Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5D

Orthogroup ID

OG0019016

Physical Location & Seq

Genomic Coordinates Forward (+)

2273367 .. 2275352

Gene Structure 1986 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5DG032500.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 996 bp

ATGGGCTCAATGAGTCTGACTTCACTTCTGGGTCATGGTTGCCGGAGTTTAGTTGCGCCGGTGGCCCTTGCGCGCACGTTGGCACTGACCCATGTTGCTCTGAGTGAACATTCGAAGAGCTACCAGCATGTGAAGGTGGCTTGGTTTTCTAAGAGGTCAAAGAAGAAGAAGAGGGTTGCATGTGAGTCTTTGAAAGAAGAGGTTACTTACCCAACTGCTGCTGCTGCTTCTGTTTATGGCTACCCATATACTCGTTTACTTCCATGTCCCTCACAGAATGGACCACCAAGAGTTGAGCACTTGGTTGTTTCCGAAGGGGGCCCTGTTCTGGAATATATATGCAAAAATCTGGATCTTCCTGCTCAGTTTGTTGCAGATCTTATCCATTTTGGAGCTGTGTATTATGCCCTTGTATGTCCAAAGCCTCCTCCAACCGCGACGCCCGAGGAAATGAGGGTATATAAAGAAACTACAGCACCATCAGTACTGAAAAAGAGAGCTTCTATAAAAGGAAAAACTGTAAGAGAAGCACAGAAGACTTTCAGGATCACACATGTAGACCAATTTGTTGAAGATGGAACGTACTTACGTGTGCATGTACACCCAAAGCGTTTTCCTAGGTGCCATGAAATTGACTGGAAATCAAGAGTTATAGCAGTAAATGAAGACTTTGTGGTGTTGGACAAACCTGCTGGTACAACAGTTGGAGGAACCACAGACAACATCGAAGAAAGTTGTGCAACCTTTACCTCCCGTGCCTTAGGACTAACAACCCCCCTGATGACCACACATCAGATTGATAATTGTACAGAAGGATGTGTTGTCTTAGCTAGGACCAAGGAGTATTGCTCAGTTTTTCATGGAAAAATCCGAGAAAAACAAGTGAAGAAACTTTATCTTGCTCTTGCTGCTGCTCCTGTGCCACTTGGAACAATTACTCACTACATGCGTCCAATTAATGTGGCTCCACGACTCATTTCAGAAGGTACTAATTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0003824 GO:0006139 GO:0006206 GO:0006213 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0008655 GO:0009058 GO:0009112 GO:0009116 GO:0009119 GO:0009451 GO:0009982 GO:0009987 GO:0016070 GO:0016853 GO:0016866 GO:0018130 GO:0019438 GO:0019858 GO:0034641 GO:0034654 GO:0043094 GO:0043170 GO:0043412 GO:0044237 GO:0044238 GO:0044249 GO:0044271 GO:0044281 GO:0046087 GO:0046131 GO:0046483 GO:0055086 GO:0071704 GO:0072527 GO:0072528 GO:0090304 GO:1901135 GO:1901360 GO:1901362 GO:1901564 GO:1901566 GO:1901576 GO:1901657

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

PseudoU_synth_2

Protein Analysis

331

Amino Acids

36.57

Weight (kDa)

9.31

Isoelectric Point (pI)

42.68

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PseudoU_synth_2	PF00849	223 - 318	2.6e-16	RNA pseudouridylate synthase

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: OG0019016)

Species	Orthologous Gene IDs
rosa_chinensis	RchiOBHm_Chr5g0003761
rosa_laevigata	RLG00000031173
rosa_multiflora	Rmu_co8372245.1_g000001
rosa_rugosa	Rorug04G0406500
rosa_samantha	Rh5AG033700 Rh5BG032100 Rh5CG036400 Rh5DG032500
rosa_wichuraiana	Rw5G003100

