Basic Information

Type: gene

Biological Identity

Species

rosa_laevigata

Chromosome

Chr4

Orthogroup ID

OG0005283

Physical Location & Seq

Genomic Coordinates Forward (+)

1373436 .. 1377380

Gene Structure 3945 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

RLM00000015776

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1233 bp

ATGGATTCAGAAGATAAGTTTCTGGCTAAAGAGTTCCTGAGGAAGGACAGGTTCAGGTTGGACTTTCCAGATAGGCGCATAGAGCTCTACTGCTGTCAAGTGGGACTAGATCTTCAGACAAGATATGGAATCATGGAAGTGCTGCTGATAGTTTCTGGAGTTCAAAGCCTCTCTTCCAGTGTGCAAAGCACTCTGGAGAAGAATGGGCATTCAGATGATTTTCTGAAATCTGGTCCCAAGAAGGAACTTTTTCGGACATGCGTTGACAAGGACAAGAAAAAGTTGGATTCCTCAAAAAACAAGATGGCTGAACTTTTGAAGACTACTAACAAGAGAAACAAAAAGCAGGAGTCAAAAAAAGCTTCTTCTAGTCCGAATAATCATCCTTCTAAAAAGCAATCCAGAAAGGGGGAAAATCCCATCCGACTGTCACCAGCTTCTGATTTTGGAGATTCTTGTAGAGCTGTTCTATCCATAGACAACACATTCTGCAAGAGATGCTCCTGCTGTATTTGTCATTTGTTTAATGACAGCAAGCACCCAAGCCTTTGGTTAGTATGTACATCTGAATCTGGTGAGGCGCGTAGATGTGAAAAGGTGGGATTGTTGATCTTGGGCAATTGTAGTTATTGTTGTGCTTCATGCGGTAAAGTTTCTGGGATACTTGGAATTTGGGAGAAGCAGCTACTCATAGCAAAGGATGCTCGACGTGTTGATGTACTCTGGGACAAGATATGCTTGACCAAGACTAAACTCGAGACAGAACTAGGTCCAATTAATGTACGTGGGATAGTCAGCAGACTATCTATTGCTGGTGATGTGCTGAAGCTCTGCTCTCTTGCAATTGAGAAAGCAGATGAATGTTGGCCAATGTTTCTAGGTTCACTTCCAACTGCCTGCATGTTTCTCTCGGAGGAAGTAACACCTTCATCTGTTGTGATTATAATGATCGGACTGTCTAATGCATCGTCTGATGACATCAAGGGCTACAAGCTCTGGTATTACAAGAGCAGAGAAGAATCACACACAAAAGAGCCTAATTGTACCTTTTCAAGATCTCAGAGAAGAATTTTGATCTCCAATTTGCAGCCTTGCAGAGAATCTCTTTCGAATCCCATCATTGAGGCAAATTCTGGTGCCACGAGGGAGTCTGAAACTACGACAGCAGTTGTGCCTTCTTCCAAATTTAAAGTTTGTGATCTTGGGAAGATACTTCTTCTGGCTCAGGCTTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0001666 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005677 GO:0006950 GO:0008150 GO:0009266 GO:0009409 GO:0009628 GO:0009892 GO:0009893 GO:0009987 GO:0010048 GO:0010468 GO:0010604 GO:0010605 GO:0010629 GO:0010638 GO:0016604 GO:0016607 GO:0017053 GO:0019222 GO:0031056 GO:0031058 GO:0031060 GO:0031062 GO:0031323 GO:0031325 GO:0031399 GO:0031401 GO:0031974 GO:0031981 GO:0032268 GO:0032270 GO:0032991 GO:0033043 GO:0033044 GO:0033554 GO:0036293 GO:0040029 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044464 GO:0045814 GO:0048518 GO:0048519 GO:0048522 GO:0050789 GO:0050794 GO:0050896 GO:0051128 GO:0051130 GO:0051171 GO:0051173 GO:0051246 GO:0051247 GO:0051569 GO:0051571 GO:0051716 GO:0060255 GO:0061085 GO:0061087 GO:0065007 GO:0070013 GO:0070417 GO:0070482 GO:0080090 GO:0090568 GO:1902275 GO:1905269 GO:2001252

