Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000002

Orthogroup ID

OG0003237

Physical Location & Seq

Genomic Coordinates Reverse (-)

17120938 .. 17123763

Gene Structure 2826 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_2G00095770.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1197 bp

ATGTCTGGTGTTCTTCTTTGGGTGGTGAGTCCGAAAGAGAATGCCACCTCTTTGCTTGGTCTTATGCCCAGAATTGGTAACCCAAAGAGGTCCAAGTTCTGCTCCAGGCTGAGTTTCTCACCTGGGATTTTAGCCTATTCAGGAGCTGTTGCTCACCCATCAAGGTCTTCAGAAGAGAGGGTCTATGAAGTGGTGCTCAAGCAAGCTGCTTTGGTGAGAGAACAGAGGAGGCCCAAAGAGAAAGCTTTGGACTTTGGTGAAGGGGTTGAAAGTAGTGATGGTATGACCAACTGGGATTTGCTGAATGAGGCTTACGATAGGTGTGGTGAGGTCTGTGCTGAGTATGCCAAGACTTTTTACTTGGGCACATTACTTATGACACCAGAGCGGAGACGAGCGGTTTGGGCAATTTATGTATGGTGCAGAAGGACTGATGAACTAGTGGATGGACCTAATGCTTCATATATCACACCTAAAGCTCTTGACAGATGGGAGAAAAGACTGACTGACCTTTTTGAAGGTCGTCCATATGATATGTATGATGCAGCTCTATCTGATACTGTCACAAAGTACCCAGTGGATATACAGCCCTTCAAGGACATGGTAGAAGGAATGAGGTTAGACTTGAGAAAGTCAAGATACCAGAACTTTGATGAACTTTACCTCTACTGCTACTATGTTGCTGGAACTGTTGGACTGATGAGTGTTCCAGTAATGGGGATCTCACCTGAATCAAAGGCTTCAACAGAGACTGTTTACAATGCTGCATTGGCCCTTGGAATTGCTAATCAGCTCACTAACATACTTAGAGATGTTGGAGAAGATGCTAGGAGAGGAAGAGTCTATCTCCCACAAGATGAGCTTGCCCAGGCTGGACTATCGGATGATGATATCTTTCGCGGGAAAGTGACAGACAAGTGGCAAAGTTTCATGAAGGGCCAAATAAAGCGAGCTAGGATGTTCTTTGATGAGGCTGAAAAAGGTGTTGGAGAGCTCAACTCAGCAAGTAGATGGCCAGTATGGGCTTCTTTGTTGCTATATAGGCAGATTCTGGATGCCATTGAAGCAAATGGTTATGACAATTTCACAAAGAGGGCTTATGTAGGAAAAGCAAAGAAGTTATTGTCATTGCCTATAGCTTATGGCAGGGCAATTATACGCCCCTCAAAATTAACTAAGCAGTTAGTGGCAAGATAA

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

398

Amino Acids

45.05

Weight (kDa)

8.94

Isoelectric Point (pI)

46.7

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
SQS_PSY	PF00494	114 - 370	7.7e-77	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

