Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr6B

Orthogroup ID

OG0001594

Physical Location & Seq

Genomic Coordinates Forward (+)

10317436 .. 10320899

Gene Structure 3464 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh6BG066100.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1326 bp

ATGCCGAATCACCTTCTCCTCCGCCGCATCCTCCTCCGTCCTCCACTCTCCTCCTCCGCCGAATCCGGCGGCGATAGGCTCTTCATCTCACCTTTCCACTACTCCCGATCTTACGCCACCACCCAACCATTTCACGAAGACAAACAAAAGCGCGGCAAAAAGTGGTTCACTCTACCTCCGTTCACTGACTCCGTAAACGGCGCCGCTTTGGGACGAGAGCTGTCTCGCAGCGTCGGCAGAGATGTGTATGCTAAACCCACAGCCGCCGCAGCCACGACGGCGCTTAAATGGGTCACCAGGTGCTGCCCTGAGATTCCCAGAAGCCTTGTCCAGAAGCTGTTTCGGTTAAGACAGGTTCGAAGAGAAGCATCTGACATGGATCAAGGTGTTCAAGCACTTAAAAGGGTGGGGGCTAAAGACTCGATGAACTTAGGAGATCGAATTTGTCTTCCTAGTTCTGTGAAAGAGTTCCCTGATGATAAACAAGAAGAGGGACATTGTAGTGAAGAAGAAGTCAAGTTTATTCGTAGTCTCGTGTTGTATAAGGATCCAGCTATTGTTGTCATCAATAAACCCCCTGGATTGCCTGTTCAGGGCGGTATTGGAATCAAAAGGAGTTTAGATGAACTGGCTGCCACTTGTTTAAGTTACGGCTTTTCAGAACCCCCTCGTCTGGTACACAGACTTGACAGAGATTGTAGTGGTATCCTTGTGATGGGACGGACACAAATAAGTGCAACAGTTTTGCATTCCCTCTTCCGTGAGAAAACTTTTGGAGCTTCAGATGATGTTATCGACCATGCTAAAGCCATTCTGCAAAGAAGGTATTGGGCACTCGTCATTGGATCTCCCAGACAACAAGAGGGGTTAATCTCCGTGCCTTTAGGAAAGTTAGAGTCACTGTTGACTGTGCTGTCTGTGCACAACTCTTCTAACCATGTGTGGGAACTACAGCTGCGTGTACACTGTGCAGAAGTTTTGGGAACACCAATAGTCGGAGACTACAAATATGGATGGCGAACGCATAAGGACTGGAAACCTGTTGCTTGGTCTAAGATTGAAAGCCATTCCAGTGAGGGGCATTCGAAGAGAACAAACATTCCTTTTGATCTCAATATGGACAGTGGAAGTATTGCCGAAAAGAATTTGCGCTTACATCTTCATTCTAAGCAAATGGTTTTGCCTAATGTGTCTCTGGCTTTGCAAAATGTGAAACTGCATGCGGAGTGTGATCTTTCAGGACTAGAATGCCTAGAATTGGTTGCTCCTATGCCTTCATACATGCAAAAAAGTTGGGATATTACAAATTCTGGTTTTGATGGGTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0001522 GO:0003674 GO:0003824 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005739 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: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:0044444 GO:0044464 GO:0046483 GO:0071704 GO:0090304 GO:1901360

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

PseudoU_synth_2

Protein Analysis

441

Amino Acids

49.31

Weight (kDa)

9.1

Isoelectric Point (pI)