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

PHD_Oberon fn3

Protein Analysis

411

Amino Acids

45.75

Weight (kDa)

8.94

Isoelectric Point (pI)

55.0

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PHD_Oberon	PF07227	156 - 199	3.1e-07	PHD - plant homeodomain finger protein
Fn3_VIN3	PF23376	305 - 367	2e-17	VIN3-like, fibronectin type-III domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

Font Size (px)

Line Width

Align Labels (Cladogram)

Image

Tree File

Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready

iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0005283)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT2G18870 AT3G24440 AT3G24440
fragaria_vesca	FvH4_1g05280
malus_domestica	MD02G1056200.v1.1 MD15G1189100.v1.1
pyrus_communis	pycom02g04520 pycom02g04530 pycom15g16940 pycom15g16950
rosa_chinensis	RchiOBHm_Chr2g0091001
rosa_laevigata	RLG00000015776 RLG00000016165
rosa_multiflora	Rmu_sc0003305.1_g000004 Rmu_sc0004626.1_g000008
rosa_roxburghii	Rroxscaffold_2G00150700 Rroxscaffold_2G00154300 Rroxscaffold_2G00154540
rosa_rugosa	Rorug01G0468700 Rorug01G0468800 Rorug02G0011400
rosa_samantha	Rh2BG020600 Rh2BG056000 Rh2CG020200 Rh2CG020500 Rh2CG021200 Rh2CG058300 Rh2DG057400
rosa_wichuraiana	Rw2G005160