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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)
AccBSI	CCGCTC	2 cut(s)	388, 398
AccII	CGCG	1 cut(s)	900
AciI	CCGC	3 cut(s)	388, 398, 900
AclWI	GGATC	1 cut(s)	728
AcoI	YGGCCR	1 cut(s)	1013
AcuI	CTGAAG	1 cut(s)	153
AfaI	GTAC	1 cut(s)	572
AfiI	CCNNNNNNNGG	2 cut(s)	74, 716
AgsI	TTSAA	5 cut(s)	269, 518, 595, 744, 1064
AhlI	ACTAGT	1 cut(s)	439
AjnI	CCWGG	3 cut(s)	104, 121, 867
AjuI	GAANNNNNNNTTGG	2 cut(s)	969, 1001
Alw21I	GWGCWC	2 cut(s)	198, 996
Alw26I	GTCTC	2 cut(s)	385, 743
AlwI	GGATC	1 cut(s)	728
AlwNI	CAGNNNCTG	3 cut(s)	146, 752, 1051
AoxI	GGCC	4 cut(s)	230, 771, 937, 1013
ApeKI	GCWGC	3 cut(s)	206, 545, 764
ArsI	GACNNNNNNTTYG	2 cut(s)	384, 416
AspS9I	GGNCC	5 cut(s)	90, 231, 449, 772, 937
AsuHPI	GGTGA	7 cut(s)	37, 111, 146, 226, 269, 338, 717
AvaII	GGWCC	2 cut(s)	90, 449
BaeGI	GKGCMC	1 cut(s)	368
BalI	TGGCCA	1 cut(s)	1015
BanII	GRGCYC	1 cut(s)	996
BbsI	GAAGAC	1 cut(s)	159
Bbv12I	GWGCWC	2 cut(s)	198, 996
BbvI	GCAGC	3 cut(s)	193, 557, 751
BccI	CCATC	5 cut(s)	166, 272, 440, 483, 1005
BciT130I	CCWGG	3 cut(s)	106, 123, 869
BcoDI	GTCTC	2 cut(s)	385, 743
BcuI	ACTAGT	1 cut(s)	439
BfaI	CTAG	3 cut(s)	440, 828, 954
BfmI	CTRYAG	1 cut(s)	1134
BisI	GCNGC	3 cut(s)	207, 546, 765
BlsI	GCNGC	3 cut(s)	208, 547, 766
Bme1390I	CCNGG	3 cut(s)	106, 123, 869
Bme18I	GGWCC	2 cut(s)	90, 449
BmgT120I	GGNCC	5 cut(s)	90, 231, 449, 772, 937
BmrFI	CCNGG	3 cut(s)	106, 123, 869
BmrI	ACTGGG	2 cut(s)	301, 569
BmsI	GCATC	3 cut(s)	532, 814, 1045
BmuI	ACTGGG	2 cut(s)	301, 569
BpiI	GAAGAC	1 cut(s)	159
BplI	GAGNNNNNCTC	4 cut(s)	831, 863, 983, 1015
BpmI	CTGGAG	1 cut(s)	88
BpuEI	CTTGAG	2 cut(s)	182, 646
BsaJI	CCNNGG	3 cut(s)	122, 775, 867
Bsc4I	CCNNNNNNNGG	2 cut(s)	74, 716
Bse1I	ACTGG	4 cut(s)	296, 575, 710, 1016
Bse3DI	GCAATG	1 cut(s)	1127
BseBI	CCWGG	3 cut(s)	106, 123, 869
BseDI	CCNNGG	3 cut(s)	122, 775, 867
BseGI	GGATG	4 cut(s)	451, 889, 963, 1060
BseLI	CCNNNNNNNGG	2 cut(s)	74, 716
BseMI	GCAATG	1 cut(s)	1127
BseMII	CTCAG	3 cut(s)	101, 330, 1014
BseNI	ACTGG	4 cut(s)	296, 575, 710, 1016
BseRI	GAGGAG	1 cut(s)	241
BseSI	GKGCMC	1 cut(s)	368
BseXI	GCAGC	3 cut(s)	193, 557, 751
BsgI	GTGCAG	1 cut(s)	442
Bsh1236I	CGCG	1 cut(s)	900
BshFI	GGCC	4 cut(s)	232, 773, 939, 1015
BsiHKAI	GWGCWC	2 cut(s)	198, 996
BslI	CCNNNNNNNGG	2 cut(s)	74, 716
BsmAI	GTCTC	2 cut(s)	385, 743
BsmBI	CGTCTC	1 cut(s)	385
BsmI	GAATGC	1 cut(s)	46
BsnI	GGCC	4 cut(s)	232, 773, 939, 1015
Bsp1286I	GDGCHC	3 cut(s)	198, 368, 996
Bsp143I	GATC	1 cut(s)	720
BspACI	CCGC	3 cut(s)	388, 398, 900
BspANI	GGCC	4 cut(s)	232, 773, 939, 1015
BspCNI	CTCAG	3 cut(s)	102, 331, 1013
BspFNI	CGCG	1 cut(s)	900
BspHI	TCATGA	1 cut(s)	930
BspPI	GGATC	1 cut(s)	728