58.12

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PseudoU_synth_2	PF00849	186 - 297	4.6e-11	RNA pseudouridylate 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: OG0001594)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G19440 AT3G19440
fragaria_vesca	FvH4_2g05120 FvH4_2g05120 FvH4_2g05120 FvH4_2g05120
malus_domestica	MD10G1097600.v1.1
prunus_persica	Prupe.8G135400_v2.0.a1 Prupe.8G135400_v2.0.a1 Prupe.8G135400_v2.0.a1
pyrus_communis	pycom01g14220 pycom10g08370
rosa_chinensis	RchiOBHm_Chr4g0415551 RchiOBHm_Chr6g0255041
rosa_laevigata	RLG00000003460 RLG00000014859 RLG00000014868 RLG00000018864 RLG00000024043 RLG00000027684
rosa_multiflora	Rmu_ssc0000011.1_g000078
rosa_roxburghii	Rroxscaffold_2G00121110 Rroxscaffold_6G00396470 Rroxscaffold_6G00402590 Rroxscaffold_7G00210260
rosa_rugosa	Rorug03G0278700 Rorug03G0278800 Rorug03G0278900 Rorug05G0556400 Rorug05G0556500
rosa_samantha	Rh1AG091300 Rh1AG167900 Rh1DG094800 Rh2BG117700 Rh2BG330200 Rh2DG118600 Rh3BG349000 Rh4CG206700 Rh5BG449900 Rh6AG035800 Rh6AG073700 Rh6BG065900 Rh6BG066100 Rh6BG131700 Rh7AG357100 Rh7CG374500
rosa_wichuraiana	Rw2G034900 Rw6G006400 Rw6G006410 Rw6G026380

