Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr6A

Orthogroup ID

OG0003550

Physical Location & Seq

Genomic Coordinates Reverse (-)

34117063 .. 34131484

Gene Structure 14422 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh6AG190900.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1308 bp

ATGGACGCAACCACTGTCGTCGACTCCCTCCGGCATAGAGTTCAGGAATTAGAGGCATTAAATGCCAAGTTGTCATCTCAACTCGCAGTTTGTCGCTGCCATCAGCAACAGGACAAGACTGAAGACTCTTCTGTAAGTTCTGATAATTTAGTTGAGAAAAGCGGGAAATCGAGCTTTCAAAGTGAGAACACCACCAAGGAGAAAGTTAAAGGGAAATTGCCAGGTTACGACACAAGGATCATGAATCACCACAGCAAGAGATATGTTGCTTTGAAAGTCATGTATTTTGGCCAAAGGTTCTATGGTTTTGCTGCTGAGGCACAGATGGATCCAACTATTGAGTCTGAAATTTTCAAAGCTCTTGAGAAGACAAGACTTTTGATTGGTGATAAGAAGGAATCACATTACTCAAGATGTGGTAGGACAGACAAGGGAGTTTCTGCTGTTGGGCAAGTGATTGCTCTCTATTTAAGATCAAACCTCAAGGAAGCATGTGAAATCAGTGAAGATCCTAGCAACCAAGAACAATATGAAGGTGAAATCGATTATGTGAGGGTGCTGAATCGAGTCCTTCCCGATGATATTCGAGTTTTTGGTTGGTGTCCTGTACCATTGGGTTTCAGTGCGAGGTTTAGCTGTCTAAGCAGGGAGTATTATTATTTATTTTGGGGAGAAAATCTGAATTTCTTGGCTATGGAGACTGCTGGTAGGAAATTTGTTGGTGAACATGACTTCAGAAACTTCTGTAAGATGGATGCTCTTAATGTGCACAACTACAGGCGGAAAATCACTTCATTTGCAATATCGCCTTGTGATGTGAGGTTTGAGGGGAGCCAGCTTTGGGCATTTAAAATCAAAGGTAGTGCTTTCCTTTGGCATCAGGTCCGATGCATGGTTGCTGTACTACTCTTGATTGGCCAAGGTCATGAATCTCCTGATGTGATAGATGCATTACTGGATACTGACAGAATTCCGAGAAAACCTCAATATGGCATGGCACCAGAGATTCCGTTGGTTCTTCAATCCTGTGAATTTGAGGGTCTCAAGTTCATTTGCTCTTCAGATGCCAGACAAGCTTTGCGCATACACTTGGCTCATGAATGTCGAAACTATCATCTCCAAGCTGCAATTTTTAATGAGGCTCTAAAATGCTGTTTTCCAGTAGAAAAAGGTGCTGAAGATCAGCGCTCCTTGGATAATGGAACAATGAAGAAGAAATCTTCCCATGTTCCACTCATGTTGCGCCCAACTGAGCGTAAGTACTGTATCTTTGAAGTTACATACGAAATGGTCGTTACAGTAATATAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0001522 GO:0003674 GO:0003824 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005737 GO:0006139 GO:0006396 GO:0006399 GO:0006400 GO:0006725 GO:0006807 GO:0008033 GO:0008150 GO:0008152 GO:0009451 GO:0009982 GO:0009987 GO:0010467 GO:0016070 GO:0016071 GO:0016556 GO:0016853 GO:0016866 GO:0031119 GO:0034470 GO:0034641 GO:0034660 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:1901360 GO:1990481

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

PseudoU_synth_1

Protein Analysis

435

Amino Acids

49.76

Weight (kDa)

7.85

Isoelectric Point (pI)

44.26

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PseudoU_synth_1	PF01416	237 - 346	1.9e-30	tRNA pseudouridine 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: OG0003550)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G34150
fragaria_vesca	FvH4_2g12780 FvH4_2g12780 FvH4_2g12780 FvH4_2g12780 FvH4_2g12780 FvH4_2g12780 FvH4_2g12780 FvH4_2g12780 FvH4_2g12780 FvH4_2g12780 FvH4_2g12780 FvH4_2g12780 FvH4_2g12780 FvH4_2g12780 FvH4_2g12780
malus_domestica	MD05G1036800.v1.1 MD05G1036900.v1.1
prunus_persica	Prupe.8G045000_v2.0.a1 Prupe.8G045000_v2.0.a1
pyrus_communis	pycom05g02710 pycom05g02720
rosa_chinensis	RchiOBHm_Chr6g0273621
rosa_laevigata	RLG00000013608
rosa_multiflora	Rmu_sc0001419.1_g000001 Rmu_sc0015671.1_g000001
rosa_roxburghii	Rroxscaffold_7G00195210
rosa_rugosa	Rorug06G0076200 Rorug06G0076300 Rorug06G0076400
rosa_samantha	Rh6AG190900 Rh6BG194400 Rh6CG194300 Rh6DG186200
rosa_wichuraiana	Rw6G016710

