Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3A

Orthogroup ID

OG0003237

Physical Location & Seq

Genomic Coordinates Forward (+)

34431455 .. 34435144

Gene Structure 3690 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3AG287700.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1269 bp

ATGTCTGTAGCATTGGTATGGATGGTTTCCCCCAACACAAAGGTGTTGAATTGCTTTGGGGTGTTGGATTCATCAAGTTTTGTTTTGGGGGATGGAAGAGCAAAGATGGGTAGGAAGCAGAAACGGGATTCATGCTGTCTGAGTAGTAGTACAGAAGTCAAGTATTTGAGCACTTCTGGCTTACAAAGTGAATCTAAATTCCGCATTTTGTCAAGCATGGTAGCCAACCCGGCTGGAGAAATAGAGGTGACATCGGAACAGAAGGTTTATGATGTGGTGCTGAAGCAGGCAGCCTTAGTGGAGAAGCAGTTGAGGACTAGTGGAGATGATGTTGATGTGAAGCCTGATATTATTCTTCCAGGGAATCTGAGCTTGTTGGGTGAAGCTTATGACAGATGCAGAGAAGTTTGTGCAGAGTATGCCAAGACTTTTTACCTGGGTACTCTGCTTATGACCCCTGAGAGAAGAAGAGCTATCTGGGCAATATATGTGTGGTGTAGAAGAACTGATGAGCTTGTTGATGGGCCTAATGCCTCACACATAACACCACAAGCTTTGGATAGGTGGGAGTCAAGGTTGGAAGATCTTTTCCAAGGTCGTCCATTCGATATGCTTGATGCTGCTTTATCAGATACAGTCACCCAATTTCCTGTTGACATTCAGCCATTCAAGGATATGATAGAGGGAATGAGAATGGACCTTAGGAAATCAATATACACGAACTTTGATGAACTATACCTCTACTGTTATTATGTTGCCGGGACTGTTGGACTAATGAGTGTTCCAGTCATGGGCATTGCACCTGATTCGCAAGCAACTACAGAGTCTGTATATAATGCTGCCTTAGCATTGGGGATTGCGAATCAGCTAACTAACATACTAAGGGATGTTGGAGAAGATGCAAGGAGAGGACGCATTTATTTACCACAGGATGAGCTGGCACAAGCTGGACTTTCTGATACTGACATATATGCTGGAAAGGTCACAGATAAATGGAGGAGTTTCATGCAGAGTCAGATTAAGAGAGCAAGGATGTTCTTTGATGAGGCAGAGAAAGGAGTCATGGAGCTCAGTGAAGCCAGCAGATGGCCGGTATTGGCGTCCCTACTTTTGTATCGCCAAATATTAGATGAGATAGAAGCTAATGACTACAACAACTTCACAAAAAGGGCTTATGTAAGCAAAGCTAAGAAATTACTTGCTTTGCCTATGGCATATACTAAATCCCTGATTCTGCCATCAAGAACACTCGAAATAAATCGAGCCTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0009507 GO:0009536 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044424 GO:0044444 GO:0044464

KEGG Pathways

Metabolic & Signaling

ko00906 ko01062 ko01100 ko01110 map00906 map01062 map01100 map01110

Pfam Domains

Protein Families

SQS_PSY

Protein Analysis

422

Amino Acids

47.48

Weight (kDa)

5.47

Isoelectric Point (pI)

55.05

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
SQS_PSY	PF00494	139 - 396	6.4e-79	Squalene/phytoene synthase

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

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

Orthologous Genes (Group: OG0003237)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G17230 AT5G17230 AT5G17230 AT5G17230
fragaria_vesca	FvH4_1g27480 FvH4_6g38780
malus_domestica	MD09G1146800.v1.1 MD09G1281300.v1.1 MD17G1133400.v1.1
prunus_persica	Prupe.3G013200_v2.0.a1 Prupe.3G013200_v2.0.a1 Prupe.3G178500_v2.0.a1
pyrus_communis	pycom09g06720 pycom09g18890 pycom17g12790
rosa_chinensis	RchiOBHm_Chr2g0152351 RchiOBHm_Chr3g0488531
rosa_laevigata	RLG00000020629 RLG00000022946
rosa_multiflora	Rmu_sc0005885.1_g000002 Rmu_sc0019526.1_g000003
rosa_roxburghii	Rroxscaffold_2G00095770 Rroxscaffold_6G00394200
rosa_rugosa	Rorug02G0432500 Rorug03G0238700 Rorug03G0238800 Rorug03G0238900 Rorug03G0239000
rosa_samantha	Rh2AG494000 Rh2BG506300 Rh2CG480300 Rh2DG517400 Rh3AG287700 Rh3CG321800 Rh3DG320600
rosa_wichuraiana	Rw2G040650 Rw3G025470