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	944
AccB1I	GGYRCC	1 cut(s)	1136
AccII	CGCG	1 cut(s)	583
AciI	CCGC	1 cut(s)	645
AcoI	YGGCCR	1 cut(s)	866
AcsI	RAATTY	4 cut(s)	669, 1068, 1129, 1184
AcuI	CTGAAG	2 cut(s)	98, 845
AfaI	GTAC	4 cut(s)	562, 720, 783, 1045
AfiI	CCNNNNNNNGG	2 cut(s)	43, 408
AflIII	ACRYGT	1 cut(s)	709
AgsI	TTSAA	3 cut(s)	164, 319, 1053
AjiI	CACGTC	1 cut(s)	710
AluBI	AGCT	7 cut(s)	85, 362, 437, 464, 685, 829, 994
AluI	AGCT	7 cut(s)	85, 362, 437, 464, 685, 829, 994
Alw21I	GWGCWC	1 cut(s)	87
Alw26I	GTCTC	1 cut(s)	752
AlwNI	CAGNNNCTG	1 cut(s)	440
Ama87I	CYCGRG	1 cut(s)	755
AoxI	GGCC	1 cut(s)	866
ApeKI	GCWGC	3 cut(s)	142, 682, 1087
ApoI	RAATTY	4 cut(s)	669, 1068, 1129, 1184
AseI	ATTAAT	1 cut(s)	777
Asp700I	GAANNNNTTC	1 cut(s)	249
AspLEI	GCGC	2 cut(s)	78, 583
AspS9I	GGNCC	2 cut(s)	233, 770
AsuHPI	GGTGA	3 cut(s)	423, 587, 827
AsuII	TTCGAA	1 cut(s)	1109
AvaI	CYCGRG	1 cut(s)	755
AvaII	GGWCC	2 cut(s)	233, 770
AxyI	CCTNAGG	1 cut(s)	38
BalI	TGGCCA	1 cut(s)	868
BanI	GGYRCC	1 cut(s)	1136
BanII	GRGCYC	1 cut(s)	87
BauI	CACGAG	1 cut(s)	1141
BbsI	GAAGAC	1 cut(s)	326
Bbv12I	GWGCWC	1 cut(s)	87
BbvI	GCAGC	3 cut(s)	129, 694, 1099
BccI	CCATC	3 cut(s)	298, 428, 1124
BciVI	GTATCC	1 cut(s)	654
BcoDI	GTCTC	1 cut(s)	752
BfaI	CTAG	4 cut(s)	107, 369, 767, 878
BfuI	GTATCC	1 cut(s)	654
BglII	AGATCT	2 cut(s)	109, 1055
BisI	GCNGC	3 cut(s)	143, 683, 1088
BlsI	GCNGC	3 cut(s)	144, 684, 1089
Bme18I	GGWCC	2 cut(s)	233, 770
BmeT110I	CYCGRG	1 cut(s)	755
BmgBI	CACGTC	1 cut(s)	710
BmgT120I	GGNCC	2 cut(s)	233, 770
BmiI	GGNNCC	2 cut(s)	235, 1138
BmsI	GCATC	3 cut(s)	488, 691, 974
BpiI	GAAGAC	1 cut(s)	326
BpmI	CTGGAG	2 cut(s)	177, 215
Bpu10I	CCTNAGC	1 cut(s)	1224
Bpu14I	TTCGAA	1 cut(s)	1109
BsaAI	YACGTR	1 cut(s)	785
Bsc4I	CCNNNNNNNGG	2 cut(s)	43, 408
Bse1I	ACTGG	1 cut(s)	177
Bse21I	CCTNAGG	1 cut(s)	38
BseGI	GGATG	3 cut(s)	382, 420, 706
BseLI	CCNNNNNNNGG	2 cut(s)	43, 408
BseMII	CTCAG	2 cut(s)	29, 1073
BseNI	ACTGG	1 cut(s)	177
BseXI	GCAGC	3 cut(s)	129, 694, 1099
Bsh1236I	CGCG	1 cut(s)	583
BshFI	GGCC	1 cut(s)	868
BshNI	GGYRCC	1 cut(s)	1136
BsiHKAI	GWGCWC	1 cut(s)	87
BsiHKCI	CYCGRG	1 cut(s)	755
BslFI	GGGAC	3 cut(s)	117, 219, 740
BslI	CCNNNNNNNGG	2 cut(s)	43, 408
BsmAI	GTCTC	1 cut(s)	752
BsmFI	GGGAC	3 cut(s)	117, 219, 740
