Basic Information

Type: gene

Biological Identity

Species

rosa_laevigata

Chromosome

Chr3

Orthogroup ID

OG0005465

Physical Location & Seq

Genomic Coordinates Forward (+)

44695350 .. 44696681

Gene Structure 1332 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

RLM00000013953

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1176 bp

ATGGGTGTGGCGGCTGATATTTTCGTGTCTTGTGCGTTGATTGATATGTATAGCAAGTGTGGGAGCATTGATGACGCTCACTGTGTTTTTGATGAGATGCCGAAGAAGACAACTGTAGGATGGAATACCATTATAGCGGGTTATGCACTTCATGGTTATAGTGAGGAGGCTTTGAGTATGTACTATGATATGCGTGATTCTGGTGTGCCGATGGACCATATTACGTTTTCCATGATCATAAGAACATGTGCAAGGTTGGCGTCGTTAGAACATGCAAAGCAAGCACATGCAGGTCTAGTTCGTCATGGTTTTGGGTTGGATATAGTGGCAAACACATCGCTCGTGGAGTTCTATAGCAAATGGGGGAGGATAGAAGATGCTCGTCATGTTTTTGATCAGATGCCTAACAAGAATGTCATATCTTGGAATGCCTTGATTGCTGGATATGGTAACCATGGTCGGGGTGATGAGGCTGTTGAGATGTTTGAGAAGATGCTTCAGGAAGGAATGGTACCCAACCATGTTACTTTTCTTGCTGTCTTGCCTGCTTGCAGTCGTTCAGGTTTATCAGAACTTGGATGGGAGATTTTTGAATCAATGAGCAGGGATTACAAGATCAAGCCCCGTGCTATGCATTATGCTTGTATGATTGAATTGCTAGGACAAGAGGGCAATTTAGATGGAGCGTTTGCATTGATAAGAACTGCTCCCTTAAAGCCTACAGCAAACATGTGGGCTGCTCTGCTGGCAGCTTGTCGAATCCATGAGAATTTAGAGCTTGGCAAAATTGCAGCCGAAGAGCTCTATGGGATGGAGCCTGAGAAGCTAAATGAAAGGCATGCCCAAACAAGAGAGATTTACGAGAAAGTGGAAGAATTGACGGTCAGGATTAGGAGACGTGGTTACATCCCTGACAAGAAGCATCTACTTCCTGATGTGGATGAACATGAGCGCATCTCAGCTTACCACAGTGAGAAACTGGCTATAGCTTACGGCTTGATAAGTACGTCAGATGGGACGCCACTGCAAATTGTGCAAGGCCATCGCATTTGCGGAGACTGCCATTCCACAATCAAGTTAATAGCTAAGGTGACTGAACGGGAAATTGTAGTGAGGGACGCCAGCAGATTCCACCACTTCAAGAATGGGAGTTGTTCTTGTGGGAATTACTGGTGA

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

DYW_deaminase PPR PPR_2

Protein Analysis

392

Amino Acids

43.94

Weight (kDa)

6.09

Isoelectric Point (pI)

43.85

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_2	PF13041	37 - 85	1.1e-11	PPR repeat family
PPR	PF01535	41 - 69	1.2e-06	PPR repeat
PPR_2	PF13041	137 - 185	1.3e-12	PPR repeat family
PPR_1	PF12854	138 - 165	3e-06	PPR repeat
PPR	PF01535	140 - 169	3.6e-09	PPR repeat
DYW_deaminase	PF14432	301 - 391	1.3e-36	DYW family of nucleic acid deaminases

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: OG0005465)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G50390
fragaria_vesca	FvH4_6g48290
malus_domestica	MD00G1131200.v1.1 MD09G1052300.v1.1
prunus_persica	Prupe.3G266400_v2.0.a1
pyrus_communis	pycom111g04370 pycom17g04780
rosa_chinensis	RchiOBHm_Chr2g0168271 RchiOBHm_Chr6g0267531
rosa_laevigata	RLG00000013953 RLG00000013992
rosa_multiflora	Rmu_co8459511.1_g000001 Rmu_sc0003354.1_g000005 Rmu_sc0012005.1_g000008
rosa_roxburghii	Rroxscaffold_2G00083250 Rroxscaffold_7G00200650
rosa_rugosa	Rorug02G0532200 Rorug02G0532200 Rorug02G0532300 Rorug06G0033600
rosa_samantha	Rh2AG601300 Rh2BG614500 Rh2BG614600 Rh6AG155000 Rh6BG155600 Rh6DG140900
rosa_wichuraiana	Rw0G012800 Rw2G049930 Rw6G013300

