Basic Information

Type: gene

Biological Identity

Species

rosa_laevigata

Chromosome

Chr1

Orthogroup ID

OG0001535

Physical Location & Seq

Genomic Coordinates Reverse (-)

15269424 .. 15270695

Gene Structure 1272 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

RLM00000001411

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1272 bp

ATGGTAAATGATATGACACAAAGTGGAGTTCCCCCTGATGCTGTTACTTACACAGGTATCCTTGATGGGCTTTTCAAAAATGGAATGGCTACAAAAGCCATGGGGATATTCACTTTAATGCTCACGAAGGGTAAAGAGCCTAATAATGTAACATGCAATGTTATGATTGATGGACTATGCAAGGAGGGGTTGATGGATGATGCTTTAAAGATCTTAGTAATGATGAAAGGGAAAGGTGTAAAGCCTGATGTAATTACTTACAACACATTACTAATGGGACTATTCTGTGATGGGAAGGTTGATGAGGCAATGAAACTTTTCAGTAAGATAACAAATGATGAGAATTTTCTTGAGCCAGATGTTATCACATATAACATGGTCATTTTGGGACTGTGCAAGGAAGGTAATCTTGATGAGGCTATGGAGATTTATCATACAATGATTGAAAGGGGCATTTCTGGTAGCTTATGTACTTATAATACTTTGATAGATAGATGCCTACGGGAAGGATTAGCTGACAAGGCCATAGAATTCTGGAGACATGCAGTGGACTTGGGAGTTATTCCTAATTCAATTACTTATGGTGTCATGATCAATGGATTTTGCAAAAATCAAATGTTCAGGGTTGCAAAAGGACTTTTTACTAAAATGAGAGCTTCTGGGATTAGTCCTACTGTAAATGACTACAACACTTTGATGTCATCATTGTGCAAGGAGGGTAGTTTGGGGCAAGCTAGGATGTTGTTTCAAGAAATGAGAACCGCAAATTATTTGCCTAGTATTGTCTCATTTAATACTATAATTGATGGAATTCTAAAAGCTGGAGATGTTAAATCTGCTAAAGAGTTGCTAGAAGACATGTTCAAATTGGGTTTAACTCCCGATATAATTACATTCTCTACATTAGTAAACCAGTTTTCAAAACTTGGGCTCTTGGATGAGGCTAGAATGTGTGTTGAGAAGATGATTACTCATGGTATTGAACCTGATGTCTTTGTATTTGATTCTTTATTAAAGGGCTATAGTTCAAAAGGTGAAACAAAAGAAATTGTTAACTTGCTTCATCAGATGGCAGACAAGGGTGTTATTCTTGACAAAGAAATAACTTCTACCATCTTGGCGTGCCTCTGTCAAATCTCTGACGATGTTGATGTGATGGAGGTTCTCCAAACTTTTTCCAAAGAGACATCAAAAGGAATAATAATTACCTGCAATGAGCTATTGATGAAAGTCGATAAATCTTACCCGGAACTTAAGTTACATGCTGCTTGA

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

424

Amino Acids

46.77

Weight (kDa)

5.13

Isoelectric Point (pI)