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB7I	CCANNNNNTGG	1 cut(s)	1086
AciI	CCGC	1 cut(s)	202
AcoI	YGGCCR	1 cut(s)	1088
AcsI	RAATTY	1 cut(s)	197
AcuI	CTGAAG	1 cut(s)	302
AcyI	GRCGYC	1 cut(s)	1100
AfaI	GTAC	2 cut(s)	151, 442
AfiI	CCNNNNNNNGG	2 cut(s)	791, 1086
AgsI	TTSAA	2 cut(s)	49, 670
AhlI	ACTAGT	1 cut(s)	317
AjnI	CCWGG	2 cut(s)	358, 435
AleI	CACNNNNGTG	1 cut(s)	41
Alw21I	GWGCWC	2 cut(s)	173, 1071
AlwNI	CAGNNNCTG	1 cut(s)	827
AoxI	GGCC	2 cut(s)	524, 1088
ApeKI	GCWGC	3 cut(s)	290, 620, 839
ApoI	RAATTY	1 cut(s)	197
AspS9I	GGNCC	2 cut(s)	524, 697
AsuC2I	CCSGG	2 cut(s)	230, 760
AsuHPI	GGTGA	3 cut(s)	259, 392, 631
AvaII	GGWCC	1 cut(s)	697
AxyI	CCTNAGG	1 cut(s)	701
BaeI	ACNNNNGTAYC	2 cut(s)	1097, 1130
BanII	GRGCYC	1 cut(s)	1071
Bbv12I	GWGCWC	2 cut(s)	173, 1071
BbvI	GCAGC	3 cut(s)	302, 607, 826
BccI	CCATC	6 cut(s)	16, 86, 100, 515, 1080, 1246
BcgI	CGANNNNNNTGC	2 cut(s)	789, 823
BciT130I	CCWGG	2 cut(s)	360, 437
BcnI	CCSGG	2 cut(s)	230, 760
BcuI	ACTAGT	1 cut(s)	317
BfaI	CTAG	2 cut(s)	318, 1267
BfmI	CTRYAG	2 cut(s)	6, 819
BglI	GCCNNNNNGGC	1 cut(s)	230
BglII	AGATCT	1 cut(s)	583
BisI	GCNGC	3 cut(s)	291, 621, 840
BlsI	GCNGC	3 cut(s)	292, 622, 841
Bme1390I	CCNGG	4 cut(s)	230, 360, 437, 760
Bme18I	GGWCC	1 cut(s)	697
BmgT120I	GGNCC	2 cut(s)	524, 697
BmrFI	CCNGG	4 cut(s)	230, 360, 437, 760
BmsI	GCATC	3 cut(s)	386, 607, 889
BpmI	CTGGAG	1 cut(s)	255
Bpu10I	CCTNAGC	1 cut(s)	844
BpuMI	CCSGG	2 cut(s)	230, 760
BsaHI	GRCGYC	1 cut(s)	1100
BsaJI	CCNNGG	3 cut(s)	359, 436, 592
BsaXI	ACNNNNNCTCC	6 cut(s)	293, 315, 323, 345, 560, 590
Bsc4I	CCNNNNNNNGG	2 cut(s)	791, 1086
Bse118I	RCCGGY	1 cut(s)	1090
Bse1I	ACTGG	1 cut(s)	785
Bse21I	CCTNAGG	1 cut(s)	701
Bse3DI	GCAATG	1 cut(s)	795
BseBI	CCWGG	2 cut(s)	360, 437
BseDI	CCNNGG	3 cut(s)	359, 436, 592
BseGI	GGATG	5 cut(s)	27, 97, 892, 937, 1038
BseLI	CCNNNNNNNGG	2 cut(s)	791, 1086
BseMI	GCAATG	1 cut(s)	795
BseMII	CTCAG	4 cut(s)	131, 359, 450, 1084
BseNI	ACTGG	1 cut(s)	785
BseRI	GAGGAG	1 cut(s)	1012
BseXI	GCAGC	3 cut(s)	302, 607, 826
BsgI	GTGCAG	1 cut(s)	432