BsmI	GAATGC	1 cut(s)	208
BsnI	GGCC	1 cut(s)	868
BsoBI	CYCGRG	1 cut(s)	755
Bsp119I	TTCGAA	1 cut(s)	1109
Bsp1286I	GDGCHC	1 cut(s)	87
Bsp1407I	TGTACA	1 cut(s)	560
Bsp143I	GATC	6 cut(s)	109, 609, 948, 1055, 1074, 1198
BspACI	CCGC	1 cut(s)	645
BspANI	GGCC	1 cut(s)	868
BspCNI	CTCAG	2 cut(s)	30, 1072
BspFNI	CGCG	1 cut(s)	583
BspLI	GGNNCC	2 cut(s)	235, 1138
BspT104I	TTCGAA	1 cut(s)	1109
BspT107I	GGYRCC	1 cut(s)	1136
BsrGI	TGTACA	1 cut(s)	560
BsrI	ACTGG	1 cut(s)	177
BssMI	GATC	6 cut(s)	109, 609, 948, 1055, 1074, 1198
BssSI	CACGAG	1 cut(s)	1141
Bst2BI	CACGAG	1 cut(s)	1141
Bst4CI	ACNGT	2 cut(s)	429, 957
Bst6I	CTCTTC	1 cut(s)	178
BstAPI	GCANNNNNTGC	2 cut(s)	498, 701
BstAUI	TGTACA	1 cut(s)	560
BstBAI	YACGTR	1 cut(s)	785
BstBI	TTCGAA	1 cut(s)	1109
BstC8I	GCNNGC	2 cut(s)	536, 898
BstDEI	CTNAG	3 cut(s)	38, 1059, 1224
BstENI	CCTNNNNNAGG	1 cut(s)	41
BstF5I	GGATG	3 cut(s)	382, 420, 706
BstFNI	CGCG	1 cut(s)	583
BstHHI	GCGC	2 cut(s)	78, 583
BstKTI	GATC	6 cut(s)	112, 612, 951, 1058, 1077, 1201
BstMAI	GTCTC	1 cut(s)	752
BstMBI	GATC	6 cut(s)	109, 609, 948, 1055, 1074, 1198
BstMWI	GCNNNNNNNGC	3 cut(s)	82, 498, 701
BstNSI	RCATGY	2 cut(s)	261, 904
BstUI	CGCG	1 cut(s)	583
BstV1I	GCAGC	3 cut(s)	129, 694, 1099
BstV2I	GAAGAC	1 cut(s)	326
BstX2I	RGATCY	2 cut(s)	109, 1055
BstXI	CCANNNNNNTGG	1 cut(s)	549
BstYI	RGATCY	2 cut(s)	109, 1055
Bsu36I	CCTNAGG	1 cut(s)	38
BsuI	GTATCC	1 cut(s)	654
BsuRI	GGCC	1 cut(s)	868
BtrI	CACGTC	1 cut(s)	710
BtsCI	GGATG	3 cut(s)	382, 420, 706
BtsIMutI	CAGTG	1 cut(s)	184
Cac8I	GCNNGC	2 cut(s)	536, 898
CaiI	CAGNNNCTG	1 cut(s)	440
CfoI	GCGC	2 cut(s)	78, 583
Cfr13I	GGNCC	2 cut(s)	233, 770
Csp6I	GTAC	4 cut(s)	561, 719, 782, 1044
CviAII	CATG	4 cut(s)	133, 258, 642, 901
CviQI	GTAC	4 cut(s)	561, 719, 782, 1044
DdeI	CTNAG	3 cut(s)	38, 1059, 1224
DpnI	GATC	6 cut(s)	111, 611, 950, 1057, 1076, 1200
DpnII	GATC	6 cut(s)	109, 609, 948, 1055, 1074, 1198
DraI	TTTAAA	1 cut(s)	1189
EaeI	YGGCCR	1 cut(s)	866
Eam1104I	CTCTTC	1 cut(s)	178
EarI	CTCTTC	1 cut(s)	178
Ecl136II	GAGCTC	1 cut(s)	85
Eco24I	GRGCYC	1 cut(s)	87
Eco47I	GGWCC	2 cut(s)	233, 770
Eco53kI	GAGCTC	1 cut(s)	85
Eco57I	CTGAAG	2 cut(s)	98, 845
Eco81I	CCTNAGG	1 cut(s)	38
Eco88I	CYCGRG	1 cut(s)	755
EcoICRI	GAGCTC	1 cut(s)	85
EcoNI	CCTNNNNNAGG	1 cut(s)	41
EcoT22I	ATGCAT	1 cut(s)	967
