Basic Information

Type: gene

Biological Identity

Species

rosa_laevigata

Chromosome

Chr1

Orthogroup ID

OG0005837

Physical Location & Seq

Genomic Coordinates Reverse (-)

24099542 .. 24101269

Gene Structure 1728 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

RLM00000001999

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1215 bp

ATGGATGCTCATTCATATAGTTTGAATCCCATTAATAGTACTGTGAGGCCAATACACTATTTGACTCAACCCCACTTTGACATAGTACCCAAAGTTGCTTCCAGTGGATTTCTTGGTATATACAAGCGATTTTCATTGCATAAGTTTTACTCATCACCATCTCGATCTTTTAGAAGGAGAGAAAATAAAAGATTAGAATCCAGTAGAAAACCAACCCTTAATGAAGCCCAATTTCAAAGGTCTGTATCCCAGTTGTTGCCTAGATTTACACCTGAAGAACTGTGCGATGTTATAACTAAGCAAGATGATCCTCTTGTGTGTTTAGAGTTGCTCAATTGGGCATCACAACAGTCACGGTTCAAACATGATGTTAACAGCTATCACATTACAATAAAGAAACTTGGTGTAGCTAAGATGTACGAAGAGATGGATGATATTGTCAACCAAGTGCTTGCTATCTCTCACATGGGTTCTGAGGCGCTTTTCAATTCCATTATCTACTTTTTCACAGAAGCTCGGAAGTTGACTAGAGCTGTCAATATATTTAAACACATGAAGAATAGTAGAAACATGGACTGTAGGCCTTCTGTTAGGACATACAATATTCTGTTTACTGCCTTTTTGAGTAGGGGATGTAATACCTACATAAATCACATGTATATGGAAACCATAAGATGTCTGTTTAGGCAAATGGTGAATGATGGGATTGAACCCGATATTTATACTTTGAATTCAATGATTAAGGGGTATGTTCTTTCCCTTCATGTGAATGATGCACTTAGAGTATTCCATCAGATGGGTGTGGTCTATAACTGCCTGCCAAACACATTTTCCTATGATTATCTCATCCATGGATTATGTGCTCAAGGCCGAACAAACAATGCTAAGCAGTTGTGCAACGAAATGAAGACTAAAGGGTTTGTCCCGAGTAGTAAATCCTACAACTCGCTTGTGAATGCTTTGGCTCTTTGTGGAGAGATTGAGGAGGCAGTGAAGTATTTGTGGGAGATGATTGAGAAGCGAAGGTCAACTGAATTCATTACTTATAAGACAGTACTTGATGAAATGTGCAGACAAGGACGGGTTGGACAAGCAATGAAGTTGCTAAAAGAATTTCAAAAGAAAGACATCCTGAGTGGGCATGCTTACAGGAAGCTCCAATATGTGCTTGAAGATGACTATGGAGATTCTGTCTCCCATACTCGATTGAGATAA

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

405

Amino Acids

47.02

Weight (kDa)

9.22

Isoelectric Point (pI)

52.37

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_2	PF13041	161 - 207	2.2e-06	PPR repeat family
PPR_2	PF13041	215 - 250	4.4e-06	PPR repeat family
PPR_3	PF13812	227 - 284	3.2e-07	Pentatricopeptide repeat domain
PPR_2	PF13041	244 - 287	1.2e-07	PPR repeat family
PPR_1	PF12854	271 - 303	1.4e-08	PPR repeat
PPR_2	PF13041	274 - 322	9.1e-13	PPR repeat family
TPR_24	PF23276	276 - 372	5.9e-06	Fungal tetratrico peptide repeats

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0005837)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT2G27800
fragaria_vesca	FvH4_3g33090 FvH4_3g33090
malus_domestica	MD03G1104000.v1.1 MD11G1131200.v1.1
prunus_persica	Prupe.6G095500_v2.0.a1
rosa_chinensis	RchiOBHm_Chr5g0060431 RchiOBHm_Chr7g0223121 RchiOBHm_Chr7g0223131
rosa_laevigata	RLG00000001999 RLG00000002000 RLG00000035363
rosa_multiflora	Rmu_sc0002192.1_g000036 Rmu_sc0002608.1_g000003
rosa_roxburghii	Rroxscaffold_1G00020390 Rroxscaffold_3G00236080
rosa_rugosa	Rorug05G0329900 Rorug07G0213100
rosa_samantha	Rh5AG394700 Rh5BG406800 Rh5CG430600 Rh5DG421900 Rh7AG358300 Rh7BG346400 Rh7CG376600 Rh7DG353700
rosa_wichuraiana	Rw5G037120 Rw7G030490