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc36I	ACCTGC	1 cut(s)	697
AccB1I	GGYRCC	1 cut(s)	621
AccI	GTMKAC	1 cut(s)	558
AccII	CGCG	2 cut(s)	73, 437
AciI	CCGC	1 cut(s)	435
AclWI	GGATC	2 cut(s)	360, 554
AcyI	GRCGYC	1 cut(s)	440
AfaI	GTAC	6 cut(s)	486, 584, 600, 697, 808, 988
AfiI	CCNNNNNNNGG	1 cut(s)	328
AflIII	ACRYGT	2 cut(s)	553, 589
AgsI	TTSAA	2 cut(s)	193, 572
AluBI	AGCT	4 cut(s)	120, 395, 500, 830
AluI	AGCT	4 cut(s)	120, 395, 500, 830
Alw21I	GWGCWC	1 cut(s)	300
AlwI	GGATC	2 cut(s)	360, 554
Ama87I	CYCGRG	1 cut(s)	443
AoxI	GGCC	2 cut(s)	63, 319
ApaI	GGGCCC	1 cut(s)	323
ApeKI	GCWGC	5 cut(s)	218, 221, 224, 908, 911
AseI	ATTAAT	1 cut(s)	957
Asp700I	GAANNNNTTC	1 cut(s)	539
AspA2I	CCTAGG	1 cut(s)	617
AspLEI	GCGC	3 cut(s)	58, 73, 75
AspS9I	GGNCC	5 cut(s)	64, 281, 319, 320, 834
AsuII	TTCGAA	1 cut(s)	113
AvaI	CYCGRG	1 cut(s)	443
AvaII	GGWCC	2 cut(s)	281, 834
AvrII	CCTAGG	1 cut(s)	617
AxyI	CCTNAGG	1 cut(s)	760
BaeGI	GKGCMC	1 cut(s)	323
BaeI	ACNNNNGTAYC	2 cut(s)	687, 720
BanI	GGYRCC	1 cut(s)	621
BanII	GRGCYC	2 cut(s)	8, 323
BbsI	GAAGAC	2 cut(s)	542, 672
Bbv12I	GWGCWC	1 cut(s)	300
BbvI	GCAGC	5 cut(s)	205, 208, 211, 895, 898
BccI	CCATC	2 cut(s)	487, 569
BfaI	CTAG	2 cut(s)	618, 831
BfmI	CTRYAG	1 cut(s)	471
BfuAI	ACCTGC	1 cut(s)	697
BglII	AGATCT	1 cut(s)	376
BisI	GCNGC	5 cut(s)	219, 222, 225, 909, 912
BlnI	CCTAGG	1 cut(s)	617
BlsI	GCNGC	5 cut(s)	220, 223, 226, 910, 913
BmcAI	AGTACT	1 cut(s)	486
Bme18I	GGWCC	2 cut(s)	281, 834
BmeT110I	CYCGRG	1 cut(s)	443
BmgT120I	GGNCC	5 cut(s)	64, 281, 319, 320, 834
BmiI	GGNNCC	5 cut(s)	320, 321, 623, 712, 966
BpiI	GAAGAC	2 cut(s)	542, 672
BplI	GAGNNNNNCTC	2 cut(s)	833, 865
Bpu14I	TTCGAA	1 cut(s)	113
BsaAI	YACGTR	1 cut(s)	590
BsaHI	GRCGYC	1 cut(s)	440
BsaJI	CCNNGG	3 cut(s)	444, 617, 837
Bsc4I	CCNNNNNNNGG	1 cut(s)	328
Bse118I	RCCGGY	1 cut(s)	58
Bse1I	ACTGG	1 cut(s)	641
Bse21I	CCTNAGG	1 cut(s)	760
BseDI	CCNNGG	3 cut(s)	444, 617, 837
BseGI	GGATG	1 cut(s)	821
BseLI	CCNNNNNNNGG	1 cut(s)	328
BseMII	CTCAG	3 cut(s)	92, 377, 864
BseNI	ACTGG	1 cut(s)	641
BsePI	GCGCGC	1 cut(s)	71
BseRI	GAGGAG	1 cut(s)	417
BseSI	GKGCMC	1 cut(s)	323