17.42

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_3	PF13812	2 - 57	9.2e-07	Pentatricopeptide repeat domain
PPR_2	PF13041	12 - 61	1.7e-13	PPR repeat family
TPR_24	PF23276	28 - 146	2.5e-07	Fungal tetratrico peptide repeats
PPR_1	PF12854	43 - 76	8.8e-09	PPR repeat
PPR_2	PF13041	47 - 94	1.8e-16	PPR repeat family
PPR	PF01535	50 - 80	1.3e-08	PPR repeat
PPR_3	PF13812	71 - 132	1.7e-09	Pentatricopeptide repeat domain
PPR_1	PF12854	78 - 109	2.5e-12	PPR repeat
PPR_2	PF13041	82 - 110	3.3e-06	PPR repeat family
PPR_3	PF13812	117 - 166	6.3e-09	Pentatricopeptide repeat domain
PPR_1	PF12854	117 - 147	3e-11	PPR repeat
PPR_2	PF13041	119 - 166	1.7e-14	PPR repeat family
PPR	PF01535	122 - 152	2.7e-08	PPR repeat
PPR_long	PF17177	132 - 253	8.3e-08	Pentacotripeptide-repeat region of PRORP
PPR_2	PF13041	157 - 203	8.9e-13	PPR repeat family
TPR_24	PF23276	166 - 283	2.2e-06	Fungal tetratrico peptide repeats
PPR_1	PF12854	186 - 218	3e-07	PPR repeat
PPR	PF01535	192 - 222	5.4e-06	PPR repeat
PPR_1	PF12854	221 - 253	3.1e-08	PPR repeat
PPR_long	PF17177	245 - 360	1.2e-08	Pentacotripeptide-repeat region of PRORP
PPR_3	PF13812	248 - 306	9.5e-08	Pentatricopeptide repeat domain
PPR_1	PF12854	257 - 287	4.6e-06	PPR repeat
PPR_2	PF13041	259 - 308	1.1e-13	PPR repeat family
PPR_1	PF12854	291 - 322	9.6e-06	PPR repeat
PPR_2	PF13041	294 - 342	7.4e-08	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: OG0001535)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT4G28010
fragaria_vesca	FvH4_3g35120 FvH4_3g35120 FvH4_3g35120 FvH4_3g35120 FvH4_3g35120 FvH4_5g33200 FvH4_5g33200 FvH4_5g33200
malus_domestica	MD08G1215500.v1.1 MD15G1399800.v1.1 MD15G1400000.v1.1
prunus_persica	Prupe.1G547200_v2.0.a1 Prupe.1G547200_v2.0.a1 Prupe.1G547200_v2.0.a1 Prupe.1G547200_v2.0.a1 Prupe.1G547200_v2.0.a1 Prupe.1G547200_v2.0.a1 Prupe.1G547200_v2.0.a1 Prupe.1G547200_v2.0.a1 Prupe.1G547200_v2.0.a1 Prupe.1G547200_v2.0.a1 Prupe.1G547200_v2.0.a1 Prupe.1G547200_v2.0.a1
pyrus_communis	pycom08g18660 pycom15g35860
rosa_chinensis	RchiOBHm_Chr5g0048941 RchiOBHm_Chr7g0231581
rosa_laevigata	RLG00000001411 RLG00000001412 RLG00000034570
rosa_multiflora	Rmu_sc0007946.1_g000003
rosa_roxburghii	Rroxscaffold_1G00032970 Rroxscaffold_3G00229080
rosa_rugosa	Rorug05G0241400 Rorug07G0267200 Rorug07G0267300
rosa_samantha	Rh5AG321400 Rh5CG357100 Rh5DG343500 Rh7AG421600 Rh7AG421700 Rh7AG421900 Rh7BG396300 Rh7CG441900 Rh7CG442200 Rh7DG414300
rosa_wichuraiana	Rw5G030330 Rw7G034790 Rw7G034880 Rw7G034900