BshFI	GGCC	2 cut(s)	526, 1090
BsiHKAI	GWGCWC	2 cut(s)	173, 1071
BsiSI	CCGG	3 cut(s)	230, 759, 1091
BslFI	GGGAC	2 cut(s)	775, 1087
BslI	CCNNNNNNNGG	2 cut(s)	791, 1086
BsmFI	GGGAC	2 cut(s)	775, 1087
BsnI	GGCC	2 cut(s)	526, 1090
Bsp1286I	GDGCHC	2 cut(s)	173, 1071
Bsp143I	GATC	1 cut(s)	583
BspACI	CCGC	1 cut(s)	202
BspANI	GGCC	2 cut(s)	526, 1090
BspCNI	CTCAG	4 cut(s)	132, 360, 451, 1083
BspQI	GCTCTTC	2 cut(s)	91, 463
BsrDI	GCAATG	1 cut(s)	795
BsrFI	RCCGGY	1 cut(s)	1090
BsrI	ACTGG	1 cut(s)	785
BssAI	RCCGGY	1 cut(s)	1090
BssECI	CCNNGG	3 cut(s)	359, 436, 592
BssMI	GATC	1 cut(s)	583
BssNI	GRCGYC	1 cut(s)	1100
BssT1I	CCWWGG	1 cut(s)	592
Bst2UI	CCWGG	2 cut(s)	360, 437
Bst4CI	ACNGT	3 cut(s)	637, 746, 766
Bst6I	CTCTTC	2 cut(s)	91, 463
BstACI	GRCGYC	1 cut(s)	1100
BstAPI	GCANNNNNTGC	1 cut(s)	419
BstC8I	GCNNGC	4 cut(s)	288, 813, 939, 1081
BstDEI	CTNAG	9 cut(s)	140, 295, 368, 459, 701, 844, 881, 1070, 1188
BstF5I	GGATG	5 cut(s)	27, 97, 892, 937, 1038
BstKTI	GATC	1 cut(s)	586
BstMBI	GATC	1 cut(s)	583
BstMWI	GCNNNNNNNGC	5 cut(s)	177, 230, 419, 479, 845
BstNI	CCWGG	2 cut(s)	360, 437
BstSCI	CCNGG	4 cut(s)	228, 358, 435, 758
BstSFI	CTRYAG	2 cut(s)	6, 819
BstV1I	GCAGC	3 cut(s)	302, 607, 826
BstX2I	RGATCY	1 cut(s)	583
BstYI	RGATCY	1 cut(s)	583
Bsu36I	CCTNAGG	1 cut(s)	701
BsuRI	GGCC	2 cut(s)	526, 1090
BtsCI	GGATG	5 cut(s)	27, 97, 892, 937, 1038
BtsIMutI	CAGTG	1 cut(s)	1078
Cac8I	GCNNGC	4 cut(s)	288, 813, 939, 1081
CaiI	CAGNNNCTG	1 cut(s)	827
Cfr10I	RCCGGY	1 cut(s)	1090
Cfr13I	GGNCC	2 cut(s)	524, 697
CseI	GACGC	2 cut(s)	921, 1089
Csp6I	GTAC	2 cut(s)	150, 441
CspCI	CAANNNNNGTGG	2 cut(s)	537, 572
CviAII	CATG	5 cut(s)	132, 217, 790, 1006, 1063
CviQI	GTAC	2 cut(s)	150, 441
DdeI	CTNAG	9 cut(s)	140, 295, 368, 459, 701, 844, 881, 1070, 1188
DpnI	GATC	1 cut(s)	585
DpnII	GATC	1 cut(s)	583
EaeI	YGGCCR	1 cut(s)	1088
Eam1104I	CTCTTC	2 cut(s)	91, 463
EarI	CTCTTC	2 cut(s)	91, 463
Ecl136II	GAGCTC	1 cut(s)	1069
Eco130I	CCWWGG	1 cut(s)	592
Eco24I	GRGCYC	1 cut(s)	1071
Eco47I	GGWCC	1 cut(s)	697
Eco53kI	GAGCTC	1 cut(s)	1069