EcoT38I	GRGCYC	1 cut(s)	87
FaeI	CATG	4 cut(s)	136, 261, 645, 904
FalI	AAGNNNNNCTT	4 cut(s)	157, 189, 722, 754
FaqI	GGGAC	3 cut(s)	117, 219, 740
FatI	CATG	4 cut(s)	132, 257, 641, 900
Fnu4HI	GCNGC	3 cut(s)	143, 683, 1088
FokI	GGATG	3 cut(s)	369, 407, 713
FriOI	GRGCYC	1 cut(s)	87
Fsp4HI	GCNGC	3 cut(s)	143, 683, 1088
FspBI	CTAG	4 cut(s)	107, 369, 767, 878
GlaI	GCGC	2 cut(s)	77, 582
GluI	GCNGC	3 cut(s)	143, 683, 1088
GsuI	CTGGAG	2 cut(s)	177, 215
HaeIII	GGCC	1 cut(s)	868
HhaI	GCGC	2 cut(s)	78, 583
Hin1II	CATG	4 cut(s)	136, 261, 645, 904
Hin6I	GCGC	2 cut(s)	76, 581
HinP1I	GCGC	2 cut(s)	76, 581
HincII	GTYRAC	1 cut(s)	265
HindII	GTYRAC	1 cut(s)	265
HindIII	AAGCTT	1 cut(s)	360
HphI	GGTGA	3 cut(s)	423, 587, 827
Hpy166II	GTNNAC	2 cut(s)	265, 884
Hpy188III	TCNNGA	7 cut(s)	37, 68, 156, 194, 402, 757, 1053
Hpy8I	GTNNAC	2 cut(s)	265, 884
Hpy99I	CGWCG	1 cut(s)	711
HpyAV	CCTTC	5 cut(s)	37, 235, 396, 936, 1185
HpyCH4III	ACNGT	2 cut(s)	429, 957
HpyCH4IV	ACGT	2 cut(s)	709, 784
HpyCH4V	TGCA	7 cut(s)	184, 492, 842, 900, 965, 1087, 1095
HpyF10VI	GCNNNNNNNGC	3 cut(s)	82, 498, 701
HpyF3I	CTNAG	3 cut(s)	38, 1059, 1224
HpySE526I	ACGT	2 cut(s)	709, 784
Hsp92II	CATG	4 cut(s)	136, 261, 645, 904
HspAI	GCGC	2 cut(s)	76, 581
Kzo9I	GATC	6 cut(s)	109, 609, 948, 1055, 1074, 1198
LmnI	GCTCC	1 cut(s)	506
Lsp1109I	GCAGC	3 cut(s)	129, 694, 1099
LweI	GCATC	3 cut(s)	488, 691, 974
MaeI	CTAG	4 cut(s)	107, 369, 767, 878
MaeII	ACGT	2 cut(s)	709, 784
MaeIII	GTNAC	2 cut(s)	429, 919
MalI	GATC	6 cut(s)	111, 611, 950, 1057, 1076, 1200
MboI	GATC	6 cut(s)	109, 609, 948, 1055, 1074, 1198
MfeI	CAATTG	2 cut(s)	619, 843
MflI	RGATCY	2 cut(s)	109, 1055
MhlI	GDGCHC	1 cut(s)	87
MlsI	TGGCCA	1 cut(s)	868
MluCI	AATT	9 cut(s)	619, 669, 774, 843, 1039, 1068, 1081, 1129, 1184
MluNI	TGGCCA	1 cut(s)	868
MlyI	GAGTC	2 cut(s)	359, 1157
MmeI	TCCRAC	4 cut(s)	39, 264, 448, 914
MnlI	CCTC	7 cut(s)	33, 179, 301, 571, 907, 1117, 1137
Mox20I	TGGCCA	1 cut(s)	868
Mph1103I	ATGCAT	1 cut(s)	967
MroXI	GAANNNNTTC	1 cut(s)	249
MscI	TGGCCA	1 cut(s)	868
MseI	TTAA	4 cut(s)	525, 777, 1188, 1231
MslI	CAYNNNNRTG	2 cut(s)	137, 213
Msp20I	TGGCCA	1 cut(s)	868
MunI	CAATTG	2 cut(s)	619, 843
Mva1269I	GAATGC	1 cut(s)	208
MvnI	CGCG	1 cut(s)	583
MwoI	GCNNNNNNNGC	3 cut(s)	82, 498, 701