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	477
Acc36I	ACCTGC	1 cut(s)	1217
AciI	CCGC	1 cut(s)	762
AcsI	RAATTY	3 cut(s)	343, 530, 810
AdeI	CACNNNGTG	1 cut(s)	23
AfaI	GTAC	1 cut(s)	472
AflII	CTTAAG	1 cut(s)	1253
AflIII	ACRYGT	1 cut(s)	858
AgsI	TTSAA	8 cut(s)	76, 446, 573, 749, 865, 921, 983, 1029
AluBI	AGCT	6 cut(s)	465, 515, 656, 734, 821, 1219
AluI	AGCT	6 cut(s)	465, 515, 656, 734, 821, 1219
Alw26I	GTCTC	3 cut(s)	532, 790, 1178
AoxI	GGCC	1 cut(s)	522
ApeKI	GCWGC	1 cut(s)	1265
ApoI	RAATTY	3 cut(s)	343, 530, 810
Asp700I	GAANNNNTTC	1 cut(s)	317
AsuC2I	CCSGG	1 cut(s)	1247
AsuHPI	GGTGA	1 cut(s)	1046
BaeI	ACNNNNGTAYC	2 cut(s)	40, 73
BanII	GRGCYC	1 cut(s)	933
BbsI	GAAGAC	1 cut(s)	861
BbvI	GCAGC	1 cut(s)	1252
BccI	CCATC	8 cut(s)	59, 164, 187, 284, 800, 1063, 1121, 1150
BciVI	GTATCC	1 cut(s)	68
BclI	TGATCA	1 cut(s)	591
BcnI	CCSGG	1 cut(s)	1247
BcoDI	GTCTC	3 cut(s)	532, 790, 1178
BfaI	CTAG	4 cut(s)	735, 777, 851, 945
BfmI	CTRYAG	1 cut(s)	1021
BfrI	CTTAAG	1 cut(s)	1253
BfuAI	ACCTGC	1 cut(s)	1217
BfuI	GTATCC	1 cut(s)	68
BglII	AGATCT	1 cut(s)	210
BisI	GCNGC	1 cut(s)	1266
BlsI	GCNGC	1 cut(s)	1267
Bme1390I	CCNGG	1 cut(s)	1247
BmrFI	CCNGG	1 cut(s)	1247
BmsI	GCATC	3 cut(s)	28, 190, 485
BpiI	GAAGAC	1 cut(s)	861
BpmI	CTGGAG	2 cut(s)	556, 843
BpuEI	CTTGAG	1 cut(s)	371
BpuMI	CCSGG	1 cut(s)	1247
BsaJI	CCNNGG	1 cut(s)	99
Bse1I	ACTGG	1 cut(s)	913
Bse3DI	GCAATG	3 cut(s)	163, 315, 1219
BseDI	CCNNGG	1 cut(s)	99
BseGI	GGATG	3 cut(s)	202, 744, 943
BseMI	GCAATG	3 cut(s)	163, 315, 1219
BseNI	ACTGG	1 cut(s)	913
BseXI	GCAGC	1 cut(s)	1252
BshFI	GGCC	1 cut(s)	524
BsiSI	CCGG	1 cut(s)	1247
BslFI	GGGAC	2 cut(s)	291, 402
BsmAI	GTCTC	3 cut(s)	532, 790, 1178
BsmFI	GGGAC	2 cut(s)	291, 402
BsnI	GGCC	1 cut(s)	524
Bsp1286I	GDGCHC	1 cut(s)	933
Bsp143I	GATC	2 cut(s)	210, 591
Bsp19I	CCATGG	1 cut(s)	99
BspACI	CCGC	1 cut(s)	762
BspANI	GGCC	1 cut(s)	524
BspHI	TCATGA	1 cut(s)	588
BspMI	ACCTGC	1 cut(s)	1217
BspTI	CTTAAG	1 cut(s)	1253
BsrDI	GCAATG	3 cut(s)	163, 315, 1219
BsrI	ACTGG	1 cut(s)	913
BssECI	CCNNGG	1 cut(s)	99
BssMI	GATC	2 cut(s)	210, 591
BssT1I	CCWWGG	1 cut(s)	99
Bst4CI	ACNGT	2 cut(s)	393, 676
BstAFI	CTTAAG	1 cut(s)	1253
BstC8I	GCNNGC	2 cut(s)	732, 1123
BstDEI	CTNAG	1 cut(s)	214