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc36I	ACCTGC	1 cut(s)	281
Acc65I	GGTACC	1 cut(s)	511
AccB1I	GGYRCC	1 cut(s)	511
AciI	CCGC	3 cut(s)	11, 137, 1053
AcsI	RAATTY	1 cut(s)	769
AcuI	CTGAAG	1 cut(s)	482
AcyI	GRCGYC	3 cut(s)	260, 1019, 1119
AfaI	GTAC	3 cut(s)	182, 513, 1006
AfiI	CCNNNNNNNGG	1 cut(s)	460
AflIII	ACRYGT	2 cut(s)	245, 729
AgsI	TTSAA	3 cut(s)	593, 653, 1141
AjiI	CACGTC	1 cut(s)	899
AluBI	AGCT	7 cut(s)	752, 778, 802, 826, 962, 989, 1085
AluI	AGCT	7 cut(s)	752, 778, 802, 826, 962, 989, 1085
Alw21I	GWGCWC	1 cut(s)	804
Alw26I	GTCTC	2 cut(s)	889, 1050
AoxI	GGCC	1 cut(s)	1039
ApeKI	GCWGC	3 cut(s)	737, 749, 791
ApoI	RAATTY	1 cut(s)	769
Asp718I	GGTACC	1 cut(s)	511
AspLEI	GCGC	1 cut(s)	954
AspS9I	GGNCC	1 cut(s)	214
AsuHPI	GGTGA	2 cut(s)	476, 1102
AvaII	GGWCC	1 cut(s)	214
BanI	GGYRCC	1 cut(s)	511
BanII	GRGCYC	1 cut(s)	804
BarI	GAAGNNNNNNTAC	2 cut(s)	495, 527
BauI	CACGAG	1 cut(s)	341
BbsI	GAAGAC	1 cut(s)	113
Bbv12I	GWGCWC	1 cut(s)	804
BbvI	GCAGC	3 cut(s)	724, 761, 803
BccI	CCATC	7 cut(s)	114, 205, 573, 674, 805, 1007, 1050
BceAI	ACGGC	1 cut(s)	1009
BcgI	CGANNNNNNTGC	4 cut(s)	318, 352, 1025, 1059
BclI	TGATCA	2 cut(s)	234, 394
BcoDI	GTCTC	2 cut(s)	889, 1050
BfaI	CTAG	2 cut(s)	296, 659
BfmI	CTRYAG	4 cut(s)	114, 352, 720, 984
BfuAI	ACCTGC	1 cut(s)	281
BisI	GCNGC	4 cut(s)	12, 738, 750, 792
BlsI	GCNGC	4 cut(s)	13, 739, 751, 793
Bme18I	GGWCC	1 cut(s)	214
BmgBI	CACGTC	1 cut(s)	899
BmgT120I	GGNCC	1 cut(s)	214
BmiI	GGNNCC	2 cut(s)	513, 816
BmsI	GCATC	6 cut(s)	87, 367, 390, 483, 931, 963
BpiI	GAAGAC	1 cut(s)	113
BplI	GAGNNNNNCTC	2 cut(s)	941, 973
Bpu10I	CCTNAGC	1 cut(s)	1086
BsaHI	GRCGYC	3 cut(s)	260, 1019, 1119
BsaJI	CCNNGG	1 cut(s)	454
BsaXI	ACNNNNNCTCC	2 cut(s)	886, 916
Bsc4I	CCNNNNNNNGG	1 cut(s)	460
Bse1I	ACTGG	2 cut(s)	984, 1175
BseDI	CCNNGG	1 cut(s)	454
BseGI	GGATG	5 cut(s)	125, 584, 816, 906, 946
BseLI	CCNNNNNNNGG	1 cut(s)	460
BseMII	CTCAG	2 cut(s)	810, 972
BseNI	ACTGG	2 cut(s)	984, 1175
BseRI	GAGGAG	1 cut(s)	179
BseXI	GCAGC	3 cut(s)	724, 761, 803
BshFI	GGCC	1 cut(s)	1041