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AasI	GACNNNNNNGTC	1 cut(s)	913
AccB1I	GGYRCC	1 cut(s)	200
AccII	CGCG	1 cut(s)	153
AclWI	GGATC	4 cut(s)	387, 542, 555, 853
AcsI	RAATTY	3 cut(s)	441, 1144, 1306
AcuI	CTGAAG	1 cut(s)	765
AcyI	GRCGYC	1 cut(s)	201
AdeI	CACNNNGTG	1 cut(s)	300
AfaI	GTAC	2 cut(s)	678, 963
AfiI	CCNNNNNNNGG	7 cut(s)	593, 673, 715, 943, 995, 1077, 1258
AgsI	TTSAA	2 cut(s)	392, 1061
AjnI	CCWGG	2 cut(s)	296, 577
AloI	GAACNNNNNNTCC	4 cut(s)	573, 605, 1084, 1116
AluBI	AGCT	5 cut(s)	220, 337, 554, 779, 955
AluI	AGCT	5 cut(s)	220, 337, 554, 779, 955
Alw21I	GWGCWC	1 cut(s)	924
Alw26I	GTCTC	4 cut(s)	228, 536, 993, 1197
Alw44I	GTGCAC	1 cut(s)	920
AlwI	GGATC	4 cut(s)	387, 542, 555, 853
AlwNI	CAGNNNCTG	2 cut(s)	303, 337
ApaLI	GTGCAC	1 cut(s)	920
ApeKI	GCWGC	5 cut(s)	228, 269, 303, 632, 955
ApoI	RAATTY	3 cut(s)	441, 1144, 1306
Asp700I	GAANNNNTTC	1 cut(s)	467
AspLEI	GCGC	4 cut(s)	153, 203, 283, 1152
AsuHPI	GGTGA	2 cut(s)	81, 286
AsuII	TTCGAA	2 cut(s)	358, 1085
BaeGI	GKGCMC	2 cut(s)	835, 924
BamHI	GGATCC	1 cut(s)	547
BanI	GGYRCC	1 cut(s)	200
BauI	CACGAG	1 cut(s)	533
BbsI	GAAGAC	2 cut(s)	144, 440
Bbv12I	GWGCWC	1 cut(s)	924
BbvI	GCAGC	5 cut(s)	240, 281, 290, 619, 942
BccI	CCATC	3 cut(s)	709, 1008, 1313
BceAI	ACGGC	3 cut(s)	214, 294, 667
BciT130I	CCWGG	2 cut(s)	298, 579
BciVI	GTATCC	1 cut(s)	716
BcoDI	GTCTC	4 cut(s)	228, 536, 993, 1197
BfaI	CTAG	3 cut(s)	453, 1244, 1253
BfmI	CTRYAG	1 cut(s)	950
BfoI	RGCGCY	2 cut(s)	204, 284
BfuI	GTATCC	1 cut(s)	716
BglI	GCCNNNNNGGC	1 cut(s)	278
Bme1390I	CCNGG	2 cut(s)	298, 579
BmiI	GGNNCC	2 cut(s)	202, 549
BmrFI	CCNGG	2 cut(s)	298, 579
BmsI	GCATC	2 cut(s)	36, 377
BpiI	GAAGAC	2 cut(s)	144, 440
Bpu14I	TTCGAA	2 cut(s)	358, 1085
BsaHI	GRCGYC	1 cut(s)	201
BsaJI	CCNNGG	1 cut(s)	577
BsaXI	ACNNNNNCTCC	2 cut(s)	160, 190
Bsc4I	CCNNNNNNNGG	7 cut(s)	593, 673, 715, 943, 995, 1077, 1258
Bse1I	ACTGG	3 cut(s)	633, 1037, 1071
BseBI	CCWGG	2 cut(s)	298, 579
BseDI	CCNNGG	1 cut(s)	577
BseGI	GGATG	2 cut(s)	27, 1019
BseLI	CCNNNNNNNGG	7 cut(s)	593, 673, 715, 943, 995, 1077, 1258
BseMII	CTCAG	1 cut(s)	300
BseNI	ACTGG	3 cut(s)	633, 1037, 1071
BseRI	GAGGAG	4 cut(s)	8, 23, 40, 43
BseSI	GKGCMC	2 cut(s)	835, 924
BseXI	GCAGC	5 cut(s)	240, 281, 290, 619, 942
BsgI	GTGCAG	1 cut(s)	990
Bsh1236I	CGCG	1 cut(s)	153
BshNI	GGYRCC	1 cut(s)	200
BsiHKAI	GWGCWC	1 cut(s)	924
BsiSI	CCGG	1 cut(s)	66
BslFI	GGGAC	3 cut(s)	225, 507, 732