BstDSI	CCRYGG	1 cut(s)	99
BstF5I	GGATG	3 cut(s)	202, 744, 943
BstKTI	GATC	2 cut(s)	213, 594
BstMAI	GTCTC	3 cut(s)	532, 790, 1178
BstMBI	GATC	2 cut(s)	210, 591
BstMWI	GCNNNNNNNGC	2 cut(s)	95, 521
BstNSI	RCATGY	4 cut(s)	156, 545, 862, 1265
BstSCI	CCNGG	1 cut(s)	1245
BstSFI	CTRYAG	1 cut(s)	1021
BstV1I	GCAGC	1 cut(s)	1252
BstV2I	GAAGAC	1 cut(s)	861
BstX2I	RGATCY	1 cut(s)	210
BstYI	RGATCY	1 cut(s)	210
BsuI	GTATCC	1 cut(s)	68
BsuRI	GGCC	1 cut(s)	524
BtgI	CCRYGG	1 cut(s)	99
BtsCI	GGATG	3 cut(s)	202, 744, 943
BtsI	GCAGTG	1 cut(s)	552
BtsIMutI	CAGTG	1 cut(s)	552
BveI	ACCTGC	1 cut(s)	1217
Cac8I	GCNNGC	2 cut(s)	732, 1123
CciI	TCATGA	1 cut(s)	588
Csp6I	GTAC	1 cut(s)	471
CviAII	CATG	8 cut(s)	100, 153, 376, 542, 589, 859, 974, 1262
CviQI	GTAC	1 cut(s)	471
DdeI	CTNAG	1 cut(s)	214
DpnI	GATC	2 cut(s)	212, 593
DpnII	GATC	2 cut(s)	210, 591
DraI	TTTAAA	1 cut(s)	207
DraIII	CACNNNGTG	1 cut(s)	23
Eco130I	CCWWGG	1 cut(s)	99
Eco24I	GRGCYC	1 cut(s)	933
EcoRI	GAATTC	2 cut(s)	530, 810
EcoT14I	CCWWGG	1 cut(s)	99
EcoT38I	GRGCYC	1 cut(s)	933
ErhI	CCWWGG	1 cut(s)	99
FaeI	CATG	8 cut(s)	103, 156, 379, 545, 592, 862, 977, 1265
FalI	AAGNNNNNCTT	2 cut(s)	393, 425
FaqI	GGGAC	2 cut(s)	291, 402
FatI	CATG	8 cut(s)	99, 152, 375, 541, 588, 858, 973, 1261
FbaI	TGATCA	1 cut(s)	591
Fnu4HI	GCNGC	1 cut(s)	1266
FokI	GGATG	3 cut(s)	209, 751, 950
FriOI	GRGCYC	1 cut(s)	933
Fsp4HI	GCNGC	1 cut(s)	1266
FspBI	CTAG	4 cut(s)	735, 777, 851, 945
GluI	GCNGC	1 cut(s)	1266
GsuI	CTGGAG	2 cut(s)	556, 843
HaeIII	GGCC	1 cut(s)	524
HapII	CCGG	1 cut(s)	1247
Hin1II	CATG	8 cut(s)	103, 156, 379, 545, 592, 862, 977, 1265
HincII	GTYRAC	1 cut(s)	1054
HindII	GTYRAC	1 cut(s)	1054
HinfI	GANTC	1 cut(s)	1004
HpaI	GTTAAC	1 cut(s)	1054
HpaII	CCGG	1 cut(s)	1247
HphI	GGTGA	1 cut(s)	1046
Hpy166II	GTNNAC	3 cut(s)	550, 910, 1054
Hpy188I	TCNGA	2 cut(s)	1068, 1141
Hpy188III	TCNNGA	8 cut(s)	124, 350, 410, 535, 589, 749, 881, 1091
Hpy8I	GTNNAC	3 cut(s)	550, 910, 1054
HpyAV	CCTTC	4 cut(s)	121, 289, 395, 500
HpyCH4III	ACNGT	2 cut(s)	393, 676
HpyCH4V	TGCA	8 cut(s)	156, 180, 396, 545, 606, 629, 711, 1212
HpyF10VI	GCNNNNNNNGC	2 cut(s)	95, 521
HpyF3I	CTNAG	1 cut(s)	214
Hsp92II	CATG	8 cut(s)	103, 156, 379, 545, 592, 862, 977, 1265