NdeII	GATC	6 cut(s)	109, 609, 948, 1055, 1074, 1198
NlaIII	CATG	4 cut(s)	136, 261, 645, 904
NlaIV	GGNNCC	2 cut(s)	235, 1138
NmuCI	GTSAC	1 cut(s)	429
NsiI	ATGCAT	1 cut(s)	967
NspI	RCATGY	2 cut(s)	261, 904
NspV	TTCGAA	1 cut(s)	1109
PaeR7I	CTCGAG	1 cut(s)	755
PctI	GAATGC	1 cut(s)	208
PdmI	GAANNNNTTC	1 cut(s)	249
PfeI	GAWTC	8 cut(s)	5, 129, 287, 452, 569, 1019, 1100, 1111
PkrI	GCNGC	3 cut(s)	144, 684, 1089
PleI	GAGTC	2 cut(s)	358, 1156
PpsI	GAGTC	2 cut(s)	358, 1156
Ppu21I	YACGTR	1 cut(s)	785
PshBI	ATTAAT	1 cut(s)	777
PsiI	TTATAA	1 cut(s)	944
Psp124BI	GAGCTC	1 cut(s)	87
PspN4I	GGNNCC	2 cut(s)	235, 1138
PspPI	GGNCC	2 cut(s)	233, 770
PstNI	CAGNNNCTG	1 cut(s)	440
PsuI	RGATCY	2 cut(s)	109, 1055
RsaI	GTAC	4 cut(s)	562, 720, 783, 1045
RsaNI	GTAC	4 cut(s)	561, 719, 782, 1044
RseI	CAYNNNNRTG	2 cut(s)	137, 213
SacI	GAGCTC	1 cut(s)	87
SaqAI	TTAA	4 cut(s)	525, 777, 1188, 1231
SatI	GCNGC	3 cut(s)	143, 683, 1088
Sau3AI	GATC	6 cut(s)	109, 609, 948, 1055, 1074, 1198
Sau96I	GGNCC	2 cut(s)	233, 770
SchI	GAGTC	2 cut(s)	359, 1157
SduI	GDGCHC	1 cut(s)	87
SfaNI	GCATC	3 cut(s)	488, 691, 974
Sfr274I	CTCGAG	1 cut(s)	755
SfuI	TTCGAA	1 cut(s)	1109
SinI	GGWCC	2 cut(s)	233, 770
SlaI	CTCGAG	1 cut(s)	755
SmiMI	CAYNNNNRTG	2 cut(s)	137, 213
SmlI	CTYRAG	1 cut(s)	755
SmoI	CTYRAG	1 cut(s)	755
Sse9I	AATT	9 cut(s)	619, 669, 774, 843, 1039, 1068, 1081, 1129, 1184
SsiI	CCGC	1 cut(s)	645
SspMI	CTAG	4 cut(s)	107, 369, 767, 878
SstI	GAGCTC	1 cut(s)	87
TaaI	ACNGT	2 cut(s)	429, 957
TaiI	ACGT	2 cut(s)	712, 787
TaqI	TCGA	3 cut(s)	706, 756, 1109
TasI	AATT	9 cut(s)	619, 669, 774, 843, 1039, 1068, 1081, 1129, 1184
TatI	WGTACW	2 cut(s)	560, 718
TfiI	GAWTC	8 cut(s)	5, 129, 287, 452, 569, 1019, 1100, 1111
Tru1I	TTAA	4 cut(s)	525, 777, 1188, 1231
Tru9I	TTAA	4 cut(s)	525, 777, 1188, 1231
TscAI	CASTG	1 cut(s)	184
TseFI	GTSAC	1 cut(s)	429
TseI	GCWGC	3 cut(s)	142, 682, 1087
Tsp45I	GTSAC	1 cut(s)	429
TspDTI	ATGAA	3 cut(s)	630, 873, 918
TspRI	CASTG	1 cut(s)	184
VpaK11BI	GGWCC	2 cut(s)	233, 770
VspI	ATTAAT	1 cut(s)	777
XagI	CCTNNNNNAGG	1 cut(s)	41
XapI	RAATTY	4 cut(s)	669, 1068, 1129, 1184
XceI	RCATGY	2 cut(s)	261, 904
XhoI	CTCGAG	1 cut(s)	755
XmnI	GAANNNNTTC	1 cut(s)	249
XspI	CTAG	4 cut(s)	107, 369, 767, 878
Zsp2I	ATGCAT	1 cut(s)	967

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