BslI	CCNNNNNNNGG	7 cut(s)	593, 673, 715, 943, 995, 1077, 1258
BsmAI	GTCTC	4 cut(s)	228, 536, 993, 1197
BsmFI	GGGAC	3 cut(s)	225, 507, 732
BsmI	GAATGC	3 cut(s)	748, 1081, 1253
Bsp119I	TTCGAA	2 cut(s)	358, 1085
Bsp1286I	GDGCHC	2 cut(s)	835, 924
Bsp1407I	TGTACA	1 cut(s)	961
Bsp143I	GATC	7 cut(s)	107, 379, 436, 547, 845, 1108, 1231
BspCNI	CTCAG	1 cut(s)	301
BspFNI	CGCG	1 cut(s)	153
BspLI	GGNNCC	2 cut(s)	202, 549
BspPI	GGATC	4 cut(s)	387, 542, 555, 853
BspQI	GCTCTTC	1 cut(s)	86
BspT104I	TTCGAA	2 cut(s)	358, 1085
BspT107I	GGYRCC	1 cut(s)	200
BsrGI	TGTACA	1 cut(s)	961
BsrI	ACTGG	3 cut(s)	633, 1037, 1071
BssECI	CCNNGG	1 cut(s)	577
BssMI	GATC	7 cut(s)	107, 379, 436, 547, 845, 1108, 1231
BssNI	GRCGYC	1 cut(s)	201
BssSI	CACGAG	1 cut(s)	533
Bst2BI	CACGAG	1 cut(s)	533
Bst2UI	CCWGG	2 cut(s)	298, 579
Bst4CI	ACNGT	5 cut(s)	742, 903, 910, 968, 1124
Bst6I	CTCTTC	6 cut(s)	86, 355, 483, 761, 934, 1082
BstACI	GRCGYC	1 cut(s)	201
BstAUI	TGTACA	1 cut(s)	961
BstBI	TTCGAA	2 cut(s)	358, 1085
BstC8I	GCNNGC	1 cut(s)	1221
BstDEI	CTNAG	4 cut(s)	309, 430, 1053, 1167
BstEII	GGTNACC	1 cut(s)	292
BstF5I	GGATG	2 cut(s)	27, 1019
BstFNI	CGCG	1 cut(s)	153
BstH2I	RGCGCY	2 cut(s)	204, 284
BstHHI	GCGC	4 cut(s)	153, 203, 283, 1152
BstKTI	GATC	7 cut(s)	110, 382, 439, 550, 848, 1111, 1234
BstMAI	GTCTC	4 cut(s)	228, 536, 993, 1197
BstMBI	GATC	7 cut(s)	107, 379, 436, 547, 845, 1108, 1231
BstMWI	GCNNNNNNNGC	4 cut(s)	234, 269, 278, 919
BstNI	CCWGG	2 cut(s)	298, 579
BstNSI	RCATGY	2 cut(s)	1223, 1285
BstPI	GGTNACC	1 cut(s)	292
BstSCI	CCNGG	2 cut(s)	296, 577
BstSFI	CTRYAG	1 cut(s)	950
BstSLI	GKGCMC	2 cut(s)	835, 924
BstUI	CGCG	1 cut(s)	153
BstV1I	GCAGC	5 cut(s)	240, 281, 290, 619, 942
BstV2I	GAAGAC	2 cut(s)	144, 440
BstX2I	RGATCY	2 cut(s)	547, 845
BstYI	RGATCY	2 cut(s)	547, 845
BsuI	GTATCC	1 cut(s)	716
BtsCI	GGATG	2 cut(s)	27, 1019
BtsIMutI	CAGTG	5 cut(s)	183, 899, 964, 1078, 1129
Cac8I	GCNNGC	1 cut(s)	1221
CaiI	CAGNNNCTG	2 cut(s)	303, 337
CfoI	GCGC	4 cut(s)	153, 203, 283, 1152
CseI	GACGC	1 cut(s)	220
CsiI	ACCWGGT	1 cut(s)	296
Csp6I	GTAC	2 cut(s)	677, 962
CviAII	CATG	5 cut(s)	376, 800, 938, 1220, 1282
CviQI	GTAC	2 cut(s)	677, 962
DdeI	CTNAG	4 cut(s)	309, 430, 1053, 1167
DinI	GGCGCC	1 cut(s)	202
DpnI	GATC	7 cut(s)	109, 381, 438, 549, 847, 1110, 1233
DpnII	GATC	7 cut(s)	107, 379, 436, 547, 845, 1108, 1231
DraIII	CACNNNGTG	1 cut(s)	300
DrdI	GACNNNNNNGTC	1 cut(s)	913