BsrBI	CCGCTC	2 cut(s)	388, 398
BsrDI	GCAATG	1 cut(s)	1127
BsrI	ACTGG	4 cut(s)	296, 575, 710, 1016
BssECI	CCNNGG	3 cut(s)	122, 775, 867
BssMI	GATC	1 cut(s)	720
BssT1I	CCWWGG	1 cut(s)	775
Bst2UI	CCWGG	3 cut(s)	106, 123, 869
Bst4CI	ACNGT	3 cut(s)	562, 691, 754
Bst6I	CTCTTC	2 cut(s)	168, 832
BstC8I	GCNNGC	3 cut(s)	204, 864, 951
BstDEI	CTNAG	5 cut(s)	110, 339, 806, 1000, 1176
BstEII	GGTNACC	1 cut(s)	77
BstF5I	GGATG	4 cut(s)	451, 889, 963, 1060
BstFNI	CGCG	1 cut(s)	900
BstKTI	GATC	1 cut(s)	723
BstMAI	GTCTC	2 cut(s)	385, 743
BstMBI	GATC	1 cut(s)	720
BstMWI	GCNNNNNNNGC	5 cut(s)	344, 404, 770, 1042, 1064
BstNI	CCWGG	3 cut(s)	106, 123, 869
BstPI	GGTNACC	1 cut(s)	77
BstSCI	CCNGG	3 cut(s)	104, 121, 867
BstSFI	CTRYAG	1 cut(s)	1134
BstSLI	GKGCMC	1 cut(s)	368
BstUI	CGCG	1 cut(s)	900
BstV1I	GCAGC	3 cut(s)	193, 557, 751
BstV2I	GAAGAC	1 cut(s)	159
BstX2I	RGATCY	1 cut(s)	720
BstYI	RGATCY	1 cut(s)	720
BsuRI	GGCC	4 cut(s)	232, 773, 939, 1015
BtsCI	GGATG	4 cut(s)	451, 889, 963, 1060
BtsIMutI	CAGTG	1 cut(s)	582
Cac8I	GCNNGC	3 cut(s)	204, 864, 951
CaiI	CAGNNNCTG	3 cut(s)	146, 752, 1051
CciI	TCATGA	1 cut(s)	930
Cfr13I	GGNCC	5 cut(s)	90, 231, 449, 772, 937
Csp6I	GTAC	1 cut(s)	571
CviAII	CATG	2 cut(s)	601, 931
CviQI	GTAC	1 cut(s)	571
DdeI	CTNAG	5 cut(s)	110, 339, 806, 1000, 1176
DpnI	GATC	1 cut(s)	722
DpnII	GATC	1 cut(s)	720
EaeI	YGGCCR	1 cut(s)	1013
Eam1104I	CTCTTC	2 cut(s)	168, 832
EarI	CTCTTC	2 cut(s)	168, 832
Ecl136II	GAGCTC	1 cut(s)	994
Eco130I	CCWWGG	1 cut(s)	775
Eco24I	GRGCYC	1 cut(s)	996
Eco32I	GATATC	1 cut(s)	892
Eco47I	GGWCC	2 cut(s)	90, 449
Eco53kI	GAGCTC	1 cut(s)	994
Eco57I	CTGAAG	1 cut(s)	153
Eco91I	GGTNACC	1 cut(s)	77
EcoICRI	GAGCTC	1 cut(s)	994
EcoO65I	GGTNACC	1 cut(s)	77
EcoRII	CCWGG	3 cut(s)	104, 121, 867
EcoRV	GATATC	1 cut(s)	892
EcoT14I	CCWWGG	1 cut(s)	775
EcoT38I	GRGCYC	1 cut(s)	996
ErhI	CCWWGG	1 cut(s)	775
Esp3I	CGTCTC	1 cut(s)	385
FaeI	CATG	2 cut(s)	604, 934
FalI	AAGNNNNNCTT	2 cut(s)	846, 878
FatI	CATG	2 cut(s)	600, 930
FauI	CCCGC	1 cut(s)	893
FauNDI	CATATG	1 cut(s)	529
Fnu4HI	GCNGC	3 cut(s)	207, 546, 765
FokI	GGATG	4 cut(s)	458, 896, 970, 1067
FriOI	GRGCYC	1 cut(s)	996
Fsp4HI	GCNGC	3 cut(s)	207, 546, 765
FspBI	CTAG	3 cut(s)	440, 828, 954
GluI	GCNGC	3 cut(s)	207, 546, 765
GsuI	CTGGAG	1 cut(s)	88
HaeIII	GGCC	4 cut(s)	232, 773, 939, 1015
Hin1II	CATG	2 cut(s)	604, 934
HindIII	AAGCTT	1 cut(s)	243
HinfI	GANTC	4 cut(s)	28, 731, 840, 1048
HphI	GGTGA	7 cut(s)	37, 111, 146, 226, 269, 338, 717
Hpy166II	GTNNAC	1 cut(s)	757
Hpy188I	TCNGA	4 cut(s)	33, 172, 556, 883
Hpy188III	TCNNGA	5 cut(s)	141, 482, 636, 931, 1052
Hpy8I	GTNNAC	1 cut(s)	757
HpyAV	CCTTC	6 cut(s)	254, 420, 512, 601, 602, 928
HpyCH4III	ACNGT	3 cut(s)	562, 691, 754