Restriction Enzyme Sites

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Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	2 cut(s)	293, 1047
AccB7I	CCANNNNNTGG	1 cut(s)	796
AclWI	GGATC	1 cut(s)	302
AcsI	RAATTY	3 cut(s)	730, 1034, 1112
AcuI	CTGAAG	1 cut(s)	294
AfaI	GTAC	4 cut(s)	40, 87, 419, 1056
AfiI	CCNNNNNNNGG	1 cut(s)	796
AflIII	ACRYGT	1 cut(s)	654
AgsI	TTSAA	9 cut(s)	25, 236, 361, 487, 710, 730, 735, 1118, 1172
AjuI	GAANNNNNNNTTGG	2 cut(s)	814, 846
AluBI	AGCT	5 cut(s)	378, 410, 515, 533, 1156
AluI	AGCT	5 cut(s)	378, 410, 515, 533, 1156
Alw21I	GWGCWC	1 cut(s)	865
Alw26I	GTCTC	1 cut(s)	1198
AlwI	GGATC	1 cut(s)	302
Ama87I	CYCGRG	1 cut(s)	925
AoxI	GGCC	3 cut(s)	47, 581, 868
ApoI	RAATTY	3 cut(s)	730, 1034, 1112
AseI	ATTAAT	1 cut(s)	33
AspLEI	GCGC	1 cut(s)	481
AsuHPI	GGTGA	2 cut(s)	147, 706
AvaI	CYCGRG	1 cut(s)	925
BbsI	GAAGAC	1 cut(s)	914
Bbv12I	GWGCWC	1 cut(s)	865
BccI	CCATC	5 cut(s)	166, 421, 695, 790, 798
BciVI	GTATCC	1 cut(s)	256
BcoDI	GTCTC	1 cut(s)	1198
BfaI	CTAG	2 cut(s)	261, 528
BfmI	CTRYAG	1 cut(s)	577
BfoI	RGCGCY	1 cut(s)	482
BfuI	GTATCC	1 cut(s)	256
BlpI	GCTNAGC	1 cut(s)	885
BmcAI	AGTACT	2 cut(s)	40, 1056
BmeT110I	CYCGRG	1 cut(s)	925
BmrI	ACTGGG	1 cut(s)	244
BmsI	GCATC	2 cut(s)	350, 763
BmuI	ACTGGG	1 cut(s)	244
BpiI	GAAGAC	1 cut(s)	914
Bpu1102I	GCTNAGC	1 cut(s)	885
BpuEI	CTTGAG	1 cut(s)	849
BsaBI	GATNNNNATC	1 cut(s)	196
BsaJI	CCNNGG	1 cut(s)	850
BsaXI	ACNNNNNCTCC	2 cut(s)	1176, 1206
Bsc4I	CCNNNNNNNGG	1 cut(s)	796
Bse1I	ACTGG	3 cut(s)	102, 201, 250
Bse3DI	GCAATG	2 cut(s)	134, 1101
Bse8I	GATNNNNATC	1 cut(s)	196
BseDI	CCNNGG	1 cut(s)	850
BseGI	GGATG	5 cut(s)	10, 436, 638, 846, 1128
BseJI	GATNNNNATC	1 cut(s)	196
BseLI	CCNNNNNNNGG	1 cut(s)	796
BseMI	GCAATG	2 cut(s)	134, 1101
BseMII	CTCAG	2 cut(s)	465, 1124
BseNI	ACTGG	3 cut(s)	102, 201, 250
BseRI	GAGGAG	1 cut(s)	998
BsgI	GTGCAG	1 cut(s)	1090
BshFI	GGCC	3 cut(s)	49, 583, 870
BsiHKAI	GWGCWC	1 cut(s)	865
BsiHKCI	CYCGRG	1 cut(s)	925
BslFI	GGGAC	1 cut(s)	908
BslI	CCNNNNNNNGG	1 cut(s)	796
BsmAI	GTCTC	1 cut(s)	1198
BsmFI	GGGAC	1 cut(s)	908
BsmI	GAATGC	1 cut(s)	961
BsnI	GGCC	3 cut(s)	49, 583, 870
BsoBI	CYCGRG	1 cut(s)	925
Bsp1286I	GDGCHC	1 cut(s)	865
Bsp143I	GATC	2 cut(s)	164, 307
Bsp1720I	GCTNAGC	1 cut(s)	885
Bsp19I	CCATGG	1 cut(s)	850
BspANI	GGCC	3 cut(s)	49, 583, 870
BspCNI	CTCAG	2 cut(s)	466, 1125
BspPI	GGATC	1 cut(s)	302
BsrDI	GCAATG	2 cut(s)	134, 1101
BsrI	ACTGG	3 cut(s)	102, 201, 250
BssECI	CCNNGG	1 cut(s)	850