DseDI	GACNNNNNNGTC	1 cut(s)	913
Eam1104I	CTCTTC	6 cut(s)	86, 355, 483, 761, 934, 1082
EarI	CTCTTC	6 cut(s)	86, 355, 483, 761, 934, 1082
EciI	GGCGGA	2 cut(s)	11, 46
Eco57I	CTGAAG	1 cut(s)	765
Eco91I	GGTNACC	1 cut(s)	292
EcoO65I	GGTNACC	1 cut(s)	292
EcoRII	CCWGG	2 cut(s)	296, 577
EgeI	GGCGCC	1 cut(s)	202
EheI	GGCGCC	1 cut(s)	202
FaeI	CATG	5 cut(s)	379, 803, 941, 1223, 1285
FaqI	GGGAC	3 cut(s)	225, 507, 732
FatI	CATG	5 cut(s)	375, 799, 937, 1219, 1281
FokI	GGATG	2 cut(s)	14, 1026
FspBI	CTAG	3 cut(s)	453, 1244, 1253
GlaI	GCGC	4 cut(s)	152, 202, 282, 1151
HaeII	RGCGCY	2 cut(s)	204, 284
HapII	CCGG	1 cut(s)	66
HgaI	GACGC	1 cut(s)	220
HhaI	GCGC	4 cut(s)	153, 203, 283, 1152
Hin1I	GRCGYC	1 cut(s)	201
Hin1II	CATG	5 cut(s)	379, 803, 941, 1223, 1285
Hin6I	GCGC	4 cut(s)	151, 201, 281, 1150
HinP1I	GCGC	4 cut(s)	151, 201, 281, 1150
HincII	GTYRAC	1 cut(s)	906
HindII	GTYRAC	1 cut(s)	906
HinfI	GANTC	7 cut(s)	7, 62, 188, 313, 419, 606, 896
HpaII	CCGG	1 cut(s)	66
HphI	GGTGA	2 cut(s)	81, 286
Hpy166II	GTNNAC	8 cut(s)	168, 183, 196, 679, 906, 922, 962, 964
Hpy188I	TCNGA	4 cut(s)	373, 661, 784, 998
Hpy188III	TCNNGA	4 cut(s)	105, 134, 331, 1239
Hpy8I	GTNNAC	8 cut(s)	168, 183, 196, 679, 906, 922, 962, 964
Hpy99I	CGWCG	2 cut(s)	236, 280
HpyAV	CCTTC	3 cut(s)	23, 816, 1284
HpyCH4III	ACNGT	5 cut(s)	742, 903, 910, 968, 1124
HpyCH4V	TGCA	8 cut(s)	737, 748, 817, 922, 971, 1204, 1219, 1285
HpyF10VI	GCNNNNNNNGC	4 cut(s)	234, 269, 278, 919
HpyF3I	CTNAG	4 cut(s)	309, 430, 1053, 1167
Hsp92I	GRCGYC	1 cut(s)	201
Hsp92II	CATG	5 cut(s)	379, 803, 941, 1223, 1285
HspAI	GCGC	4 cut(s)	151, 201, 281, 1150
KasI	GGCGCC	1 cut(s)	200
Kzo9I	GATC	7 cut(s)	107, 379, 436, 547, 845, 1108, 1231
LguI	GCTCTTC	1 cut(s)	86
LmnI	GCTCC	2 cut(s)	776, 1270
Lsp1109I	GCAGC	5 cut(s)	240, 281, 290, 619, 942
LweI	GCATC	2 cut(s)	36, 377
MabI	ACCWGGT	1 cut(s)	296
MaeI	CTAG	3 cut(s)	453, 1244, 1253
MaeIII	GTNAC	3 cut(s)	292, 647, 897
MalI	GATC	7 cut(s)	109, 381, 438, 549, 847, 1110, 1233
MboI	GATC	7 cut(s)	107, 379, 436, 547, 845, 1108, 1231
MflI	RGATCY	2 cut(s)	547, 845
MhlI	GDGCHC	2 cut(s)	835, 924
MluCI	AATT	4 cut(s)	441, 1144, 1256, 1306
Mly113I	GGCGCC	1 cut(s)	201
MlyI	GAGTC	3 cut(s)	182, 413, 905
MmeI	TCCRAC	1 cut(s)	976
MroXI	GAANNNNTTC	1 cut(s)	467
MseI	TTAA	5 cut(s)	285, 347, 399, 644, 869
MslI	CAYNNNNRTG	2 cut(s)	501, 1071
MspA1I	CMGCKG	1 cut(s)	955
MspI	CCGG	1 cut(s)	66