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc16I	TGCGCA	1 cut(s)	1082
AccB1I	GGYRCC	1 cut(s)	997
AccI	GTMKAC	1 cut(s)	21
AciI	CCGC	2 cut(s)	162, 781
AclWI	GGATC	4 cut(s)	245, 323, 336, 503
AcoI	YGGCCR	2 cut(s)	289, 916
AcsI	RAATTY	5 cut(s)	348, 682, 713, 969, 1031
AcuI	CTGAAG	4 cut(s)	141, 718, 1044, 1197
AfaI	GTAC	3 cut(s)	609, 903, 1262
AfeI	AGCGCT	1 cut(s)	1187
AfiI	CCNNNNNNNGG	3 cut(s)	841, 892, 989
AgsI	TTSAA	5 cut(s)	179, 274, 355, 1022, 1274
AjnI	CCWGG	1 cut(s)	220
AluBI	AGCT	6 cut(s)	174, 359, 636, 838, 1076, 1124
AluI	AGCT	6 cut(s)	174, 359, 636, 838, 1076, 1124
Alw21I	GWGCWC	1 cut(s)	771
Alw26I	GTCTC	2 cut(s)	692, 1046
Alw44I	GTGCAC	1 cut(s)	767
AlwI	GGATC	4 cut(s)	245, 323, 336, 503
Aor51HI	AGCGCT	1 cut(s)	1187
AoxI	GGCC	2 cut(s)	289, 916
ApaLI	GTGCAC	1 cut(s)	767
ApeKI	GCWGC	3 cut(s)	96, 311, 1124
ApoI	RAATTY	5 cut(s)	348, 682, 713, 969, 1031
ArsI	GACNNNNNNTTYG	2 cut(s)	361, 393
AspLEI	GCGC	3 cut(s)	1083, 1188, 1245
AspS9I	GGNCC	1 cut(s)	883
AsuHPI	GGTGA	4 cut(s)	239, 398, 548, 734
AvaII	GGWCC	1 cut(s)	883
BaeGI	GKGCMC	1 cut(s)	771
BalI	TGGCCA	2 cut(s)	291, 918
BamHI	GGATCC	1 cut(s)	328
BanI	GGYRCC	1 cut(s)	997
BbsI	GAAGAC	2 cut(s)	129, 374
Bbv12I	GWGCWC	1 cut(s)	771
BbvCI	CCTCAGC	1 cut(s)	315
BbvI	GCAGC	3 cut(s)	83, 298, 1111
BccI	CCATC	3 cut(s)	108, 319, 745
BciT130I	CCWGG	1 cut(s)	222
BciVI	GTATCC	1 cut(s)	952
BcoDI	GTCTC	2 cut(s)	692, 1046
BfaI	CTAG	1 cut(s)	513
BfmI	CTRYAG	1 cut(s)	775
BfoI	RGCGCY	1 cut(s)	1189
BfuI	GTATCC	1 cut(s)	952
BisI	GCNGC	3 cut(s)	97, 312, 1125
BlsI	GCNGC	3 cut(s)	98, 313, 1126
BmcAI	AGTACT	1 cut(s)	1262
Bme1390I	CCNGG	1 cut(s)	222
Bme18I	GGWCC	1 cut(s)	883
BmgT120I	GGNCC	1 cut(s)	883
BmiI	GGNNCC	3 cut(s)	330, 833, 999
BmrFI	CCNGG	1 cut(s)	222
BmsI	GCATC	5 cut(s)	745, 878, 886, 937, 1054
BpiI	GAAGAC	2 cut(s)	129, 374
BplI	GAGNNNNNCTC	2 cut(s)	967, 999
Bpu10I	CCTNAGC	1 cut(s)	315
BpuEI	CTTGAG	4 cut(s)	383, 394, 467, 1028
Bsa29I	ATCGAT	1 cut(s)	543
BsaI	GGTCTC	1 cut(s)	1046
BsaJI	CCNNGG	3 cut(s)	195, 919, 1191
Bsc4I	CCNNNNNNNGG	3 cut(s)	841, 892, 989
Bse1I	ACTGG	2 cut(s)	960, 1160
BseBI	CCWGG	1 cut(s)	222
BseCI	ATCGAT	1 cut(s)	543
BseDI	CCNNGG	3 cut(s)	195, 919, 1191
BseGI	GGATG	1 cut(s)	760
BseLI	CCNNNNNNNGG	3 cut(s)	841, 892, 989
BseMII	CTCAG	2 cut(s)	306, 1242
