	287, 288, 365
BmrFI	CCNGG	3 cut(s)	74, 283, 284
BmsI	GCATC	1 cut(s)	421
BpiI	GAAGAC	2 cut(s)	124, 612
BpmI	CTGGAG	2 cut(s)	95, 339
Bpu10I	CCTNAGC	1 cut(s)	411
BpuEI	CTTGAG	1 cut(s)	86
BpuMI	CCSGG	2 cut(s)	283, 284
BsaHI	GRCGYC	1 cut(s)	81
BsaJI	CCNNGG	2 cut(s)	180, 282
Bsc4I	CCNNNNNNNGG	3 cut(s)	166, 283, 482
BseBI	CCWGG	1 cut(s)	74
BseDI	CCNNGG	2 cut(s)	180, 282
BseGI	GGATG	1 cut(s)	93
BseLI	CCNNNNNNNGG	3 cut(s)	166, 283, 482
BseMII	CTCAG	2 cut(s)	408, 425
BseRI	GAGGAG	5 cut(s)	28, 66, 548, 580, 629
Bsh1236I	CGCG	1 cut(s)	31
BshFI	GGCC	1 cut(s)	159
BshNI	GGYRCC	1 cut(s)	363
BsiHKAI	GWGCWC	2 cut(s)	72, 303
BsiHKCI	CYCGRG	1 cut(s)	282
BsiSI	CCGG	1 cut(s)	283
BslFI	GGGAC	1 cut(s)	272
BslI	CCNNNNNNNGG	3 cut(s)	166, 283, 482
BsmAI	GTCTC	1 cut(s)	363
BsmFI	GGGAC	1 cut(s)	272
BsnI	GGCC	1 cut(s)	159
BsoBI	CYCGRG	1 cut(s)	282
Bsp1286I	GDGCHC	2 cut(s)	72, 303
Bsp143I	GATC	3 cut(s)	39, 129, 214
BspACI	CCGC	3 cut(s)	167, 482, 516
BspANI	GGCC	1 cut(s)	159
BspCNI	CTCAG	2 cut(s)	409, 424
BspFNI	CGCG	1 cut(s)	31
BspHI	TCATGA	1 cut(s)	592
BspLI	GGNNCC	3 cut(s)	287, 288, 365
BspMI	ACCTGC	1 cut(s)	154
BspPI	GGATC	2 cut(s)	124, 209
BspT107I	GGYRCC	1 cut(s)	363
BssECI	CCNNGG	2 cut(s)	180, 282
BssMI	GATC	3 cut(s)	39, 129, 214
BssNAI	GTATAC	1 cut(s)	492
BssNI	GRCGYC	1 cut(s)	81
BssT1I	CCWWGG	1 cut(s)	180
Bst1107I	GTATAC	1 cut(s)	492
Bst2UI	CCWGG	1 cut(s)	74
Bst4CI	ACNGT	1 cut(s)	227
Bst6I	CTCTTC	1 cut(s)	452
BstACI	GRCGYC	1 cut(s)	81
BstC8I	GCNNGC	6 cut(s)	161, 165, 303, 368, 518, 657
BstDEI	CTNAG	2 cut(s)	411, 417
BstEII	GGTNACC	1 cut(s)	141
BstF5I	GGATG	1 cut(s)	93
BstFNI	CGCG	1 cut(s)	31
BstHHI	GCGC	1 cut(s)	33
BstKTI	GATC	3 cut(s)	42, 132, 217
BstMAI	GTCTC	1 cut(s)	363
BstMBI	GATC	3 cut(s)	39, 129, 214
BstNI	CCWGG	1 cut(s)	74
BstNSI	RCATGY	1 cut(s)	659
BstPI	GGTNACC	1 cut(s)	141
BstSCI	CCNGG	3 cut(s)	72, 281, 282
BstUI	CGCG	1 cut(s)	31
BstV2I	GAAGAC	2 cut(s)	124, 612
BstXI	CCANNNNNNTGG	1 cut(s)	244
BstZ17I	GTATAC	1 cut(s)	492
BsuRI	GGCC	1 cut(s)	159
BtgZI	GCGATG	1 cut(s)	554
BtsCI	GGATG	1 cut(s)	93
BtsIMutI	CAGTG	1 cut(s)	232
BveI	ACCTGC	1 cut(s)	154
Cac8I	GCNNGC	6 cut(s)	161, 165, 303, 368, 518, 657
CciI	TCATGA	1 cut(s)	592