MspR9I	CCNGG	2 cut(s)	298, 579
Mva1269I	GAATGC	3 cut(s)	748, 1081, 1253
MvaI	CCWGG	2 cut(s)	298, 579
MvnI	CGCG	1 cut(s)	153
MwoI	GCNNNNNNNGC	4 cut(s)	234, 269, 278, 919
NarI	GGCGCC	1 cut(s)	201
NdeII	GATC	7 cut(s)	107, 379, 436, 547, 845, 1108, 1231
NlaIII	CATG	5 cut(s)	379, 803, 941, 1223, 1285
NlaIV	GGNNCC	2 cut(s)	202, 549
NmuCI	GTSAC	2 cut(s)	292, 897
NspI	RCATGY	2 cut(s)	1223, 1285
NspV	TTCGAA	2 cut(s)	358, 1085
PaeI	GCATGC	1 cut(s)	1223
PciSI	GCTCTTC	1 cut(s)	86
PctI	GAATGC	3 cut(s)	748, 1081, 1253
PdmI	GAANNNNTTC	1 cut(s)	467
PfeI	GAWTC	4 cut(s)	7, 62, 313, 606
PleI	GAGTC	3 cut(s)	182, 413, 904
PluTI	GGCGCC	1 cut(s)	204
PpsI	GAGTC	3 cut(s)	182, 413, 904
Psp6I	CCWGG	2 cut(s)	296, 577
PspEI	GGTNACC	1 cut(s)	292
PspGI	CCWGG	2 cut(s)	296, 577
PspN4I	GGNNCC	2 cut(s)	202, 549
PstNI	CAGNNNCTG	2 cut(s)	303, 337
PsuI	RGATCY	2 cut(s)	547, 845
PvuII	CAGCTG	1 cut(s)	955
RsaI	GTAC	2 cut(s)	678, 963
RsaNI	GTAC	2 cut(s)	677, 962
RseI	CAYNNNNRTG	2 cut(s)	501, 1071
SapI	GCTCTTC	1 cut(s)	86
SaqAI	TTAA	5 cut(s)	285, 347, 399, 644, 869
Sau3AI	GATC	7 cut(s)	107, 379, 436, 547, 845, 1108, 1231
SchI	GAGTC	3 cut(s)	182, 413, 905
ScrFI	CCNGG	2 cut(s)	298, 579
SduI	GDGCHC	2 cut(s)	835, 924
SexAI	ACCWGGT	1 cut(s)	296
SfaNI	GCATC	2 cut(s)	36, 377
SfcI	CTRYAG	1 cut(s)	950
SfoI	GGCGCC	1 cut(s)	202
SfuI	TTCGAA	2 cut(s)	358, 1085
SmiMI	CAYNNNNRTG	2 cut(s)	501, 1071
SphI	GCATGC	1 cut(s)	1223
Sse9I	AATT	4 cut(s)	441, 1144, 1256, 1306
SspDI	GGCGCC	1 cut(s)	200
SspMI	CTAG	3 cut(s)	453, 1244, 1253
StyD4I	CCNGG	2 cut(s)	296, 577
TaaI	ACNGT	5 cut(s)	742, 903, 910, 968, 1124
TaqI	TCGA	5 cut(s)	358, 422, 439, 795, 1085
TasI	AATT	4 cut(s)	441, 1144, 1256, 1306
TatI	WGTACW	1 cut(s)	961
TauI	GCSGC	6 cut(s)	27, 72, 156, 206, 266, 269
TfiI	GAWTC	4 cut(s)	7, 62, 313, 606
Tru1I	TTAA	5 cut(s)	285, 347, 399, 644, 869
Tru9I	TTAA	5 cut(s)	285, 347, 399, 644, 869
TscAI	CASTG	5 cut(s)	190, 906, 971, 1078, 1129
TseFI	GTSAC	2 cut(s)	292, 897
TseI	GCWGC	5 cut(s)	228, 269, 303, 632, 955
Tsp45I	GTSAC	2 cut(s)	292, 897
TspDTI	ATGAA	5 cut(s)	73, 440, 639, 1151, 1266
TspGWI	ACGGA	6 cut(s)	26, 168, 181, 736, 749, 865
TspRI	CASTG	5 cut(s)	190, 906, 971, 1078, 1129
VneI	GTGCAC	1 cut(s)	920
XapI	RAATTY	3 cut(s)	441, 1144, 1306
XceI	RCATGY	2 cut(s)	1223, 1285
XmnI	GAANNNNTTC	1 cut(s)	467
XspI	CTAG	3 cut(s)	453, 1244, 1253

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