HpyCH4V	TGCA	3 cut(s)	423, 545, 767
HpyF10VI	GCNNNNNNNGC	5 cut(s)	344, 404, 770, 1042, 1064
HpyF3I	CTNAG	5 cut(s)	110, 339, 806, 1000, 1176
Hsp92II	CATG	2 cut(s)	604, 934
Kzo9I	GATC	1 cut(s)	720
LmnI	GCTCC	2 cut(s)	107, 143
Lsp1109I	GCAGC	3 cut(s)	193, 557, 751
LweI	GCATC	3 cut(s)	532, 814, 1045
MaeI	CTAG	3 cut(s)	440, 828, 954
MaeIII	GTNAC	3 cut(s)	77, 562, 907
MalI	GATC	1 cut(s)	722
MbiI	CCGCTC	2 cut(s)	388, 398
MboI	GATC	1 cut(s)	720
MboII	GAAGA	5 cut(s)	5, 159, 185, 833, 849
MflI	RGATCY	1 cut(s)	720
MhlI	GDGCHC	3 cut(s)	198, 368, 996
MlsI	TGGCCA	1 cut(s)	1015
MluCI	AATT	6 cut(s)	72, 408, 780, 1081, 1152, 1169
MluNI	TGGCCA	1 cut(s)	1015
MlyI	GAGTC	2 cut(s)	37, 849
MmeI	TCCRAC	3 cut(s)	673, 796, 967
Mox20I	TGGCCA	1 cut(s)	1015
MscI	TGGCCA	1 cut(s)	1015
MseI	TTAA	1 cut(s)	1172
Msp20I	TGGCCA	1 cut(s)	1015
MspR9I	CCNGG	3 cut(s)	106, 123, 869
Mva1269I	GAATGC	1 cut(s)	46
MvaI	CCWGG	3 cut(s)	106, 123, 869
MvnI	CGCG	1 cut(s)	900
MwoI	GCNNNNNNNGC	5 cut(s)	344, 404, 770, 1042, 1064
NdeI	CATATG	1 cut(s)	529
NdeII	GATC	1 cut(s)	720
NlaIII	CATG	2 cut(s)	604, 934
NmuCI	GTSAC	2 cut(s)	562, 907
PagI	TCATGA	1 cut(s)	930
PctI	GAATGC	1 cut(s)	46
PfeI	GAWTC	2 cut(s)	731, 1048
PkrI	GCNGC	3 cut(s)	208, 547, 766
PleI	GAGTC	2 cut(s)	36, 848
PpsI	GAGTC	2 cut(s)	36, 848
Psp124BI	GAGCTC	1 cut(s)	996
Psp6I	CCWGG	3 cut(s)	104, 121, 867
PspEI	GGTNACC	1 cut(s)	77
PspGI	CCWGG	3 cut(s)	104, 121, 867
PspPI	GGNCC	5 cut(s)	90, 231, 449, 772, 937
PstNI	CAGNNNCTG	3 cut(s)	146, 752, 1051
PsuI	RGATCY	1 cut(s)	720
RsaI	GTAC	1 cut(s)	572
RsaNI	GTAC	1 cut(s)	571
SacI	GAGCTC	1 cut(s)	996
SaqAI	TTAA	1 cut(s)	1172
SatI	GCNGC	3 cut(s)	207, 546, 765
Sau3AI	GATC	1 cut(s)	720
Sau96I	GGNCC	5 cut(s)	90, 231, 449, 772, 937
SchI	GAGTC	2 cut(s)	37, 849
ScrFI	CCNGG	3 cut(s)	106, 123, 869
SduI	GDGCHC	3 cut(s)	198, 368, 996
SfaNI	GCATC	3 cut(s)	532, 814, 1045
SfcI	CTRYAG	1 cut(s)	1134
SinI	GGWCC	2 cut(s)	90, 449
SmlI	CTYRAG	2 cut(s)	197, 625
SmoI	CTYRAG	2 cut(s)	197, 625
SpeI	ACTAGT	1 cut(s)	439
Sse9I	AATT	6 cut(s)	72, 408, 780, 1081, 1152, 1169
SsiI	CCGC	3 cut(s)	388, 398, 900
SspMI	CTAG	3 cut(s)	440, 828, 954
SstI	GAGCTC	1 cut(s)	996
StyD4I	CCNGG	3 cut(s)	104, 121, 867
StyI	CCWWGG	1 cut(s)	775
TaaI	ACNGT	3 cut(s)	562, 691, 754
TasI	AATT	6 cut(s)	72, 408, 780, 1081, 1152, 1169
TfiI	GAWTC	2 cut(s)	731, 1048
Tru1I	TTAA	1 cut(s)	1172
Tru9I	TTAA	1 cut(s)	1172
TscAI	CASTG	1 cut(s)	582
TseFI	GTSAC	2 cut(s)	562, 907
TseI	GCWGC	3 cut(s)	206, 545, 764
Tsp45I	GTSAC	2 cut(s)	562, 907
TspDTI	ATGAA	6 cut(s)	201, 450, 450, 669, 919, 947
TspRI	CASTG	1 cut(s)	582
VpaK11BI	GGWCC	2 cut(s)	90, 449
XspI	CTAG	3 cut(s)	440, 828, 954

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