CfoI	GCGC	1 cut(s)	33
Cfr13I	GGNCC	2 cut(s)	169, 286
Cfr9I	CCCGGG	1 cut(s)	282
CviAII	CATG	2 cut(s)	593, 656
DdeI	CTNAG	2 cut(s)	411, 417
DpnI	GATC	3 cut(s)	41, 131, 216
DpnII	GATC	3 cut(s)	39, 129, 214
Eam1104I	CTCTTC	1 cut(s)	452
EarI	CTCTTC	1 cut(s)	452
EciI	GGCGGA	1 cut(s)	182
Ecl136II	GAGCTC	2 cut(s)	70, 301
Eco130I	CCWWGG	1 cut(s)	180
Eco24I	GRGCYC	2 cut(s)	72, 303
Eco47I	GGWCC	2 cut(s)	169, 286
Eco53kI	GAGCTC	2 cut(s)	70, 301
Eco88I	CYCGRG	1 cut(s)	282
Eco91I	GGTNACC	1 cut(s)	141
EcoICRI	GAGCTC	2 cut(s)	70, 301
EcoO109I	RGGNCCY	1 cut(s)	286
EcoO65I	GGTNACC	1 cut(s)	141
EcoRII	CCWGG	1 cut(s)	72
EcoT14I	CCWWGG	1 cut(s)	180
EcoT38I	GRGCYC	2 cut(s)	72, 303
ErhI	CCWWGG	1 cut(s)	180
FaeI	CATG	2 cut(s)	596, 659
FalI	AAGNNNNNCTT	2 cut(s)	593, 625
FaqI	GGGAC	1 cut(s)	272
FatI	CATG	2 cut(s)	592, 655
FauI	CCCGC	2 cut(s)	475, 509
FblI	GTMKAC	1 cut(s)	491
FokI	GGATG	1 cut(s)	80
FriOI	GRGCYC	2 cut(s)	72, 303
FspBI	CTAG	5 cut(s)	60, 155, 197, 209, 296
GlaI	GCGC	1 cut(s)	32
GsuI	CTGGAG	2 cut(s)	95, 339
HaeIII	GGCC	1 cut(s)	159
HapII	CCGG	1 cut(s)	283
HhaI	GCGC	1 cut(s)	33
Hin1I	GRCGYC	1 cut(s)	81
Hin1II	CATG	2 cut(s)	596, 659
Hin6I	GCGC	1 cut(s)	31
HinP1I	GCGC	1 cut(s)	31
HinfI	GANTC	2 cut(s)	321, 502
HpaII	CCGG	1 cut(s)	283
HphI	GGTGA	1 cut(s)	135
Hpy166II	GTNNAC	1 cut(s)	492
Hpy188I	TCNGA	4 cut(s)	39, 116, 129, 219
Hpy188III	TCNNGA	3 cut(s)	133, 318, 593
Hpy8I	GTNNAC	1 cut(s)	492
Hpy99I	CGWCG	2 cut(s)	13, 116
HpyAV	CCTTC	4 cut(s)	12, 442, 457, 595
HpyCH4III	ACNGT	1 cut(s)	227
HpyCH4IV	ACGT	1 cut(s)	81
HpyCH4V	TGCA	3 cut(s)	331, 621, 655
HpyF3I	CTNAG	2 cut(s)	411, 417
HpySE526I	ACGT	1 cut(s)	81
Hsp92I	GRCGYC	1 cut(s)	81
Hsp92II	CATG	2 cut(s)	596, 659
HspAI	GCGC	1 cut(s)	31
KflI	GGGWCCC	1 cut(s)	286
Kzo9I	GATC	3 cut(s)	39, 129, 214
LmnI	GCTCC	1 cut(s)	75
LweI	GCATC	1 cut(s)	421
MaeI	CTAG	5 cut(s)	60, 155, 197, 209, 296
MaeII	ACGT	1 cut(s)	81
MaeIII	GTNAC	2 cut(s)	141, 175
MalI	GATC	3 cut(s)	41, 131, 216
MboI	GATC	3 cut(s)	39, 129, 214
MboII	GAAGA	7 cut(s)	129, 433, 469, 538, 610, 617, 656
MhlI	GDGCHC	2 cut(s)	72, 303
MluCI	AATT	4 cut(s)	136, 272, 391, 624
MlyI	GAGTC	1 cut(s)	330
MmeI	TCCRAC	3 cut(s)	94, 242, 360