BssMI	GATC	2 cut(s)	164, 307
BssT1I	CCWWGG	1 cut(s)	850
Bst4CI	ACNGT	6 cut(s)	43, 282, 351, 357, 578, 1054
Bst6I	CTCTTC	1 cut(s)	417
BstC8I	GCNNGC	3 cut(s)	453, 818, 1143
BstDEI	CTNAG	6 cut(s)	297, 411, 474, 779, 885, 1133
BstDSI	CCRYGG	1 cut(s)	850
BstF5I	GGATG	5 cut(s)	10, 436, 638, 846, 1128
BstH2I	RGCGCY	1 cut(s)	482
BstHHI	GCGC	1 cut(s)	481
BstKTI	GATC	2 cut(s)	167, 310
BstMAI	GTCTC	1 cut(s)	1198
BstMBI	GATC	2 cut(s)	164, 307
BstNSI	RCATGY	2 cut(s)	658, 1145
BstSFI	CTRYAG	1 cut(s)	577
BstV2I	GAAGAC	1 cut(s)	914
BsuI	GTATCC	1 cut(s)	256
BsuRI	GGCC	3 cut(s)	49, 583, 870
BtgI	CCRYGG	1 cut(s)	850
BtgZI	GCGATG	1 cut(s)	300
BtsCI	GGATG	5 cut(s)	10, 436, 638, 846, 1128
BtsI	GCAGTG	1 cut(s)	996
BtsIMutI	CAGTG	2 cut(s)	109, 996
Cac8I	GCNNGC	3 cut(s)	453, 818, 1143
CfoI	GCGC	1 cut(s)	481
Csp6I	GTAC	4 cut(s)	39, 86, 418, 1055
CviAII	CATG	8 cut(s)	365, 466, 553, 571, 655, 764, 851, 1142
CviQI	GTAC	4 cut(s)	39, 86, 418, 1055
DdeI	CTNAG	6 cut(s)	297, 411, 474, 779, 885, 1133
DpnI	GATC	2 cut(s)	166, 309
DpnII	GATC	2 cut(s)	164, 307
DraI	TTTAAA	1 cut(s)	547
Eam1104I	CTCTTC	1 cut(s)	417
EarI	CTCTTC	1 cut(s)	417
Eco130I	CCWWGG	1 cut(s)	850
Eco147I	AGGCCT	1 cut(s)	583
Eco57I	CTGAAG	1 cut(s)	294
Eco88I	CYCGRG	1 cut(s)	925
EcoRI	GAATTC	2 cut(s)	730, 1034
EcoT14I	CCWWGG	1 cut(s)	850
ErhI	CCWWGG	1 cut(s)	850
FaeI	CATG	8 cut(s)	368, 469, 556, 574, 658, 767, 854, 1145
FaqI	GGGAC	1 cut(s)	908
FatI	CATG	8 cut(s)	364, 465, 552, 570, 654, 763, 850, 1141
FokI	GGATG	5 cut(s)	17, 443, 645, 833, 1115
FspBI	CTAG	2 cut(s)	261, 528
GlaI	GCGC	1 cut(s)	480
HaeII	RGCGCY	1 cut(s)	482
HaeIII	GGCC	3 cut(s)	49, 583, 870
HhaI	GCGC	1 cut(s)	481
Hin1II	CATG	8 cut(s)	368, 469, 556, 574, 658, 767, 854, 1145
Hin6I	GCGC	1 cut(s)	479
HinP1I	GCGC	1 cut(s)	479
HincII	GTYRAC	4 cut(s)	373, 442, 525, 1029
HindII	GTYRAC	4 cut(s)	373, 442, 525, 1029
HinfI	GANTC	4 cut(s)	25, 64, 197, 1187
HpaI	GTTAAC	1 cut(s)	373
HphI	GGTGA	2 cut(s)	147, 706
Hpy166II	GTNNAC	5 cut(s)	373, 442, 525, 612, 1029
Hpy188I	TCNGA	3 cut(s)	475, 519, 795
Hpy188III	TCNNGA	3 cut(s)	162, 925, 1132
Hpy8I	GTNNAC	5 cut(s)	373, 442, 525, 612, 1029
HpyAV	CCTTC	4 cut(s)	168, 594, 770, 1017
HpyCH4III	ACNGT	6 cut(s)	43, 282, 351, 357, 578, 1054
HpyCH4V	TGCA	4 cut(s)	139, 776, 897, 1071
HpyF3I	CTNAG	6 cut(s)	297, 411, 474, 779, 885, 1133
Hsp92II	CATG	8 cut(s)	368, 469, 556, 574, 658, 767, 854, 1145
HspAI	GCGC	1 cut(s)	479
KspAI	GTTAAC	1 cut(s)	373
Kzo9I	GATC	2 cut(s)	164, 307