BseXI	GCAGC	5 cut(s)	205, 208, 211, 895, 898
Bsh1236I	CGCG	2 cut(s)	73, 437
BshFI	GGCC	2 cut(s)	65, 321
BshNI	GGYRCC	1 cut(s)	621
BsiHKAI	GWGCWC	1 cut(s)	300
BsiHKCI	CYCGRG	1 cut(s)	443
BsiSI	CCGG	2 cut(s)	43, 59
BslFI	GGGAC	1 cut(s)	252
BslI	CCNNNNNNNGG	1 cut(s)	328
BsmFI	GGGAC	1 cut(s)	252
BsnI	GGCC	2 cut(s)	65, 321
BsoBI	CYCGRG	1 cut(s)	443
Bsp119I	TTCGAA	1 cut(s)	113
Bsp120I	GGGCCC	1 cut(s)	319
Bsp1286I	GDGCHC	3 cut(s)	8, 300, 323
Bsp1407I	TGTACA	2 cut(s)	598, 806
Bsp143I	GATC	3 cut(s)	352, 376, 546
BspACI	CCGC	1 cut(s)	435
BspANI	GGCC	2 cut(s)	65, 321
BspCNI	CTCAG	3 cut(s)	93, 376, 863
BspFNI	CGCG	2 cut(s)	73, 437
BspLI	GGNNCC	5 cut(s)	320, 321, 623, 712, 966
BspMI	ACCTGC	1 cut(s)	697
BspPI	GGATC	2 cut(s)	360, 554
BspQI	GCTCTTC	1 cut(s)	110
BspT104I	TTCGAA	1 cut(s)	113
BspT107I	GGYRCC	1 cut(s)	621
BsrFI	RCCGGY	1 cut(s)	58
BsrGI	TGTACA	2 cut(s)	598, 806
BsrI	ACTGG	1 cut(s)	641
BssAI	RCCGGY	1 cut(s)	58
BssECI	CCNNGG	3 cut(s)	444, 617, 837
BssHII	GCGCGC	1 cut(s)	71
BssMI	GATC	3 cut(s)	352, 376, 546
BssNI	GRCGYC	1 cut(s)	440
BssT1I	CCWWGG	2 cut(s)	617, 837
Bst4CI	ACNGT	2 cut(s)	520, 703
Bst6I	CTCTTC	3 cut(s)	110, 164, 192
BstACI	GRCGYC	1 cut(s)	440
BstAUI	TGTACA	2 cut(s)	598, 806
BstBAI	YACGTR	1 cut(s)	590
BstBI	TTCGAA	1 cut(s)	113
BstC8I	GCNNGC	1 cut(s)	73
BstDEI	CTNAG	6 cut(s)	101, 150, 363, 760, 826, 850
BstF5I	GGATG	1 cut(s)	821
BstFNI	CGCG	2 cut(s)	73, 437
BstHHI	GCGC	3 cut(s)	58, 73, 75
BstKTI	GATC	3 cut(s)	355, 379, 549
BstMBI	GATC	3 cut(s)	352, 376, 546
BstMWI	GCNNNNNNNGC	3 cut(s)	62, 224, 908
BstNSI	RCATGY	5 cut(s)	131, 183, 557, 599, 949
BstSFI	CTRYAG	1 cut(s)	471
BstSLI	GKGCMC	1 cut(s)	323
BstUI	CGCG	2 cut(s)	73, 437
BstV1I	GCAGC	5 cut(s)	205, 208, 211, 895, 898
BstV2I	GAAGAC	2 cut(s)	542, 672
BstX2I	RGATCY	2 cut(s)	352, 376
BstYI	RGATCY	2 cut(s)	352, 376
Bsu36I	CCTNAGG	1 cut(s)	760
BsuRI	GGCC	2 cut(s)	65, 321
BtsCI	GGATG	1 cut(s)	821
BtsIMutI	CAGTG	1 cut(s)	83
BveI	ACCTGC	1 cut(s)	697
Cac8I	GCNNGC	1 cut(s)	73
CfoI	GCGC	3 cut(s)	58, 73, 75
Cfr10I	RCCGGY	1 cut(s)	58
Cfr13I	GGNCC	5 cut(s)	64, 281, 319, 320, 834
CseI	GACGC	2 cut(s)	448, 938