BshNI	GGYRCC	1 cut(s)	511
BsiHKAI	GWGCWC	1 cut(s)	804
BslFI	GGGAC	2 cut(s)	1030, 1130
BslI	CCNNNNNNNGG	1 cut(s)	460
BsmAI	GTCTC	2 cut(s)	889, 1050
BsmBI	CGTCTC	1 cut(s)	889
BsmFI	GGGAC	2 cut(s)	1030, 1130
BsmI	GAATGC	1 cut(s)	433
BsnI	GGCC	1 cut(s)	1041
Bsp1286I	GDGCHC	1 cut(s)	804
Bsp143I	GATC	3 cut(s)	234, 394, 615
Bsp19I	CCATGG	1 cut(s)	454
BspACI	CCGC	3 cut(s)	11, 137, 1053
BspANI	GGCC	1 cut(s)	1041
BspCNI	CTCAG	2 cut(s)	811, 971
BspLI	GGNNCC	2 cut(s)	513, 816
BspMI	ACCTGC	1 cut(s)	281
BspQI	GCTCTTC	1 cut(s)	792
BspT107I	GGYRCC	1 cut(s)	511
BsrI	ACTGG	2 cut(s)	984, 1175
BssECI	CCNNGG	1 cut(s)	454
BssMI	GATC	3 cut(s)	234, 394, 615
BssNI	GRCGYC	3 cut(s)	260, 1019, 1119
BssSI	CACGAG	1 cut(s)	341
BssT1I	CCWWGG	1 cut(s)	454
Bst2BI	CACGAG	1 cut(s)	341
Bst4CI	ACNGT	4 cut(s)	83, 115, 883, 971
Bst6I	CTCTTC	1 cut(s)	792
BstACI	GRCGYC	3 cut(s)	260, 1019, 1119
BstAPI	GCANNNNNTGC	1 cut(s)	1033
BstC8I	GCNNGC	6 cut(s)	282, 546, 550, 747, 840, 1123
BstDEI	CTNAG	3 cut(s)	819, 958, 1086
BstDSI	CCRYGG	1 cut(s)	454
BstEII	GGTNACC	1 cut(s)	449
BstF5I	GGATG	5 cut(s)	125, 584, 816, 906, 946
BstHHI	GCGC	1 cut(s)	954
BstKTI	GATC	3 cut(s)	237, 397, 618
BstMAI	GTCTC	2 cut(s)	889, 1050
BstMBI	GATC	3 cut(s)	234, 394, 615
BstMWI	GCNNNNNNNGC	8 cut(s)	143, 257, 281, 437, 746, 823, 1033, 1059
BstNSI	RCATGY	5 cut(s)	249, 275, 290, 733, 842
BstPI	GGTNACC	1 cut(s)	449
BstSFI	CTRYAG	4 cut(s)	114, 352, 720, 984
BstV1I	GCAGC	3 cut(s)	724, 761, 803
BstV2I	GAAGAC	1 cut(s)	113
BsuRI	GGCC	1 cut(s)	1041
BtgI	CCRYGG	1 cut(s)	454
BtgZI	GCGATG	2 cut(s)	321, 1028
BtrI	CACGTC	1 cut(s)	899
BtsCI	GGATG	5 cut(s)	125, 584, 816, 906, 946
BtsI	GCAGTG	1 cut(s)	1022
BtsIMutI	CAGTG	3 cut(s)	79, 976, 1022
BveI	ACCTGC	1 cut(s)	281
Cac8I	GCNNGC	6 cut(s)	282, 546, 550, 747, 840, 1123
CfoI	GCGC	1 cut(s)	954
Cfr13I	GGNCC	1 cut(s)	214
CseI	GACGC	4 cut(s)	83, 249, 1027, 1127
Csp6I	GTAC	3 cut(s)	181, 512, 1005
CviQI	GTAC	3 cut(s)	181, 512, 1005
DdeI	CTNAG	3 cut(s)	819, 958, 1086
DpnI	GATC	3 cut(s)	236, 396, 617
DpnII	GATC	3 cut(s)	234, 394, 615