LmnI	GCTCC	1 cut(s)	1161
LpnPI	CCDG	7 cut(s)	115, 214, 263, 285, 830, 1135, 1145
LweI	GCATC	2 cut(s)	350, 763
MaeI	CTAG	2 cut(s)	261, 528
MaeIII	GTNAC	1 cut(s)	351
MalI	GATC	2 cut(s)	166, 309
MboI	GATC	2 cut(s)	164, 307
MboII	GAAGA	5 cut(s)	287, 434, 568, 919, 1184
MfeI	CAATTG	1 cut(s)	334
MhlI	GDGCHC	1 cut(s)	865
MluCI	AATT	6 cut(s)	230, 334, 487, 730, 1034, 1112
MlyI	GAGTC	1 cut(s)	58
MmeI	TCCRAC	1 cut(s)	1066
MnlI	CCTC	5 cut(s)	39, 321, 469, 976, 979
MseI	TTAA	5 cut(s)	33, 219, 372, 546, 741
MslI	CAYNNNNRTG	2 cut(s)	659, 768
MunI	CAATTG	1 cut(s)	334
Mva1269I	GAATGC	1 cut(s)	961
NcoI	CCATGG	1 cut(s)	850
NdeII	GATC	2 cut(s)	164, 307
NlaIII	CATG	8 cut(s)	368, 469, 556, 574, 658, 767, 854, 1145
NmuCI	GTSAC	1 cut(s)	351
NspI	RCATGY	2 cut(s)	658, 1145
PaeI	GCATGC	1 cut(s)	1145
PceI	AGGCCT	1 cut(s)	583
PciI	ACATGT	1 cut(s)	654
PctI	GAATGC	1 cut(s)	961
PfeI	GAWTC	3 cut(s)	25, 197, 1187
PflMI	CCANNNNNTGG	1 cut(s)	796
PleI	GAGTC	1 cut(s)	58
PpsI	GAGTC	1 cut(s)	58
PscI	ACATGT	1 cut(s)	654
PshBI	ATTAAT	1 cut(s)	33
PsiI	TTATAA	2 cut(s)	293, 1047
RsaI	GTAC	4 cut(s)	40, 87, 419, 1056
RsaNI	GTAC	4 cut(s)	39, 86, 418, 1055
RseI	CAYNNNNRTG	2 cut(s)	659, 768
SaqAI	TTAA	5 cut(s)	33, 219, 372, 546, 741
Sau3AI	GATC	2 cut(s)	164, 307
ScaI	AGTACT	2 cut(s)	40, 1056
SchI	GAGTC	1 cut(s)	58
SduI	GDGCHC	1 cut(s)	865
SetI	ASST	9 cut(s)	242, 274, 380, 412, 517, 535, 644, 1028, 1158
SfaNI	GCATC	2 cut(s)	350, 763
SfcI	CTRYAG	1 cut(s)	577
SmiMI	CAYNNNNRTG	2 cut(s)	659, 768
SmlI	CTYRAG	1 cut(s)	864
SmoI	CTYRAG	1 cut(s)	864
SphI	GCATGC	1 cut(s)	1145
Sse9I	AATT	6 cut(s)	230, 334, 487, 730, 1034, 1112
SseBI	AGGCCT	1 cut(s)	583
SspI	AATATT	1 cut(s)	604
SspMI	CTAG	2 cut(s)	261, 528
StuI	AGGCCT	1 cut(s)	583
StyI	CCWWGG	1 cut(s)	850
TaaI	ACNGT	6 cut(s)	43, 282, 351, 357, 578, 1054
TaqI	TCGA	2 cut(s)	163, 1204
TasI	AATT	6 cut(s)	230, 334, 487, 730, 1034, 1112
TatI	WGTACW	2 cut(s)	38, 1054
TfiI	GAWTC	3 cut(s)	25, 197, 1187
Tru1I	TTAA	5 cut(s)	33, 219, 372, 546, 741
Tru9I	TTAA	5 cut(s)	33, 219, 372, 546, 741
TscAI	CASTG	2 cut(s)	109, 996
TseFI	GTSAC	1 cut(s)	351
Tsp45I	GTSAC	1 cut(s)	351
TspDTI	ATGAA	8 cut(s)	123, 237, 569, 752, 920, 1027, 1077, 1112
TspRI	CASTG	2 cut(s)	109, 996
Van91I	CCANNNNNTGG	1 cut(s)	796
VspI	ATTAAT	1 cut(s)	33
XapI	RAATTY	3 cut(s)	730, 1034, 1112
XceI	RCATGY	2 cut(s)	658, 1145
XspI	CTAG	2 cut(s)	261, 528
ZrmI	AGTACT	2 cut(s)	40, 1056

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