Ksp22I	TGATCA	1 cut(s)	591
KspAI	GTTAAC	1 cut(s)	1054
Kzo9I	GATC	2 cut(s)	210, 591
Lsp1109I	GCAGC	1 cut(s)	1252
LweI	GCATC	3 cut(s)	28, 190, 485
MaeI	CTAG	4 cut(s)	735, 777, 851, 945
MaeIII	GTNAC	3 cut(s)	43, 148, 1257
MalI	GATC	2 cut(s)	212, 593
MboI	GATC	2 cut(s)	210, 591
MboII	GAAGA	2 cut(s)	866, 973
MflI	RGATCY	1 cut(s)	210
MhlI	GDGCHC	1 cut(s)	933
MnlI	CCTC	7 cut(s)	178, 298, 409, 709, 934, 1136, 1153
MroXI	GAANNNNTTC	1 cut(s)	317
MseI	TTAA	8 cut(s)	116, 206, 792, 831, 875, 1013, 1053, 1254
MslI	CAYNNNNRTG	3 cut(s)	116, 695, 706
MspCI	CTTAAG	1 cut(s)	1253
MspI	CCGG	1 cut(s)	1247
MspR9I	CCNGG	1 cut(s)	1247
MwoI	GCNNNNNNNGC	2 cut(s)	95, 521
NciI	CCSGG	1 cut(s)	1247
NcoI	CCATGG	1 cut(s)	99
NdeII	GATC	2 cut(s)	210, 591
NlaIII	CATG	8 cut(s)	103, 156, 379, 545, 592, 862, 977, 1265
NspI	RCATGY	4 cut(s)	156, 545, 862, 1265
PagI	TCATGA	1 cut(s)	588
PciI	ACATGT	1 cut(s)	858
PdmI	GAANNNNTTC	1 cut(s)	317
PfeI	GAWTC	1 cut(s)	1004
PkrI	GCNGC	1 cut(s)	1267
PscI	ACATGT	1 cut(s)	858
PsiI	TTATAA	1 cut(s)	477
PsrI	GAACNNNNNNTAC	1 cut(s)	1242
PsuI	RGATCY	1 cut(s)	210
RsaI	GTAC	1 cut(s)	472
RsaNI	GTAC	1 cut(s)	471
RseI	CAYNNNNRTG	3 cut(s)	116, 695, 706
SaqAI	TTAA	8 cut(s)	116, 206, 792, 831, 875, 1013, 1053, 1254
SatI	GCNGC	1 cut(s)	1266
Sau3AI	GATC	2 cut(s)	210, 591
ScrFI	CCNGG	1 cut(s)	1247
SduI	GDGCHC	1 cut(s)	933
SfaNI	GCATC	3 cut(s)	28, 190, 485
SfcI	CTRYAG	1 cut(s)	1021
SmiMI	CAYNNNNRTG	3 cut(s)	116, 695, 706
SmlI	CTYRAG	2 cut(s)	350, 1253
SmoI	CTYRAG	2 cut(s)	350, 1253
SsiI	CCGC	1 cut(s)	762
SspMI	CTAG	4 cut(s)	735, 777, 851, 945
StyD4I	CCNGG	1 cut(s)	1245
StyI	CCWWGG	1 cut(s)	99
TaaI	ACNGT	2 cut(s)	393, 676
TaqI	TCGA	1 cut(s)	1233
TatI	WGTACW	1 cut(s)	470
TfiI	GAWTC	1 cut(s)	1004
Tru1I	TTAA	8 cut(s)	116, 206, 792, 831, 875, 1013, 1053, 1254
Tru9I	TTAA	8 cut(s)	116, 206, 792, 831, 875, 1013, 1053, 1254
TscAI	CASTG	1 cut(s)	552
TseI	GCWGC	1 cut(s)	1265
TspDTI	ATGAA	4 cut(s)	239, 326, 1052, 1241
TspRI	CASTG	1 cut(s)	552
Vha464I	CTTAAG	1 cut(s)	1253
XapI	RAATTY	3 cut(s)	343, 530, 810
XceI	RCATGY	4 cut(s)	156, 545, 862, 1265
XmnI	GAANNNNTTC	1 cut(s)	317
XspI	CTAG	4 cut(s)	735, 777, 851, 945

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