Csp6I	GTAC	6 cut(s)	485, 583, 599, 696, 807, 987
CspCI	CAANNNNNGTGG	2 cut(s)	942, 977
CviQI	GTAC	6 cut(s)	485, 583, 599, 696, 807, 987
DdeI	CTNAG	6 cut(s)	101, 150, 363, 760, 826, 850
DpnI	GATC	3 cut(s)	354, 378, 548
DpnII	GATC	3 cut(s)	352, 376, 546
Eam1104I	CTCTTC	3 cut(s)	110, 164, 192
EarI	CTCTTC	3 cut(s)	110, 164, 192
Eco130I	CCWWGG	2 cut(s)	617, 837
Eco24I	GRGCYC	2 cut(s)	8, 323
Eco47I	GGWCC	2 cut(s)	281, 834
Eco81I	CCTNAGG	1 cut(s)	760
Eco88I	CYCGRG	1 cut(s)	443
EcoO109I	RGGNCCY	2 cut(s)	319, 320
EcoT14I	CCWWGG	2 cut(s)	617, 837
EcoT38I	GRGCYC	2 cut(s)	8, 323
ErhI	CCWWGG	2 cut(s)	617, 837
FaqI	GGGAC	1 cut(s)	252
FblI	GTMKAC	1 cut(s)	558
Fnu4HI	GCNGC	5 cut(s)	219, 222, 225, 909, 912
FokI	GGATG	1 cut(s)	828
FriOI	GRGCYC	2 cut(s)	8, 323
Fsp4HI	GCNGC	5 cut(s)	219, 222, 225, 909, 912
FspBI	CTAG	2 cut(s)	618, 831
GlaI	GCGC	3 cut(s)	57, 72, 74
GluI	GCNGC	5 cut(s)	219, 222, 225, 909, 912
HaeIII	GGCC	2 cut(s)	65, 321
HapII	CCGG	2 cut(s)	43, 59
HgaI	GACGC	2 cut(s)	448, 938
HhaI	GCGC	3 cut(s)	58, 73, 75
Hin1I	GRCGYC	1 cut(s)	440
Hin6I	GCGC	3 cut(s)	56, 71, 73
HinP1I	GCGC	3 cut(s)	56, 71, 73
HinfI	GANTC	3 cut(s)	13, 185, 972
HpaII	CCGG	2 cut(s)	43, 59
Hpy166II	GTNNAC	4 cut(s)	107, 257, 559, 601
Hpy188I	TCNGA	6 cut(s)	18, 102, 313, 795, 872, 982
Hpy188III	TCNNGA	4 cut(s)	329, 350, 544, 645
Hpy8I	GTNNAC	4 cut(s)	107, 257, 559, 601
Hpy99I	CGWCG	1 cut(s)	442
HpyAV	CCTTC	4 cut(s)	127, 308, 806, 977
HpyCH4III	ACNGT	2 cut(s)	520, 703
HpyCH4IV	ACGT	3 cut(s)	77, 581, 589
HpyCH4V	TGCA	5 cut(s)	179, 342, 374, 595, 740
HpyF10VI	GCNNNNNNNGC	3 cut(s)	62, 224, 908
HpyF3I	CTNAG	6 cut(s)	101, 150, 363, 760, 826, 850
HpySE526I	ACGT	3 cut(s)	77, 581, 589
Hsp92I	GRCGYC	1 cut(s)	440
HspAI	GCGC	3 cut(s)	56, 71, 73
Kzo9I	GATC	3 cut(s)	352, 376, 546
LguI	GCTCTTC	1 cut(s)	110
LmnI	GCTCC	3 cut(s)	392, 919, 970
Lsp1109I	GCAGC	5 cut(s)	205, 208, 211, 895, 898
MaeI	CTAG	2 cut(s)	618, 831
MaeII	ACGT	3 cut(s)	77, 581, 589
MaeIII	GTNAC	1 cut(s)	202
MalI	GATC	3 cut(s)	354, 378, 548
MboI	GATC	3 cut(s)	352, 376, 546
MflI	RGATCY	2 cut(s)	352, 376
MhlI	GDGCHC	3 cut(s)	8, 300, 323
MluCI	AATT	6 cut(s)	563, 630, 802, 933, 954, 991