Eam1104I	CTCTTC	1 cut(s)	792
EarI	CTCTTC	1 cut(s)	792
Ecl136II	GAGCTC	1 cut(s)	802
Eco130I	CCWWGG	1 cut(s)	454
Eco24I	GRGCYC	1 cut(s)	804
Eco47I	GGWCC	1 cut(s)	214
Eco53kI	GAGCTC	1 cut(s)	802
Eco57I	CTGAAG	1 cut(s)	482
Eco91I	GGTNACC	1 cut(s)	449
EcoICRI	GAGCTC	1 cut(s)	802
EcoO65I	GGTNACC	1 cut(s)	449
EcoT14I	CCWWGG	1 cut(s)	454
EcoT22I	ATGCAT	1 cut(s)	636
EcoT38I	GRGCYC	1 cut(s)	804
ErhI	CCWWGG	1 cut(s)	454
Esp3I	CGTCTC	1 cut(s)	889
FaqI	GGGAC	2 cut(s)	1030, 1130
FauI	CCCGC	1 cut(s)	130
FbaI	TGATCA	2 cut(s)	234, 394
Fnu4HI	GCNGC	4 cut(s)	12, 738, 750, 792
FokI	GGATG	5 cut(s)	132, 591, 823, 893, 953
FriOI	GRGCYC	1 cut(s)	804
Fsp4HI	GCNGC	4 cut(s)	12, 738, 750, 792
FspBI	CTAG	2 cut(s)	296, 659
GlaI	GCGC	1 cut(s)	953
GluI	GCNGC	4 cut(s)	12, 738, 750, 792
HaeIII	GGCC	1 cut(s)	1041
HgaI	GACGC	4 cut(s)	83, 249, 1027, 1127
HhaI	GCGC	1 cut(s)	954
Hin1I	GRCGYC	3 cut(s)	260, 1019, 1119
Hin6I	GCGC	1 cut(s)	952
HinP1I	GCGC	1 cut(s)	952
HinfI	GANTC	4 cut(s)	197, 593, 759, 1128
HphI	GGTGA	2 cut(s)	476, 1102
Hpy188I	TCNGA	3 cut(s)	399, 571, 1012
Hpy188III	TCNNGA	4 cut(s)	500, 886, 932, 1141
Hpy99I	CGWCG	1 cut(s)	265
HpyAV	CCTTC	1 cut(s)	497
HpyCH4III	ACNGT	4 cut(s)	83, 115, 883, 971
HpyCH4IV	ACGT	3 cut(s)	224, 898, 1007
HpyF10VI	GCNNNNNNNGC	8 cut(s)	143, 257, 281, 437, 746, 823, 1033, 1059
HpyF3I	CTNAG	3 cut(s)	819, 958, 1086
HpySE526I	ACGT	3 cut(s)	224, 898, 1007
Hsp92I	GRCGYC	3 cut(s)	260, 1019, 1119
HspAI	GCGC	1 cut(s)	952
KpnI	GGTACC	1 cut(s)	515
Ksp22I	TGATCA	2 cut(s)	234, 394
Kzo9I	GATC	3 cut(s)	234, 394, 615
LguI	GCTCTTC	1 cut(s)	792
LmnI	GCTCC	4 cut(s)	63, 683, 712, 814
Lsp1109I	GCAGC	3 cut(s)	724, 761, 803
LweI	GCATC	6 cut(s)	87, 367, 390, 483, 931, 963
MaeI	CTAG	2 cut(s)	296, 659
MaeII	ACGT	3 cut(s)	224, 898, 1007
MaeIII	GTNAC	4 cut(s)	449, 523, 902, 1090
MalI	GATC	3 cut(s)	236, 396, 617
MboI	GATC	3 cut(s)	234, 394, 615
MboII	GAAGA	6 cut(s)	115, 118, 386, 502, 809, 884
MhlI	GDGCHC	1 cut(s)	804
MluCI	AATT	8 cut(s)	653, 673, 769, 786, 875, 1029, 1104, 1165
MmeI	TCCRAC	1 cut(s)	297