BseNI	ACTGG	2 cut(s)	960, 1160
BseSI	GKGCMC	1 cut(s)	771
BseXI	GCAGC	3 cut(s)	83, 298, 1111
BshFI	GGCC	2 cut(s)	291, 918
BshNI	GGYRCC	1 cut(s)	997
BshVI	ATCGAT	1 cut(s)	543
BsiHKAI	GWGCWC	1 cut(s)	771
BsiSI	CCGG	1 cut(s)	31
BslI	CCNNNNNNNGG	3 cut(s)	841, 892, 989
BsmAI	GTCTC	2 cut(s)	692, 1046
BsnI	GGCC	2 cut(s)	291, 918
Bso31I	GGTCTC	1 cut(s)	1046
Bsp1286I	GDGCHC	1 cut(s)	771
Bsp143I	GATC	5 cut(s)	237, 328, 473, 508, 1180
BspACI	CCGC	2 cut(s)	162, 781
BspANI	GGCC	2 cut(s)	291, 918
BspCNI	CTCAG	2 cut(s)	307, 1243
BspDI	ATCGAT	1 cut(s)	543
BspHI	TCATGA	3 cut(s)	240, 925, 1096
BspLI	GGNNCC	3 cut(s)	330, 833, 999
BspPI	GGATC	4 cut(s)	245, 323, 336, 503
BspQI	GCTCTTC	1 cut(s)	1063
BspT107I	GGYRCC	1 cut(s)	997
BspTNI	GGTCTC	1 cut(s)	1046
BsrI	ACTGG	2 cut(s)	960, 1160
BssECI	CCNNGG	3 cut(s)	195, 919, 1191
BssMI	GATC	5 cut(s)	237, 328, 473, 508, 1180
BssT1I	CCWWGG	3 cut(s)	195, 919, 1191
Bst2UI	CCWGG	1 cut(s)	222
Bst4CI	ACNGT	3 cut(s)	16, 1265, 1300
Bst6I	CTCTTC	2 cut(s)	133, 1063
BstAPI	GCANNNNNTGC	1 cut(s)	62
BstC8I	GCNNGC	1 cut(s)	836
BstDEI	CTNAG	3 cut(s)	315, 641, 1251
BstF5I	GGATG	1 cut(s)	760
BstH2I	RGCGCY	1 cut(s)	1189
BstHHI	GCGC	3 cut(s)	1083, 1188, 1245
BstKTI	GATC	5 cut(s)	240, 331, 476, 511, 1183
BstMAI	GTCTC	2 cut(s)	692, 1046
BstMBI	GATC	5 cut(s)	237, 328, 473, 508, 1180
BstMWI	GCNNNNNNNGC	4 cut(s)	62, 317, 642, 1073
BstNI	CCWGG	1 cut(s)	222
BstNSI	RCATGY	1 cut(s)	495
BstSCI	CCNGG	1 cut(s)	220
BstSFI	CTRYAG	1 cut(s)	775
BstSLI	GKGCMC	1 cut(s)	771
BstV1I	GCAGC	3 cut(s)	83, 298, 1111
BstV2I	GAAGAC	2 cut(s)	129, 374
BstX2I	RGATCY	2 cut(s)	328, 508
BstYI	RGATCY	2 cut(s)	328, 508
Bsu15I	ATCGAT	1 cut(s)	543
BsuI	GTATCC	1 cut(s)	952
BsuRI	GGCC	2 cut(s)	291, 918
BsuTUI	ATCGAT	1 cut(s)	543
BtsCI	GGATG	1 cut(s)	760
BtsIMutI	CAGTG	3 cut(s)	12, 508, 628
Cac8I	GCNNGC	1 cut(s)	836
CciI	TCATGA	3 cut(s)	240, 925, 1096
CfoI	GCGC	3 cut(s)	1083, 1188, 1245
Cfr13I	GGNCC	1 cut(s)	883
ClaI	ATCGAT	1 cut(s)	543
CseI	GACGC	1 cut(s)	14
Csp6I	GTAC	3 cut(s)	608, 902, 1261
CspCI	CAANNNNNGTGG	2 cut(s)	1221, 1256
CviQI	GTAC	3 cut(s)	608, 902, 1261
DdeI	CTNAG	3 cut(s)	315, 641, 1251
DpnI	GATC	5 cut(s)	239, 330, 475, 510, 1182
DpnII	GATC	5 cut(s)	237, 328, 473, 508, 1180
DraI	TTTAAA	1 cut(s)	850
EaeI	YGGCCR	2 cut(s)	289, 916
Eam1104I	CTCTTC	2 cut(s)	133, 1063