MlyI	GAGTC	3 cut(s)	22, 194, 966
MmeI	TCCRAC	3 cut(s)	455, 660, 685
MroXI	GAANNNNTTC	1 cut(s)	539
MseI	TTAA	2 cut(s)	957, 994
MspI	CCGG	2 cut(s)	43, 59
MvnI	CGCG	2 cut(s)	73, 437
MwoI	GCNNNNNNNGC	3 cut(s)	62, 224, 908
NdeII	GATC	3 cut(s)	352, 376, 546
NlaIV	GGNNCC	5 cut(s)	320, 321, 623, 712, 966
NspI	RCATGY	5 cut(s)	131, 183, 557, 599, 949
NspV	TTCGAA	1 cut(s)	113
PauI	GCGCGC	1 cut(s)	71
PciI	ACATGT	1 cut(s)	553
PciSI	GCTCTTC	1 cut(s)	110
PdmI	GAANNNNTTC	1 cut(s)	539
PkrI	GCNGC	5 cut(s)	220, 223, 226, 910, 913
PleI	GAGTC	3 cut(s)	21, 193, 966
PpsI	GAGTC	3 cut(s)	21, 193, 966
Ppu21I	YACGTR	1 cut(s)	590
PscI	ACATGT	1 cut(s)	553
PshBI	ATTAAT	1 cut(s)	957
PspN4I	GGNNCC	5 cut(s)	320, 321, 623, 712, 966
PspOMI	GGGCCC	1 cut(s)	319
PspPI	GGNCC	5 cut(s)	64, 281, 319, 320, 834
PsuI	RGATCY	2 cut(s)	352, 376
PteI	GCGCGC	1 cut(s)	71
RsaI	GTAC	6 cut(s)	486, 584, 600, 697, 808, 988
RsaNI	GTAC	6 cut(s)	485, 583, 599, 696, 807, 987
SapI	GCTCTTC	1 cut(s)	110
SaqAI	TTAA	2 cut(s)	957, 994
SatI	GCNGC	5 cut(s)	219, 222, 225, 909, 912
Sau3AI	GATC	3 cut(s)	352, 376, 546
Sau96I	GGNCC	5 cut(s)	64, 281, 319, 320, 834
ScaI	AGTACT	1 cut(s)	486
SchI	GAGTC	3 cut(s)	22, 194, 966
SduI	GDGCHC	3 cut(s)	8, 300, 323
SfcI	CTRYAG	1 cut(s)	471
SfuI	TTCGAA	1 cut(s)	113
SgrAI	CRCCGGYG	1 cut(s)	58
SinI	GGWCC	2 cut(s)	281, 834
Sse9I	AATT	6 cut(s)	563, 630, 802, 933, 954, 991
SsiI	CCGC	1 cut(s)	435
SspMI	CTAG	2 cut(s)	618, 831
StyI	CCWWGG	2 cut(s)	617, 837
TaaI	ACNGT	2 cut(s)	520, 703
TaiI	ACGT	3 cut(s)	80, 584, 592
TaqI	TCGA	2 cut(s)	113, 726
TasI	AATT	6 cut(s)	563, 630, 802, 933, 954, 991
TatI	WGTACW	3 cut(s)	484, 598, 806
Tru1I	TTAA	2 cut(s)	957, 994
Tru9I	TTAA	2 cut(s)	957, 994
TscAI	CASTG	1 cut(s)	90
TseI	GCWGC	5 cut(s)	218, 221, 224, 908, 911
TspDTI	ATGAA	3 cut(s)	642, 678, 848
TspRI	CASTG	1 cut(s)	90
VpaK11BI	GGWCC	2 cut(s)	281, 834
VspI	ATTAAT	1 cut(s)	957
XceI	RCATGY	5 cut(s)	131, 183, 557, 599, 949
XmaJI	CCTAGG	1 cut(s)	617
XmiI	GTMKAC	1 cut(s)	558
XmnI	GAANNNNTTC	1 cut(s)	539
XspI	CTAG	2 cut(s)	618, 831
ZrmI	AGTACT	1 cut(s)	486

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