MnlI	CCTC	6 cut(s)	157, 160, 360, 463, 661, 1107
Mph1103I	ATGCAT	1 cut(s)	636
MseI	TTAA	2 cut(s)	713, 1079
Mva1269I	GAATGC	1 cut(s)	433
MwoI	GCNNNNNNNGC	8 cut(s)	143, 257, 281, 437, 746, 823, 1033, 1059
NcoI	CCATGG	1 cut(s)	454
NdeII	GATC	3 cut(s)	234, 394, 615
NlaIV	GGNNCC	2 cut(s)	513, 816
NmuCI	GTSAC	1 cut(s)	1090
NsiI	ATGCAT	1 cut(s)	636
NspI	RCATGY	5 cut(s)	249, 275, 290, 733, 842
PaeI	GCATGC	1 cut(s)	842
PciI	ACATGT	2 cut(s)	245, 729
PciSI	GCTCTTC	1 cut(s)	792
PctI	GAATGC	1 cut(s)	433
PfeI	GAWTC	4 cut(s)	197, 593, 759, 1128
PkrI	GCNGC	4 cut(s)	13, 739, 751, 793
PscI	ACATGT	2 cut(s)	245, 729
Psp124BI	GAGCTC	1 cut(s)	804
PspEI	GGTNACC	1 cut(s)	449
PspN4I	GGNNCC	2 cut(s)	513, 816
PspPI	GGNCC	1 cut(s)	214
RsaI	GTAC	3 cut(s)	182, 513, 1006
RsaNI	GTAC	3 cut(s)	181, 512, 1005
SacI	GAGCTC	1 cut(s)	804
SapI	GCTCTTC	1 cut(s)	792
SaqAI	TTAA	2 cut(s)	713, 1079
SatI	GCNGC	4 cut(s)	12, 738, 750, 792
Sau3AI	GATC	3 cut(s)	234, 394, 615
Sau96I	GGNCC	1 cut(s)	214
SduI	GDGCHC	1 cut(s)	804
SfaNI	GCATC	6 cut(s)	87, 367, 390, 483, 931, 963
SfcI	CTRYAG	4 cut(s)	114, 352, 720, 984
SinI	GGWCC	1 cut(s)	214
SphI	GCATGC	1 cut(s)	842
Sse9I	AATT	8 cut(s)	653, 673, 769, 786, 875, 1029, 1104, 1165
SsiI	CCGC	3 cut(s)	11, 137, 1053
SspMI	CTAG	2 cut(s)	296, 659
SstI	GAGCTC	1 cut(s)	804
StyI	CCWWGG	1 cut(s)	454
TaaI	ACNGT	4 cut(s)	83, 115, 883, 971
TaiI	ACGT	3 cut(s)	227, 901, 1010
TaqI	TCGA	1 cut(s)	757
TasI	AATT	8 cut(s)	653, 673, 769, 786, 875, 1029, 1104, 1165
TatI	WGTACW	1 cut(s)	180
TauI	GCSGC	1 cut(s)	14
TfiI	GAWTC	4 cut(s)	197, 593, 759, 1128
Tru1I	TTAA	2 cut(s)	713, 1079
Tru9I	TTAA	2 cut(s)	713, 1079
TscAI	CASTG	3 cut(s)	86, 976, 1029
TseFI	GTSAC	1 cut(s)	1090
TseI	GCWGC	3 cut(s)	737, 749, 791
Tsp45I	GTSAC	1 cut(s)	1090
TspDTI	ATGAA	3 cut(s)	140, 846, 957
TspRI	CASTG	3 cut(s)	86, 976, 1029
VpaK11BI	GGWCC	1 cut(s)	214
XapI	RAATTY	1 cut(s)	769
XceI	RCATGY	5 cut(s)	249, 275, 290, 733, 842
XcmI	CCANNNNNNNNNTGG	1 cut(s)	1142
XspI	CTAG	2 cut(s)	296, 659
Zsp2I	ATGCAT	1 cut(s)	636

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