EarI	CTCTTC	2 cut(s)	133, 1063
EciI	GGCGGA	1 cut(s)	796
Eco130I	CCWWGG	3 cut(s)	195, 919, 1191
Eco31I	GGTCTC	1 cut(s)	1046
Eco47I	GGWCC	1 cut(s)	883
Eco47III	AGCGCT	1 cut(s)	1187
Eco57I	CTGAAG	4 cut(s)	141, 718, 1044, 1197
EcoRI	GAATTC	1 cut(s)	969
EcoRII	CCWGG	1 cut(s)	220
EcoT14I	CCWWGG	3 cut(s)	195, 919, 1191
EcoT22I	ATGCAT	2 cut(s)	893, 952
ErhI	CCWWGG	3 cut(s)	195, 919, 1191
FauI	CCCGC	1 cut(s)	155
FblI	GTMKAC	1 cut(s)	21
Fnu4HI	GCNGC	3 cut(s)	97, 312, 1125
FokI	GGATG	1 cut(s)	767
Fsp4HI	GCNGC	3 cut(s)	97, 312, 1125
FspBI	CTAG	1 cut(s)	513
FspI	TGCGCA	1 cut(s)	1082
GlaI	GCGC	3 cut(s)	1082, 1187, 1244
GluI	GCNGC	3 cut(s)	97, 312, 1125
HaeII	RGCGCY	1 cut(s)	1189
HaeIII	GGCC	2 cut(s)	291, 918
HapII	CCGG	1 cut(s)	31
HgaI	GACGC	1 cut(s)	14
HhaI	GCGC	3 cut(s)	1083, 1188, 1245
Hin6I	GCGC	3 cut(s)	1081, 1186, 1243
HinP1I	GCGC	3 cut(s)	1081, 1186, 1243
HincII	GTYRAC	1 cut(s)	22
HindII	GTYRAC	1 cut(s)	22
HindIII	AAGCTT	1 cut(s)	1074
HinfI	GANTC	9 cut(s)	23, 125, 244, 341, 398, 562, 567, 929, 1006
HpaII	CCGG	1 cut(s)	31
HphI	GGTGA	4 cut(s)	239, 398, 548, 734
Hpy166II	GTNNAC	3 cut(s)	22, 725, 769
Hpy188I	TCNGA	7 cut(s)	142, 346, 681, 737, 887, 975, 1063
Hpy188III	TCNNGA	9 cut(s)	44, 241, 362, 411, 575, 910, 926, 935, 1097
Hpy8I	GTNNAC	3 cut(s)	22, 725, 769
Hpy99I	CGWCG	1 cut(s)	23
HpyAV	CCTTC	3 cut(s)	388, 527, 581
HpyCH4III	ACNGT	3 cut(s)	16, 1265, 1300
HpyCH4V	TGCA	5 cut(s)	769, 800, 891, 950, 1127
HpyF10VI	GCNNNNNNNGC	4 cut(s)	62, 317, 642, 1073
HpyF3I	CTNAG	3 cut(s)	315, 641, 1251
HspAI	GCGC	3 cut(s)	1081, 1186, 1243
Kzo9I	GATC	5 cut(s)	237, 328, 473, 508, 1180
LguI	GCTCTTC	1 cut(s)	1063
LmnI	GCTCC	2 cut(s)	831, 1193
Lsp1109I	GCAGC	3 cut(s)	83, 298, 1111
LweI	GCATC	5 cut(s)	745, 878, 886, 937, 1054
MaeI	CTAG	1 cut(s)	513
MaeIII	GTNAC	3 cut(s)	224, 1276, 1294
MalI	GATC	5 cut(s)	239, 330, 475, 510, 1182
MboI	GATC	5 cut(s)	237, 328, 473, 508, 1180
MflI	RGATCY	2 cut(s)	328, 508
MhlI	GDGCHC	1 cut(s)	771
MlsI	TGGCCA	2 cut(s)	291, 918
MluCI	AATT	9 cut(s)	47, 145, 215, 348, 682, 713, 969, 1031, 1128
MluNI	TGGCCA	2 cut(s)	291, 918
MlyI	GAGTC	4 cut(s)	17, 119, 350, 576
MmeI	TCCRAC	1 cut(s)	356
Mox20I	TGGCCA	2 cut(s)	291, 918
Mph1103I	ATGCAT	2 cut(s)	893, 952
MscI	TGGCCA	2 cut(s)	291, 918
MseI	TTAA	6 cut(s)	59, 207, 470, 762, 849, 1134