Eco57I	CTGAAG	1 cut(s)	302
Eco81I	CCTNAGG	1 cut(s)	701
EcoICRI	GAGCTC	1 cut(s)	1069
EcoRII	CCWGG	2 cut(s)	358, 435
EcoT14I	CCWWGG	1 cut(s)	592
EcoT38I	GRGCYC	1 cut(s)	1071
ErhI	CCWWGG	1 cut(s)	592
FaeI	CATG	5 cut(s)	135, 220, 793, 1009, 1066
FalI	AAGNNNNNCTT	2 cut(s)	936, 968
FaqI	GGGAC	2 cut(s)	775, 1087
FatI	CATG	5 cut(s)	131, 216, 789, 1005, 1062
Fnu4HI	GCNGC	3 cut(s)	291, 621, 840
FokI	GGATG	5 cut(s)	34, 104, 899, 944, 1045
FriOI	GRGCYC	1 cut(s)	1071
Fsp4HI	GCNGC	3 cut(s)	291, 621, 840
FspBI	CTAG	2 cut(s)	318, 1267
GluI	GCNGC	3 cut(s)	291, 621, 840
GsuI	CTGGAG	1 cut(s)	255
HaeIII	GGCC	2 cut(s)	526, 1090
HapII	CCGG	3 cut(s)	230, 759, 1091
HgaI	GACGC	2 cut(s)	921, 1089
Hin1I	GRCGYC	1 cut(s)	1100
Hin1II	CATG	5 cut(s)	135, 220, 793, 1009, 1066
HincII	GTYRAC	1 cut(s)	655
HindII	GTYRAC	1 cut(s)	655
HindIII	AAGCTT	2 cut(s)	384, 552
HpaII	CCGG	3 cut(s)	230, 759, 1091
HphI	GGTGA	3 cut(s)	259, 392, 631
Hpy166II	GTNNAC	1 cut(s)	655
Hpy188I	TCNGA	6 cut(s)	141, 256, 369, 631, 958, 1017
Hpy188III	TCNNGA	1 cut(s)	1242
Hpy8I	GTNNAC	1 cut(s)	655
HpyAV	CCTTC	1 cut(s)	256
HpyCH4III	ACNGT	3 cut(s)	637, 746, 766
HpyCH4V	TGCA	5 cut(s)	399, 413, 800, 902, 1009
HpyF10VI	GCNNNNNNNGC	5 cut(s)	177, 230, 419, 479, 845
HpyF3I	CTNAG	9 cut(s)	140, 295, 368, 459, 701, 844, 881, 1070, 1188
Hsp92I	GRCGYC	1 cut(s)	1100
Hsp92II	CATG	5 cut(s)	135, 220, 793, 1009, 1066
Kzo9I	GATC	1 cut(s)	583
LguI	GCTCTTC	2 cut(s)	91, 463
LmnI	GCTCC	1 cut(s)	1066
Lsp1109I	GCAGC	3 cut(s)	302, 607, 826
LweI	GCATC	3 cut(s)	386, 607, 889
MaeI	CTAG	2 cut(s)	318, 1267
MaeIII	GTNAC	3 cut(s)	247, 637, 982
MalI	GATC	1 cut(s)	585
MboI	GATC	1 cut(s)	583
MboII	GAAGA	7 cut(s)	108, 347, 477, 480, 513, 593, 908
MflI	RGATCY	1 cut(s)	583
MhlI	GDGCHC	2 cut(s)	173, 1071
MluCI	AATT	4 cut(s)	49, 197, 644, 1193
MlyI	GAGTC	4 cut(s)	578, 833, 1021, 1068
MmeI	TCCRAC	4 cut(s)	45, 558, 748, 871
MnlI	CCTC	8 cut(s)	238, 306, 544, 676, 749, 902, 990, 1039
MseI	TTAA	1 cut(s)	1020
MslI	CAYNNNNRTG	2 cut(s)	16, 41
MspI	CCGG	3 cut(s)	230, 759, 1091