MseI	TTAA	1 cut(s)	341
MspA1I	CMGCKG	1 cut(s)	163
MspI	CCGG	1 cut(s)	283
MspR9I	CCNGG	3 cut(s)	74, 283, 284
MvaI	CCWGG	1 cut(s)	74
MvnI	CGCG	1 cut(s)	31
NciI	CCSGG	2 cut(s)	283, 284
NdeII	GATC	3 cut(s)	39, 129, 214
NlaIII	CATG	2 cut(s)	596, 659
NlaIV	GGNNCC	3 cut(s)	287, 288, 365
NmuCI	GTSAC	2 cut(s)	141, 175
NspI	RCATGY	1 cut(s)	659
PaeI	GCATGC	1 cut(s)	659
PagI	TCATGA	1 cut(s)	592
PaqCI	CACCTGC	1 cut(s)	154
PfeI	GAWTC	1 cut(s)	502
PflFI	GACNNNGTC	1 cut(s)	25
PfoI	TCCNGGA	1 cut(s)	72
PleI	GAGTC	1 cut(s)	329
PpsI	GAGTC	1 cut(s)	329
PpuMI	RGGWCCY	1 cut(s)	286
Psp124BI	GAGCTC	2 cut(s)	72, 303
Psp5II	RGGWCCY	1 cut(s)	286
Psp6I	CCWGG	1 cut(s)	72
PspEI	GGTNACC	1 cut(s)	141
PspGI	CCWGG	1 cut(s)	72
PspN4I	GGNNCC	3 cut(s)	287, 288, 365
PspPI	GGNCC	2 cut(s)	169, 286
PspPPI	RGGWCCY	1 cut(s)	286
PsyI	GACNNNGTC	1 cut(s)	25
PvuII	CAGCTG	1 cut(s)	163
SacI	GAGCTC	2 cut(s)	72, 303
SaqAI	TTAA	1 cut(s)	341
Sau3AI	GATC	3 cut(s)	39, 129, 214
Sau96I	GGNCC	2 cut(s)	169, 286
SchI	GAGTC	1 cut(s)	330
ScrFI	CCNGG	3 cut(s)	74, 283, 284
SduI	GDGCHC	2 cut(s)	72, 303
SetI	ASST	9 cut(s)	29, 72, 84, 148, 165, 186, 198, 303, 444
SfaNI	GCATC	1 cut(s)	421
SinI	GGWCC	2 cut(s)	169, 286
SmaI	CCCGGG	1 cut(s)	284
SmlI	CTYRAG	1 cut(s)	65
SmoI	CTYRAG	1 cut(s)	65
SphI	GCATGC	1 cut(s)	659
Sse9I	AATT	4 cut(s)	136, 272, 391, 624
SsiI	CCGC	3 cut(s)	167, 482, 516
SspI	AATATT	1 cut(s)	264
SspMI	CTAG	5 cut(s)	60, 155, 197, 209, 296
SstI	GAGCTC	2 cut(s)	72, 303
StyD4I	CCNGG	3 cut(s)	72, 281, 282
StyI	CCWWGG	1 cut(s)	180
TaaI	ACNGT	1 cut(s)	227
TaiI	ACGT	1 cut(s)	84
TaqI	TCGA	3 cut(s)	11, 49, 240
TasI	AATT	4 cut(s)	136, 272, 391, 624
TfiI	GAWTC	1 cut(s)	502
Tru1I	TTAA	1 cut(s)	341
Tru9I	TTAA	1 cut(s)	341
TscAI	CASTG	1 cut(s)	232
TseFI	GTSAC	2 cut(s)	141, 175
Tsp45I	GTSAC	2 cut(s)	141, 175
TspDTI	ATGAA	1 cut(s)	470
TspMI	CCCGGG	1 cut(s)	282
TspRI	CASTG	1 cut(s)	232
Tth111I	GACNNNGTC	1 cut(s)	25
VpaK11BI	GGWCC	2 cut(s)	169, 286
XapI	RAATTY	1 cut(s)	272
XceI	RCATGY	1 cut(s)	659
XmaI	CCCGGG	1 cut(s)	282
XmiI	GTMKAC	1 cut(s)	491
XspI	CTAG	5 cut(s)	60, 155, 197, 209, 296
ZraI	GACGTC	1 cut(s)	82

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