Msp20I	TGGCCA	2 cut(s)	291, 918
MspI	CCGG	1 cut(s)	31
MspR9I	CCNGG	1 cut(s)	222
MvaI	CCWGG	1 cut(s)	222
MwoI	GCNNNNNNNGC	4 cut(s)	62, 317, 642, 1073
NdeII	GATC	5 cut(s)	237, 328, 473, 508, 1180
NlaIV	GGNNCC	3 cut(s)	330, 833, 999
NsbI	TGCGCA	1 cut(s)	1082
NsiI	ATGCAT	2 cut(s)	893, 952
NspI	RCATGY	1 cut(s)	495
PagI	TCATGA	3 cut(s)	240, 925, 1096
PciSI	GCTCTTC	1 cut(s)	1063
PcsI	WCGNNNNNNNCGW	1 cut(s)	1290
PfeI	GAWTC	5 cut(s)	244, 398, 562, 929, 1006
PkrI	GCNGC	3 cut(s)	98, 313, 1126
PleI	GAGTC	4 cut(s)	17, 119, 349, 575
PpsI	GAGTC	4 cut(s)	17, 119, 349, 575
Psp6I	CCWGG	1 cut(s)	220
PspGI	CCWGG	1 cut(s)	220
PspN4I	GGNNCC	3 cut(s)	330, 833, 999
PspPI	GGNCC	1 cut(s)	883
PsuI	RGATCY	2 cut(s)	328, 508
RsaI	GTAC	3 cut(s)	609, 903, 1262
RsaNI	GTAC	3 cut(s)	608, 902, 1261
SalI	GTCGAC	1 cut(s)	20
SapI	GCTCTTC	1 cut(s)	1063
SaqAI	TTAA	6 cut(s)	59, 207, 470, 762, 849, 1134
SatI	GCNGC	3 cut(s)	97, 312, 1125
Sau3AI	GATC	5 cut(s)	237, 328, 473, 508, 1180
Sau96I	GGNCC	1 cut(s)	883
ScaI	AGTACT	1 cut(s)	1262
SchI	GAGTC	4 cut(s)	17, 119, 350, 576
ScrFI	CCNGG	1 cut(s)	222
SduI	GDGCHC	1 cut(s)	771
SfaNI	GCATC	5 cut(s)	745, 878, 886, 937, 1054
SfcI	CTRYAG	1 cut(s)	775
SinI	GGWCC	1 cut(s)	883
SmlI	CTYRAG	4 cut(s)	362, 409, 482, 1043
SmoI	CTYRAG	4 cut(s)	362, 409, 482, 1043
Sse9I	AATT	9 cut(s)	47, 145, 215, 348, 682, 713, 969, 1031, 1128
SsiI	CCGC	2 cut(s)	162, 781
SspMI	CTAG	1 cut(s)	513
StyD4I	CCNGG	1 cut(s)	220
StyI	CCWWGG	3 cut(s)	195, 919, 1191
TaaI	ACNGT	3 cut(s)	16, 1265, 1300
TaqI	TCGA	6 cut(s)	21, 170, 543, 565, 586, 1105
TasI	AATT	9 cut(s)	47, 145, 215, 348, 682, 713, 969, 1031, 1128
TatI	WGTACW	2 cut(s)	901, 1260
TfiI	GAWTC	5 cut(s)	244, 398, 562, 929, 1006
Tru1I	TTAA	6 cut(s)	59, 207, 470, 762, 849, 1134
Tru9I	TTAA	6 cut(s)	59, 207, 470, 762, 849, 1134
TscAI	CASTG	3 cut(s)	19, 508, 628
TseI	GCWGC	3 cut(s)	96, 311, 1124
TspDTI	ATGAA	7 cut(s)	257, 546, 783, 942, 1039, 1113, 1223
TspGWI	ACGGA	1 cut(s)	999
TspRI	CASTG	3 cut(s)	19, 508, 628
VneI	GTGCAC	1 cut(s)	767
VpaK11BI	GGWCC	1 cut(s)	883
XapI	RAATTY	5 cut(s)	348, 682, 713, 969, 1031
XceI	RCATGY	1 cut(s)	495
XcmI	CCANNNNNNNNNTGG	1 cut(s)	299
XmiI	GTMKAC	1 cut(s)	21
XspI	CTAG	1 cut(s)	513
ZrmI	AGTACT	1 cut(s)	1262
Zsp2I	ATGCAT	2 cut(s)	893, 952

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