MspR9I	CCNGG	4 cut(s)	230, 360, 437, 760
MvaI	CCWGG	2 cut(s)	360, 437
MwoI	GCNNNNNNNGC	5 cut(s)	177, 230, 419, 479, 845
NciI	CCSGG	2 cut(s)	230, 760
NdeII	GATC	1 cut(s)	583
NlaIII	CATG	5 cut(s)	135, 220, 793, 1009, 1066
NmuCI	GTSAC	3 cut(s)	247, 637, 982
OliI	CACNNNNGTG	1 cut(s)	41
PciSI	GCTCTTC	2 cut(s)	91, 463
PfeI	GAWTC	7 cut(s)	68, 128, 191, 364, 806, 862, 1231
PflMI	CCANNNNNTGG	1 cut(s)	1086
PkrI	GCNGC	3 cut(s)	292, 622, 841
PleI	GAGTC	4 cut(s)	577, 832, 1020, 1067
PpsI	GAGTC	4 cut(s)	577, 832, 1020, 1067
Psp124BI	GAGCTC	1 cut(s)	1071
Psp6I	CCWGG	2 cut(s)	358, 435
PspGI	CCWGG	2 cut(s)	358, 435
PspPI	GGNCC	2 cut(s)	524, 697
PstNI	CAGNNNCTG	1 cut(s)	827
PsuI	RGATCY	1 cut(s)	583
RsaI	GTAC	2 cut(s)	151, 442
RsaNI	GTAC	2 cut(s)	150, 441
RseI	CAYNNNNRTG	2 cut(s)	16, 41
SacI	GAGCTC	1 cut(s)	1071
SapI	GCTCTTC	2 cut(s)	91, 463
SaqAI	TTAA	1 cut(s)	1020
SatI	GCNGC	3 cut(s)	291, 621, 840
Sau3AI	GATC	1 cut(s)	583
Sau96I	GGNCC	2 cut(s)	524, 697
SchI	GAGTC	4 cut(s)	578, 833, 1021, 1068
ScrFI	CCNGG	4 cut(s)	230, 360, 437, 760
SduI	GDGCHC	2 cut(s)	173, 1071
SfaNI	GCATC	3 cut(s)	386, 607, 889
SfcI	CTRYAG	2 cut(s)	6, 819
SinI	GGWCC	1 cut(s)	697
SmiMI	CAYNNNNRTG	2 cut(s)	16, 41
SpeI	ACTAGT	1 cut(s)	317
Sse9I	AATT	4 cut(s)	49, 197, 644, 1193
SsiI	CCGC	1 cut(s)	202
SspI	AATATT	1 cut(s)	1125
SspMI	CTAG	2 cut(s)	318, 1267
SstI	GAGCTC	1 cut(s)	1071
StyD4I	CCNGG	4 cut(s)	228, 358, 435, 758
StyI	CCWWGG	1 cut(s)	592
TaaI	ACNGT	3 cut(s)	637, 746, 766
TaqI	TCGA	3 cut(s)	606, 1251, 1261
TasI	AATT	4 cut(s)	49, 197, 644, 1193
TatI	WGTACW	1 cut(s)	149
TfiI	GAWTC	7 cut(s)	68, 128, 191, 364, 806, 862, 1231
Tru1I	TTAA	1 cut(s)	1020
Tru9I	TTAA	1 cut(s)	1020
TscAI	CASTG	1 cut(s)	1078
TseFI	GTSAC	3 cut(s)	247, 637, 982
TseI	GCWGC	3 cut(s)	290, 620, 839
Tsp45I	GTSAC	3 cut(s)	247, 637, 982
TspDTI	ATGAA	4 cut(s)	60, 120, 744, 994
TspRI	CASTG	1 cut(s)	1078
Van91I	CCANNNNNTGG	1 cut(s)	1086
VpaK11BI	GGWCC	1 cut(s)	697
XapI	RAATTY	1 cut(s)	197
XspI	CTAG	2 cut(s)	318, 1267

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